| Title: | Exploratory Analysis of Genetic and Genomic Data |
|---|---|
| Description: | Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods. |
| Authors: | Thibaut Jombart [aut]  ,
Zhian N. Kamvar [aut, cre] ,
Caitlin Collins [ctb],
Roman Lustrik [ctb],
Marie-Pauline Beugin [ctb],
Brian J. Knaus [ctb],
Peter Solymos [ctb],
Vladimir Mikryukov [ctb],
Klaus Schliep [ctb],
Tiago Maié [ctb],
Libor Morkovsky [ctb],
Ismail Ahmed [ctb],
Anne Cori [ctb],
Federico Calboli [ctb],
RJ Ewing [ctb],
Frédéric Michaud [ctb],
Rebecca DeCamp [ctb],
Alexandre Courtiol [ctb] ,
Lindsay V. Clark [ctb] ,
Pavel Dimens [ctb] |
| Maintainer: | Zhian N. Kamvar <[email protected]> |
| License: | GPL (>=2) |
| Version: | 2.1.10 |
| Built: | 2024-11-15 05:23:06 UTC |
| Source: | https://github.com/thibautjombart/adegenet |
These functions are internal C routines used in adegenet. Do not use them unless you know what you are doing.
.internal_C_routines.internal_C_routines
An object of class NULL of length 0.
Thibaut Jombart
These functions are under development. Please email the author before using them for published results.
a.score(x, n.sim=10, ...) optim.a.score(x, n.pca=1:ncol(x$tab), smart=TRUE, n=10, plot=TRUE, n.sim=10, n.da=length(levels(x$grp)), ...)a.score(x, n.sim=10, ...) optim.a.score(x, n.pca=1:ncol(x$tab), smart=TRUE, n=10, plot=TRUE, n.sim=10, n.da=length(levels(x$grp)), ...)
x |
a |
n.pca |
a vector of |
smart |
a |
n |
an |
plot |
a |
n.sim |
an |
n.da |
an |
... |
further arguments passed to other methods; currently unused.. |
The Discriminant Analysis of Principal Components seeks a reduced space inside which observations are best discriminated into pre-defined groups. One way to assess the quality of the discrimination is looking at re-assignment of individuals to their prior group, successful re-assignment being a sign of strong discrimination.
However, when the original space is very large, ad hoc solutions can be found, which discriminate very well the sampled individuals but would perform poorly on new samples. In such a case, DAPC re-assignment would be high even for randomly chosen clusters. The a-score measures this bias. It is computed as (Pt-Pr), where Pt is the reassignment probability using the true cluster, and Pr is the reassignment probability for randomly permuted clusters. A a-score close to one is a sign that the DAPC solution is both strongly discriminating and stable, while low values (toward 0 or lower) indicate either weak discrimination or instability of the results.
The a-score can serve as a criterion for choosing the optimal number of
PCs in the PCA step of DAPC, i.e. the number of PC maximizing the
a-score. Two procedures are implemented in optim.a.score. The
smart procedure selects evenly distributed number of PCs in a
pre-defined range, compute the a-score for each, and then interpolate
the results using splines, predicting an approximate optimal number of
PCs. The other procedure (when smart is FALSE) performs the
computations for all number of PCs request by the user. The 'optimal'
number is then the one giving the highest mean a-score (computed over
the groups).
=== a.score ===a.score returns a list with the following components:
tab |
a matrix of a-scores with groups in columns and simulations in row. |
pop.score |
a vector giving the mean a-score for each population. |
mean |
the overall mean a-score. |
=== optim.a.score ===optima.score returns a list with the following components:
pop.score |
a list giving the mean a-score of the populations for each number of retained PC (each element of the list corresponds to a number of retained PCs). |
mean |
a vector giving the overall mean a-score for each number of retained PCs. |
pred |
(only when |
best |
the optimal number of PCs to be retained. |
Thibaut Jombart [email protected]
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
- find.clusters: to identify clusters without prior.
- dapc: the Discriminant Analysis of Principal
Components (DAPC)
An accessor is a function that allows to interact with slots of an
object in a convenient way. Several accessors are available for genind or
genpop objects. The operator "$" and "$<-" are used to
access the slots, being equivalent to "@" and "@<-".
The operator "[" is a flexible way to subset data by individuals,
populations, alleles, and loci. When using a matrix-like syntax,
subsetting will apply to the dimensios of the @tab slot. In addition,
specific arguments loc and pop can be used to indicate
subsets of loci and populations. The argument drop is a logical
indicating if alleles becoming non-polymorphic in a new dataset should
be removed (default: FALSE). Examples:
"obj[i,j]" returns "obj" with a subset 'i' of individuals and 'j' of
alleles.
"obj[1:10,]" returns an object with only the first 10 genotypes (if
"obj" is a genind) or the first 10 populations (if
"obj" is a genpop)
"obj[1:10, 5:10]" returns an object keeping the first 10 entities and
the alleles 5 to 10.
"obj[loc=c(1,3)]" returns an object keeping only the 1st and 3rd
loci, using locNames(obj) as reference; logicals, or named loci
also work; this overrides other subsetting of alleles.
"obj[pop=2:4]" returns an object keeping only individuals from the
populations 2, 3 and 4, using popNames(obj) as reference;
logicals, or named populations also work; this overrides other
subsetting of individuals.
"obj[i=1:2, drop=TRUE]" returns an object keeping only the first
two individuals (or populations), dropping the alleles no longer
present in the data.
The argument treatOther handles the treatment of objects in the
@other slot (see details). The argument drop can be set
to TRUE to drop alleles that are no longer represented in the subset.
nInd(x, ...) nLoc(x, ...) nAll(x, onlyObserved = FALSE, ...) nPop(x, ...) pop(x) indNames(x, ...) ## S4 method for signature 'genind' indNames(x, ...) locNames(x, ...) ## S4 method for signature 'genind' locNames(x, withAlleles=FALSE, ...) ## S4 method for signature 'genpop' locNames(x, withAlleles=FALSE, ...) popNames(x, ...) ## S4 method for signature 'genind' popNames(x, ...) popNames(x, ...) ## S4 method for signature 'genpop' popNames(x, ...) ploidy(x, ...) ## S4 method for signature 'genind' ploidy(x, ...) ## S4 method for signature 'genpop' ploidy(x, ...) ## S4 method for signature 'genind' other(x, ...) ## S4 method for signature 'genpop' other(x, ...)nInd(x, ...) nLoc(x, ...) nAll(x, onlyObserved = FALSE, ...) nPop(x, ...) pop(x) indNames(x, ...) ## S4 method for signature 'genind' indNames(x, ...) locNames(x, ...) ## S4 method for signature 'genind' locNames(x, withAlleles=FALSE, ...) ## S4 method for signature 'genpop' locNames(x, withAlleles=FALSE, ...) popNames(x, ...) ## S4 method for signature 'genind' popNames(x, ...) popNames(x, ...) ## S4 method for signature 'genpop' popNames(x, ...) ploidy(x, ...) ## S4 method for signature 'genind' ploidy(x, ...) ## S4 method for signature 'genpop' ploidy(x, ...) ## S4 method for signature 'genind' other(x, ...) ## S4 method for signature 'genpop' other(x, ...)
x |
|
onlyObserved |
a logical indicating whether the allele count should
also include the alleles with onlyObserved columns in the matrix. Defaults
to |
withAlleles |
a logical indicating whether the result should be of the form [locus name].[allele name], instead of [locus name]. |
... |
further arguments to be passed to other methods (currently not used). |
The "[" operator can treat elements in the @other slot as
well. For instance, if obj@other$xy contains spatial
coordinates, the obj[1:3, ]@other$xy will contain the spatial
coordinates of the genotypes (or population) 1,2 and 3. This is
handled through the argument treatOther, a logical defaulting
to TRUE. If set to FALSE, the @other returned unmodified.
Note that only matrix-like, vector-like and lists can be proceeded in
@other. Other kind of objects will issue a warning an be
returned as they are, unless the argument quiet is left to
TRUE, its default value.
The drop argument can be set to TRUE to retain only alleles
that are present in the subset. To achieve better control of
polymorphism of the data, see isPoly.
nAll() reflects the number of columns per locus present in the current
gen object. If onlyObserved = TRUE, then the number of columns with at
least one non-missing allele is shown.
returns the number of individuals in the genind object
returns the number of loci
returns the number of observed alleles in each locus
returns the number of populations
returns a factor assigning individuals to populations.
replacement method for the @pop slot of an
object.
returns the names of populations.
sets the names of populations using a vector of
length nPop(x).
returns the names of individuals.
sets the names of individuals using a vector of
length nInd(x).
returns the names of markers and/or alleles.
sets the names of markers using a vector of
length nLoc(x).
returns a factor that defines which locus each column of the @tab slot belongs to
returns the ploidy of the data.
sets the ploidy of the data using an integer.
returns the alleles of each locus.
sets the alleles of each locus using a list with one character vector for each locus.
returns the content of the @other slot
(misc. information); returns NULL if the slot is onlyObserved or of
length zero.
sets the content of the @other slot
(misc. information); the provided value needs to be a list; it
not, provided value will be stored within a list.
Thibaut Jombart [email protected]
data(nancycats) nancycats pop(nancycats) # get the populations indNames(nancycats) # get the labels of individuals locNames(nancycats) # get the labels of the loci alleles(nancycats) # get the alleles nAll(nancycats) # count the number of alleles head(tab(nancycats)) # get allele counts # get allele frequencies, replace NAs head(tab(nancycats, freq = TRUE, NA.method = "mean")) # let's isolate populations 4 and 8 popNames(nancycats) obj <- nancycats[pop=c(4, 8)] obj popNames(obj) pop(obj) nAll(obj, onlyObserved = TRUE) # count number of alleles among these two populations nAll(obj) # count number of columns in the data all(nAll(obj, onlyObserved = TRUE) == lengths(alleles(obj))) # will be FALSE since drop = FALSE all(nAll(obj) == lengths(alleles(obj))) # will be FALSE since drop = FALSE # let's isolate two markers, fca23 and fca90 locNames(nancycats) obj <- nancycats[loc=c("fca23","fca90")] obj locNames(obj) # illustrate pop obj <- nancycats[sample(1:100, 10)] pop(obj) pop(obj) <- rep(c('b', 'a'), each = 5) pop(obj) # illustrate locNames locNames(obj) locNames(obj, withAlleles = TRUE) locNames(obj)[1] <- "newLocus" locNames(obj) locNames(obj, withAlleles=TRUE) # illustrate how 'other' slot is handled data(sim2pop) nInd(sim2pop) other(sim2pop[1:6]) # xy is subsetted automatically other(sim2pop[1:6, treatOther=FALSE]) # xy is left as isdata(nancycats) nancycats pop(nancycats) # get the populations indNames(nancycats) # get the labels of individuals locNames(nancycats) # get the labels of the loci alleles(nancycats) # get the alleles nAll(nancycats) # count the number of alleles head(tab(nancycats)) # get allele counts # get allele frequencies, replace NAs head(tab(nancycats, freq = TRUE, NA.method = "mean")) # let's isolate populations 4 and 8 popNames(nancycats) obj <- nancycats[pop=c(4, 8)] obj popNames(obj) pop(obj) nAll(obj, onlyObserved = TRUE) # count number of alleles among these two populations nAll(obj) # count number of columns in the data all(nAll(obj, onlyObserved = TRUE) == lengths(alleles(obj))) # will be FALSE since drop = FALSE all(nAll(obj) == lengths(alleles(obj))) # will be FALSE since drop = FALSE # let's isolate two markers, fca23 and fca90 locNames(nancycats) obj <- nancycats[loc=c("fca23","fca90")] obj locNames(obj) # illustrate pop obj <- nancycats[sample(1:100, 10)] pop(obj) pop(obj) <- rep(c('b', 'a'), each = 5) pop(obj) # illustrate locNames locNames(obj) locNames(obj, withAlleles = TRUE) locNames(obj)[1] <- "newLocus" locNames(obj) locNames(obj, withAlleles=TRUE) # illustrate how 'other' slot is handled data(sim2pop) nInd(sim2pop) other(sim2pop[1:6]) # xy is subsetted automatically other(sim2pop[1:6, treatOther=FALSE]) # xy is left as is
The function adegenetServer opens up a web page providing a
simple user interface for some of the functionalities implemented in
adegenet. These servers have been developed using the package
shiny.
Currently available servers include:
DAPC: a server for the Discriminant Analysis of
Principal Components (see ?dapc)
adegenetServer(what=c("DAPC"))adegenetServer(what=c("DAPC"))
what |
a character string indicating which server to start; currently accepted values are: "DAPC" |
The function invisibly returns NULL.
Thibaut Jombart [email protected] Caitlin Collins
## Not run: ## this opens a web page for DAPC adegenetServer() ## End(Not run)## Not run: ## this opens a web page for DAPC adegenetServer() ## End(Not run)
This package is devoted to the multivariate analysis of genetic markers
data. These data can be codominant markers (e.g. microsatellites) or
presence/absence data (e.g. AFLP), and have any level of ploidy. 'adegenet'
defines three formal (S4) classes:
- genind: a class for
data of individuals ("genind" stands for genotypes-individuals).
-
genpop: a class for data of groups of individuals ("genpop"
stands for genotypes-populations)
- genlight: a class for
genome-wide SNP data
For more information about these classes, type "class ? genind", "class ?
genpop", or "?genlight".
Essential functionalities of the package are presented througout 4
tutorials, accessible using adegenetTutorial(which="name-below"):
- basics: introduction to the package.
- spca: multivariate
analysis of spatial genetic patterns.
- dapc: population structure
and group assignment using DAPC.
- genomics: introduction to the
class genlight for the handling and analysis of genome-wide
SNP data.
Note: In older versions of adegenet, these tutorials were avilable as
vignettes, accessible through the function vignette("name-below",
package="adegenet"):
- adegenet-basics.
-
adegenet-spca.
- adegenet-dapc.
-
adegenet-genomics.
Important functions are also summarized below.
=== IMPORTING DATA ===
= TO GENIND OBJECTS = adegenet imports
data to genind object from the following softwares:
-
STRUCTURE: see read.structure
- GENETIX: see
read.genetix
- FSTAT: see read.fstat
-
Genepop: see read.genepop
To import data from any of these
formats, you can also use the general function
import2genind.
In addition, it can extract polymorphic sites from nucleotide and amino-acid
alignments:
- DNA files: use read.dna from the ape
package, and then extract SNPs from DNA alignments using
DNAbin2genind.
- protein sequences alignments: polymorphic sites can be extracted from
protein sequences alignments in alignment format (package
seqinr, see as.alignment) using the function
alignment2genind.
The function fasta2DNAbin allows for reading fasta files into
DNAbin object with minimum RAM requirements.
It is also possible to read genotypes coded by character strings from a
data.frame in which genotypes are in rows, markers in columns. For this, use
df2genind. Note that df2genind can be used for
any level of ploidy.
= TO GENLIGHT OBJECTS =
SNP data can be read from the following
formats:
- PLINK: see function read.PLINK
- .snp
(adegenet's own format): see function read.snp
SNP can also be extracted from aligned DNA sequences with the fasta format,
using fasta2genlight
=== EXPORTING DATA ===adegenet exports data from
Genotypes can also be recoded from a genind object into a
data.frame of character strings, using any separator between alleles. This
covers formats from many softwares like GENETIX or STRUCTURE. For this, see
genind2df.
Also note that the pegas package imports genind objects
using the function as.loci.
=== MANIPULATING DATA ===
Several functions allow one to manipulate
genind or genpop objects
-
genind2genpop: convert a genind object to a
genpop
- seploc: creates one object per
marker; for genlight objects, creates blocks of SNPs.
-
seppop: creates one object per population
-
- tab: access the allele data (counts or frequencies) of an object
(genind and genpop)
-
x[i,j]: create a new object keeping only genotypes (or populations) indexed
by 'i' and the alleles indexed by 'j'.
- makefreq: returns
a table of allelic frequencies from a genpop object.
-
repool merges genoptypes from different gene pools into one
single genind object.
- propTyped returns the
proportion of available (typed) data, by individual, population, and/or
locus.
- selPopSize subsets data, retaining only genotypes
from a population whose sample size is above a given level.
-
pop sets the population of a set of genotypes.
=== ANALYZING DATA ===
Several functions allow to use usual, and less
usual analyses:
- HWE.test.genind: performs HWE test for all
populations and loci combinations
- dist.genpop: computes 5
genetic distances among populations.
- monmonier:
implementation of the Monmonier algorithm, used to seek genetic boundaries
among individuals or populations. Optimized boundaries can be obtained using
optimize.monmonier. Object of the class monmonier can be
plotted and printed using the corresponding methods.
-
spca: implements Jombart et al. (2008) spatial Principal
Component Analysis
- global.rtest: implements Jombart et
al. (2008) test for global spatial structures
-
local.rtest: implements Jombart et al. (2008) test for local
spatial structures
- propShared: computes the proportion of
shared alleles in a set of genotypes (i.e. from a genind object)
-
propTyped: function to investigate missing data in several ways
- scaleGen: generic method to scale genind or
genpop before a principal component analysis
-
Hs: computes the average expected heterozygosity by population
in a genpop. Classically Used as a measure of genetic
diversity.
- find.clusters and dapc: implement
the Discriminant Analysis of Principal Component (DAPC, Jombart et al.,
2010).
- seqTrack: implements the SeqTrack algorithm for
recontructing transmission trees of pathogens (Jombart et al., 2010) .glPca: implements PCA for genlight objects.
-
gengraph: implements some simple graph-based clustering using
genetic data. - snpposi.plot and snpposi.test:
visualize the distribution of SNPs on a genetic sequence and test their
randomness. - adegenetServer: opens up a web interface for
some functionalities of the package (DAPC with cross validation and feature
selection).
=== GRAPHICS ===
- colorplot: plots points with associated
values for up to three variables represented by colors using the RGB system;
useful for spatial mapping of principal components.
-
loadingplot: plots loadings of variables. Useful for
representing the contribution of alleles to a given principal component in a
multivariate method.
- scatter.dapc: scatterplots for DAPC
results.
- compoplot: plots membership probabilities from a
DAPC object.
=== SIMULATING DATA ===
- hybridize: implements
hybridization between two populations.
- haploGen:
simulates genealogies of haplotypes, storing full genomes. glSim: simulates simple genlight objects.
=== DATASETS ===
- H3N2: Seasonal influenza (H3N2) HA
segment data.
- dapcIllus: Simulated data illustrating the
DAPC.
- eHGDP: Extended HGDP-CEPH dataset.
-
microbov: Microsatellites genotypes of 15 cattle breeds.
-
nancycats: Microsatellites genotypes of 237 cats from 17
colonies of Nancy (France).
- rupica: Microsatellites
genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains
(France).
- sim2pop: Simulated genotypes of two
georeferenced populations.
- spcaIllus: Simulated data
illustrating the sPCA.
For more information, visit the adegenet website using the function
adegenetWeb.
Tutorials are available via the command adegenetTutorial.
To cite adegenet, please use the reference given by
citation("adegenet") (or see references below).
Thibaut Jombart <[email protected]>
Developers: Zhian N. Kamvar <[email protected]>,
Caitlin Collins <[email protected]>,
Ismail Ahmed <[email protected]>,
Federico Calboli, Tobias Erik Reiners, Peter
Solymos, Anne Cori,
Contributed datasets from: Katayoun
Moazami-Goudarzi, Denis Laloë, Dominique Pontier, Daniel Maillard, Francois
Balloux.
Jombart T. (2008) adegenet: a R package for the multivariate
analysis of genetic markers Bioinformatics 24: 1403-1405. doi:
10.1093/bioinformatics/btn129
Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi: 10.1093/bioinformatics/btr521
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
principal components: a new method for the analysis of genetically
structured populations. BMC Genetics 11:94. doi:10.1186/1471-2156-11-94
Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease outbreaks
from genetic data: a graph approach. Heredity. doi:
10.1038/hdy.2010.78.
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. (2008) Revealing
cryptic spatial patterns in genetic variability by a new multivariate
method. Heredity, 101, 92–103.
See adegenet website: http://adegenet.r-forge.r-project.org/
Please post your questions on 'the adegenet forum': [email protected]
adegenet is related to several packages, in particular:
-
ade4 for multivariate analysis
- pegas for population
genetics tools
- ape for phylogenetics and DNA data handling
-
seqinr for handling nucleic and proteic sequences
- shiny
for R-based web interfaces
These functions simply open websites or documents available online providing resources for adegenet.
adegenetWeb() adegenetTutorial( which = c("basics", "spca", "dapc", "genomics", "strata", "snapclust") ) adegenetIssues()adegenetWeb() adegenetTutorial( which = c("basics", "spca", "dapc", "genomics", "strata", "snapclust") ) adegenetIssues()
which |
a character string indicating which tutorial to open (see details) |
adegenetWeb opens adegenet's website
adegenetTutorial opens adegenet tutorials
adegenetIssues opens the issue page on github; this is used to report a bug or post a feature request.
Available tutorials are:
'basics': general introduction to adegenet; covers basic data structures, import/export, handling, and a number of population genetics methods
'spca': spatial genetic structures using the spatial Principal Component Analysis
'dapc': population structure using the Discriminant Analysis of Principal Components
'genomics': handling large genome-wide SNP data using adegenet
'strata': introduction to hierarchical population structure in adegenet
'snapclust': introduction to fast maximum-likelihood genetic clustering using snapclust
Do not use. We work on that stuff. Contact us if interested.
## S3 method for class 'snapclust' AIC(object, ...)## S3 method for class 'snapclust' AIC(object, ...)
object |
An object returned by the function |
... |
Further arguments for compatibility with the |
Thibaut Jombart [email protected]
snapclust to generate clustering solutions.
Do not use. We work on that stuff. Contact us if interested.
AICc(object, ...) ## S3 method for class 'snapclust' AICc(object, ...)AICc(object, ...) ## S3 method for class 'snapclust' AICc(object, ...)
object |
An object returned by the function |
... |
Further arguments for compatibility with the |
Thibaut Jombart [email protected]
snapclust to generate clustering solutions.
These S3 and S4 methods are used to coerce genind and
genpop objects to matrix-like objects. In most cases,
this is equivalent to calling the @tab slot. An exception to
this is the convertion to ktab objects used in the
ade4 package as inputs for K-tables methods (e.g. Multiple Coinertia
Analysis).
as(object, Class)
objectClassthe name of the class to which the object should
be coerced, for instance "data.frame" or "matrix".
from one object class to another using
as(object,"Class"), where the object is of the old
class and the returned object is of the new class "Class".
Thibaut Jombart [email protected]
## Not run: data(microbov) x <- tab(microbov,NA.method="mean") as(x[1:3],"data.frame") ## dudi functions attempt to convert their first argument ## to a data.frame; so they can be used on genind/genpop objects. ## perform a PCA pca1 <- dudi.pca(x, scale=FALSE, scannf=FALSE) pca1 x <- genind2genpop(microbov,miss="chi2") x <- as(x,"ktab") class(x) ## perform a STATIS analysis statis1 <- statis(x, scannf=FALSE) statis1 plot(statis1) ## End(Not run)## Not run: data(microbov) x <- tab(microbov,NA.method="mean") as(x[1:3],"data.frame") ## dudi functions attempt to convert their first argument ## to a data.frame; so they can be used on genind/genpop objects. ## perform a PCA pca1 <- dudi.pca(x, scale=FALSE, scannf=FALSE) pca1 x <- genind2genpop(microbov,miss="chi2") x <- as(x,"ktab") class(x) ## perform a STATIS analysis statis1 <- statis(x, scannf=FALSE) statis1 plot(statis1) ## End(Not run)
The class genlight is a formal (S4) class for storing a genotypes
of binary SNPs in a compact way, using a bit-level coding scheme. New
instances of this class are best created using new; see the
manpage of genlight for more information on this point.
As a shortcut, conversion methods can be used to convert various
objects into a genlight object. Conversions can be
achieved using S3-style (as.genlight(x)) or S4-style
(as(x,"genlight") procedures. All of them call upon the
constructor (new) of genlight objects.
Conversion is currently available from the following objects: - matrix of type integer/numeric - data.frame with integer/numeric data - list of vectors of integer/numeric type
Thibaut Jombart ([email protected])
Related class:
- SNPbin, for storing individual genotypes of
binary SNPs
- genind
## Not run: ## data to be converted dat <- list(toto=c(1,1,0,0,2,2,1,2,NA), titi=c(NA,1,1,0,1,1,1,0,0), tata=c(NA,0,3, NA,1,1,1,0,0)) ## using the constructor x1 <- new("genlight", dat) x1 ## using 'as' methods x2 <- as.genlight(dat) x3 <- as(dat, "genlight") identical(x1,x2) identical(x1,x3) ## End(Not run)## Not run: ## data to be converted dat <- list(toto=c(1,1,0,0,2,2,1,2,NA), titi=c(NA,1,1,0,1,1,1,0,0), tata=c(NA,0,3, NA,1,1,1,0,0)) ## using the constructor x1 <- new("genlight", dat) x1 ## using 'as' methods x2 <- as.genlight(dat) x3 <- as(dat, "genlight") identical(x1,x2) identical(x1,x3) ## End(Not run)
The class SNPbin is a formal (S4) class for storing a genotype
of binary SNPs in a compact way, using a bit-level coding scheme. New
instances of this class are best created using new; see the
manpage of SNPbin for more information on this point.
As a shortcut, conversion methods can be used to convert various
objects into a SNPbin object. Conversions can be
achieved using S3-style (as.SNPbin(x)) or S4-style
(as(x,"SNPbin") procedures. All of them call upon the
constructor (new) of SNPbin objects.
Conversion is currently available from the following objects: - integer vectors - numeric vectors
Thibaut Jombart ([email protected])
Related class:
- SNPbin
- genlight, for storing multiple binary SNP
genotypes.
## Not run: ## data to be converted dat <- c(1,0,0,2,1,1,1,2,2,1,1,0,0,1) ## using the constructor x1 <- new("SNPbin", dat) x1 ## using 'as' methods x2 <- as.SNPbin(dat) x3 <- as(dat, "SNPbin") identical(x1,x2) identical(x1,x3) ## End(Not run)## Not run: ## data to be converted dat <- c(1,0,0,2,1,1,1,2,2,1,1,0,0,1) ## using the constructor x1 <- new("SNPbin", dat) x1 ## using 'as' methods x2 <- as.SNPbin(dat) x3 <- as(dat, "SNPbin") identical(x1,x2) identical(x1,x3) ## End(Not run)
adegenet implements a number of auxiliary procedures that might be of interest for users. These include graphical tools to translate variables (numeric or factors) onto a color scale, adding transparency to existing colors, pre-defined color palettes, extra functions to access documentation, and low-level treatment of character vectors.
These functions are mostly auxiliary procedures used internally in
adegenet.
These items include:
num2col: translates a numeric vector into colors.
fac2col: translates a factor into colors.
any2col: translates a vector of type numeric, character
or factor into colors.
transp: adds transparency to a vector of colors. Note that
transparent colors are not supported on some graphical devices.
corner: adds text to a corner of a figure.
checkType: checks the type of markers being used in a
function and issues an error if appropriate.
.rmspaces: remove peripheric spaces in a character string.
.genlab: generate labels in a correct alphanumeric ordering.
.readExt: read the extension of a given file.
Color palettes include:
bluepal: white -> dark blue
redpal: white -> dark red
greenpal: white -> dark green
greypal: white -> dark grey
flame: gold -> red
azur: gold -> blue
seasun: blue -> gold -> red
lightseasun: blue -> gold -> red (light variant)
deepseasun: blue -> gold -> red (deep variant)
spectral: red -> yellow -> blue (RColorBrewer variant)
wasp: gold -> brown -> black
funky: many colors
virid: adaptation of the viridis palette, from
the viridis package.
hybridpal: reorder a color palette (virid by
default) to display sharp contrast between the first two colors, and
interpolated colors after; ideal for datasets where two parental
populations are provided first, followed by various degrees of
hybrids.
.genlab(base, n) corner(text, posi="topleft", inset=0.1, ...) num2col(x, col.pal=heat.colors, reverse=FALSE, x.min=min(x,na.rm=TRUE), x.max=max(x,na.rm=TRUE), na.col="transparent") fac2col(x, col.pal=funky, na.col="transparent", seed=NULL) any2col(x, col.pal=seasun, na.col="transparent") transp(col, alpha=.5) hybridpal(col.pal = virid).genlab(base, n) corner(text, posi="topleft", inset=0.1, ...) num2col(x, col.pal=heat.colors, reverse=FALSE, x.min=min(x,na.rm=TRUE), x.max=max(x,na.rm=TRUE), na.col="transparent") fac2col(x, col.pal=funky, na.col="transparent", seed=NULL) any2col(x, col.pal=seasun, na.col="transparent") transp(col, alpha=.5) hybridpal(col.pal = virid)
base |
a character string forming the base of the labels |
n |
the number of labels to generate |
text |
a character string to be added to the plot |
posi |
a character matching any combinations of "top/bottom" and "left/right". |
inset |
a vector of two numeric values (recycled if needed) indicating the inset, as a fraction of the plotting region. |
... |
further arguments to be passed to |
x |
a numeric vector (for |
col.pal |
a function generating colors according to a given palette. |
reverse |
a logical stating whether the palette should be inverted (TRUE), or not (FALSE, default). |
x.min |
the minimal value from which to start the color scale |
x.max |
the maximal value from which to start the color scale |
na.col |
the color to be used for missing values (NAs) |
seed |
a seed for R's random number generated, used to fix the random permutation of colors in the palette used; if NULL, no randomization is used and the colors are taken from the palette according to the ordering of the levels. |
col |
a vector of colors |
alpha |
a numeric value between 0 and 1 representing the alpha coefficient; 0: total transparency; 1: no transparency. |
For .genlab, a character vector of size "n".
num2col and fac2col return a vector of
colors. any2col returns a list with the following components:
$col (a vector of colors), $leg.col (colors for the
legend), and $leg.txt (text for the legend).
Thibaut Jombart [email protected]
The R package RColorBrewer, proposing a nice selection of color
palettes. The viridis package, with many excellent palettes.
.genlab("Locus-",11) ## transparent colors using "transp" plot(rnorm(1000), rnorm(1000), col=transp("blue",.3), pch=20, cex=4) ## numeric values to color using num2col plot(1:100, col=num2col(1:100), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=bluepal), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=flame), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=wasp), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=azur,rev=TRUE), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=spectral), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=virid), pch=20, cex=4) ## factor as colors using fac2col dat <- cbind(c(rnorm(50,8), rnorm(100), rnorm(150,3), rnorm(50,10)),c(rnorm(50,1),rnorm(100),rnorm(150,3), rnorm(50,5))) fac <- rep(letters[1:4], c(50,100,150,50)) plot(dat, col=fac2col(fac), pch=19, cex=4) plot(dat, col=transp(fac2col(fac)), pch=19, cex=4) plot(dat, col=transp(fac2col(fac,seed=2)), pch=19, cex=4) ## use of any2col x <- factor(1:10) col.info <- any2col(x, col.pal=funky) plot(x, col=col.info$col, main="Use of any2col on a factor") legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white") x <- 100:1 col.info <- any2col(x, col.pal=wasp) barplot(x, col=col.info$col, main="Use of any2col on a numeric") legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white").genlab("Locus-",11) ## transparent colors using "transp" plot(rnorm(1000), rnorm(1000), col=transp("blue",.3), pch=20, cex=4) ## numeric values to color using num2col plot(1:100, col=num2col(1:100), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=bluepal), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=flame), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=wasp), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=azur,rev=TRUE), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=spectral), pch=20, cex=4) plot(1:100, col=num2col(1:100, col.pal=virid), pch=20, cex=4) ## factor as colors using fac2col dat <- cbind(c(rnorm(50,8), rnorm(100), rnorm(150,3), rnorm(50,10)),c(rnorm(50,1),rnorm(100),rnorm(150,3), rnorm(50,5))) fac <- rep(letters[1:4], c(50,100,150,50)) plot(dat, col=fac2col(fac), pch=19, cex=4) plot(dat, col=transp(fac2col(fac)), pch=19, cex=4) plot(dat, col=transp(fac2col(fac,seed=2)), pch=19, cex=4) ## use of any2col x <- factor(1:10) col.info <- any2col(x, col.pal=funky) plot(x, col=col.info$col, main="Use of any2col on a factor") legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white") x <- 100:1 col.info <- any2col(x, col.pal=wasp) barplot(x, col=col.info$col, main="Use of any2col on a numeric") legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white")
Do not use. We work on that stuff. Contact us if interested.
## S3 method for class 'snapclust' BIC(object, ...)## S3 method for class 'snapclust' BIC(object, ...)
object |
An object returned by the function |
... |
Further arguments for compatibility with the |
Thibaut Jombart [email protected]
snapclust to generate clustering solutions.
The function chooseCN is a simple interface to build a connection
network (CN) from xy coordinates. The user chooses from 6 types of graph and
one additional weighting scheme. chooseCN calls functions from
appropriate packages, handles non-unique coordinates and returns a
connection network either with classe nb or listw. For graph
types 1-4, duplicated locations are not accepted and will issue an error.
chooseCN( xy, ask = TRUE, type = NULL, result.type = "nb", d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, plot.nb = TRUE, edit.nb = FALSE, check.duplicates = TRUE )chooseCN( xy, ask = TRUE, type = NULL, result.type = "nb", d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, plot.nb = TRUE, edit.nb = FALSE, check.duplicates = TRUE )
xy |
an matrix or data.frame with two columns for x and y coordinates. |
ask |
a logical stating whether graph should be chosen interactively
(TRUE,default) or not (FALSE). Set to FALSE if |
type |
an integer giving the type of graph (see details). |
result.type |
a character giving the class of the returned object.
Either "nb" (default) or "listw", both from |
d1 |
the minimum distance between any two neighbours. Used if
|
d2 |
the maximum distance between any two neighbours. Used if
|
k |
the number of neighbours per point. Used if |
a |
the exponent of the inverse distance matrix. Used if |
dmin |
the minimum distance between any two distinct points. Used to
avoid infinite spatial proximities (defined as the inversed spatial
distances). Used if |
plot.nb |
a logical stating whether the resulting graph should be plotted (TRUE, default) or not (FALSE). |
edit.nb |
a logical stating whether the resulting graph should be edited manually for corrections (TRUE) or not (FALSE, default). |
check.duplicates |
a logical indicating if duplicate coordinates should be detected; this can be an issue for some graphs; TRUE by default. |
There are 7 kinds of graphs proposed:
Delaunay triangulation (type 1)
Gabriel graph (type 2)
Relative neighbours (type 3)
Minimum spanning
tree (type 4)
Neighbourhood by distance (type 5)
K nearests neighbours
(type 6)
Inverse distances (type 7)
The last option (type=7) is not a true neighbouring graph: all sites are
neighbours, but the spatial weights are directly proportional to the
inversed spatial distances.
Also not that in this case, the output of the
function is always a listw object, even if nb was
requested.
The choice of the connection network has been discuted on the adegenet forum. Please search the archives from adegenet website (section 'contact') using 'graph' as keyword.
Returns a connection network having the class nb or
listw. The xy coordinates are passed as attribute to the created
object.
Thibaut Jombart [email protected]
## Not run: data(nancycats) par(mfrow=c(2,2)) cn1 <- chooseCN(nancycats@other$xy,ask=FALSE,type=1) cn2 <- chooseCN(nancycats@other$xy,ask=FALSE,type=2) cn3 <- chooseCN(nancycats@other$xy,ask=FALSE,type=3) cn4 <- chooseCN(nancycats@other$xy,ask=FALSE,type=4) par(mfrow=c(1,1)) ## End(Not run)## Not run: data(nancycats) par(mfrow=c(2,2)) cn1 <- chooseCN(nancycats@other$xy,ask=FALSE,type=1) cn2 <- chooseCN(nancycats@other$xy,ask=FALSE,type=2) cn3 <- chooseCN(nancycats@other$xy,ask=FALSE,type=3) cn4 <- chooseCN(nancycats@other$xy,ask=FALSE,type=4) par(mfrow=c(1,1)) ## End(Not run)
The colorplot function represents a cloud of points with colors
corresponding to a combination of 1,2 or 3 quantitative variables,
assigned to RGB (Red, Green, Blue) channels. For instance, this can be useful to
represent up to 3 principal components in space. Note that the
property of such representation to convey multidimensional information
has not been investigated.
colorplot is a S3 generic function. Methods are defined for
particular objects, like spca objects.
colorplot(...) ## Default S3 method: colorplot(xy, X, axes=NULL, add.plot=FALSE, defaultLevel=0, transp=FALSE, alpha=.5, ...)colorplot(...) ## Default S3 method: colorplot(xy, X, axes=NULL, add.plot=FALSE, defaultLevel=0, transp=FALSE, alpha=.5, ...)
xy |
a numeric matrix with two columns (e.g. a matrix of spatial coordinates. |
X |
a matrix-like containing numeric values that are translated into the RGB system. Variables are considered to be in columns. |
axes |
the index of the columns of X to be represented. Up to three axes can be chosen. If null, up to the first three columns of X are used. |
add.plot |
a logical stating whether the colorplot should be added to the existing plot (defaults to FALSE). |
defaultLevel |
a numeric value between 0 and 1, giving the default level in a color for which values are not specified. Used whenever less than three axes are specified. |
transp |
a logical stating whether the produced colors should be transparent (TRUE) or not (FALSE, default). |
alpha |
the alpha level for transparency, between 0 (fully
transparent) and 1 (not transparent); see |
... |
further arguments to be passed to other methods. In
|
Invisibly returns a vector of colours used in the plot.
Thibaut Jombart [email protected]
# a toy example xy <- expand.grid(1:10,1:10) df <- data.frame(x=1:100, y=100:1, z=runif(100,0,100)) colorplot(xy,df,cex=10,main="colorplot: toy example") ## Not run: # a genetic example using a sPCA if(require(spdep)){ data(spcaIllus) dat3 <- spcaIllus$dat3 spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1) colorplot(spca3, cex=4, main="colorplot: a sPCA example") text(spca3$xy[,1], spca3$xy[,2], dat3$pop) mtext("P1-P2 in cline\tP3 random \tP4 local repulsion") } ## End(Not run)# a toy example xy <- expand.grid(1:10,1:10) df <- data.frame(x=1:100, y=100:1, z=runif(100,0,100)) colorplot(xy,df,cex=10,main="colorplot: toy example") ## Not run: # a genetic example using a sPCA if(require(spdep)){ data(spcaIllus) dat3 <- spcaIllus$dat3 spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1) colorplot(spca3, cex=4, main="colorplot: a sPCA example") text(spca3$xy[,1], spca3$xy[,2], dat3$pop) mtext("P1-P2 in cline\tP3 random \tP4 local repulsion") } ## End(Not run)
The compoplot uses a barplot to represent the group assignment probability of individuals to several groups. It is a generic with methods for the following objects:
compoplot(x, ...) ## S3 method for class 'matrix' compoplot( x, col.pal = funky, border = NA, subset = NULL, show.lab = FALSE, lab = rownames(x), legend = TRUE, txt.leg = colnames(x), n.col = 4, posi = NULL, cleg = 0.8, bg = transp("white"), ... ) ## S3 method for class 'dapc' compoplot(x, only.grp = NULL, border = NA, ...) ## S3 method for class 'snapclust' compoplot(x, border = NA, ...)compoplot(x, ...) ## S3 method for class 'matrix' compoplot( x, col.pal = funky, border = NA, subset = NULL, show.lab = FALSE, lab = rownames(x), legend = TRUE, txt.leg = colnames(x), n.col = 4, posi = NULL, cleg = 0.8, bg = transp("white"), ... ) ## S3 method for class 'dapc' compoplot(x, only.grp = NULL, border = NA, ...) ## S3 method for class 'snapclust' compoplot(x, border = NA, ...)
x |
an object to be used for plotting (see description) |
... |
further arguments to be passed to |
col.pal |
a color palette to be used for the groups; defaults to |
border |
a color for the border of the barplot; use |
subset |
a subset of individuals to retain |
show.lab |
a logical indicating if individual labels should be displayed |
lab |
a vector of individual labels; if NULL, row.names of the matrix are used |
legend |
a logical indicating whether a legend should be provided for the colors |
txt.leg |
a character vector to be used for the legend |
n.col |
the number of columns to be used for the legend |
posi |
the position of the legend |
cleg |
a size factor for the legend |
bg |
the background to be used for the legend |
only.grp |
a subset of groups to retain |
matrix: a matrix with individuals in row and genetic clusters in
column, each entry being an assignment probability of the corresponding
individual to the corresponding group
dapc: the output of the dapc function; in this case,
group assignments are based upon geometric criteria in the discriminant space
snapclust: the output of the snapclust function; in
this case, group assignments are based upon the likelihood of genotypes
belonging to their groups
Thibaut Jombart [email protected]
The original implementation of monmonier in package
adegenet returns path coordinates, coords.monmonier
additionally displays identities of the original points of the network,
based on original coordinates.
coords.monmonier(x)coords.monmonier(x)
x |
an object of class |
Returns a list with elements according to the x$nrun result of the monmonier object.
Corresponding path points are in the same order as in the original object.
run1 (run2, ...): for each run, a list containing a matrix giving the
original points in the network (first and second,
indicating pairs of neighbours). Path coordinates are stored in
columns x.hw and y.hw. first and second
are integers referring to the row numbers in the x$xy matrix of
the original monmonier object.
Peter Solymos, [email protected]
## Not run: if(require(spdep)){ load(system.file("files/mondata1.rda",package="adegenet")) cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE) mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2,nrun=3) mon1$run1 mon1$run2 mon1$run3 path.coords <- coords.monmonier(mon1) path.coords } ## End(Not run)## Not run: if(require(spdep)){ load(system.file("files/mondata1.rda",package="adegenet")) cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE) mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2,nrun=3) mon1$run1 mon1$run2 mon1$run3 path.coords <- coords.monmonier(mon1) path.coords } ## End(Not run)
These functions implement the Discriminant Analysis of Principal
Components (DAPC, Jombart et al. 2010). This method descibes the
diversity between pre-defined groups. When groups are unknown, use
find.clusters to infer genetic clusters. See 'details' section
for a succint description of the method, and
vignette("adegenet-dapc") for a tutorial. Graphical methods for
DAPC are documented in scatter.dapc (see
?scatter.dapc).
dapc is a generic function performing the DAPC on the following
types of objects:
- data.frame (only numeric data)
- matrix (only numeric data)
- genind objects (genetic markers)
- genlight objects (genome-wide SNPs)
These methods all return an object with class dapc.
Functions that can be applied to these objects are (the ".dapc" can be ommitted):
- print.dapc: prints the content of a dapc object.
- summary.dapc: extracts useful information from a dapc
object.
- predict.dapc: predicts group memberships based on DAPC results.
- xvalDapc: performs cross-validation of DAPC using varying
numbers of PCs (and keeping the number of discriminant functions
fixed); it currently has methods for data.frame and matrix.
DAPC implementation calls upon dudi.pca from the
ade4 package (except for genlight objects)
and lda from the MASS package. The
predict procedure uses predict.lda from the
MASS package.
as.lda is a generic with a method for dapc object which
converts these objects into outputs similar to that of
lda.default.
## S3 method for class 'data.frame' dapc(x, grp, n.pca=NULL, n.da=NULL, center=TRUE, scale=FALSE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE, pca.select=c("nbEig","percVar"), perc.pca=NULL, ..., dudi=NULL) ## S3 method for class 'matrix' dapc(x, ...) ## S3 method for class 'genind' dapc(x, pop=NULL, n.pca=NULL, n.da=NULL, scale=FALSE, truenames=TRUE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE, pca.select=c("nbEig","percVar"), perc.pca=NULL, ...) ## S3 method for class 'genlight' dapc(x, pop=NULL, n.pca=NULL, n.da=NULL, scale=FALSE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE, pca.select=c("nbEig", "percVar"), perc.pca=NULL, glPca=NULL, ...) ## S3 method for class 'dudi' dapc(x, grp, ...) ## S3 method for class 'dapc' print(x, ...) ## S3 method for class 'dapc' summary(object, ...) ## S3 method for class 'dapc' predict(object, newdata, prior = object$prior, dimen, method = c("plug-in", "predictive", "debiased"), ...)## S3 method for class 'data.frame' dapc(x, grp, n.pca=NULL, n.da=NULL, center=TRUE, scale=FALSE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE, pca.select=c("nbEig","percVar"), perc.pca=NULL, ..., dudi=NULL) ## S3 method for class 'matrix' dapc(x, ...) ## S3 method for class 'genind' dapc(x, pop=NULL, n.pca=NULL, n.da=NULL, scale=FALSE, truenames=TRUE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE, pca.select=c("nbEig","percVar"), perc.pca=NULL, ...) ## S3 method for class 'genlight' dapc(x, pop=NULL, n.pca=NULL, n.da=NULL, scale=FALSE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE, pca.select=c("nbEig", "percVar"), perc.pca=NULL, glPca=NULL, ...) ## S3 method for class 'dudi' dapc(x, grp, ...) ## S3 method for class 'dapc' print(x, ...) ## S3 method for class 'dapc' summary(object, ...) ## S3 method for class 'dapc' predict(object, newdata, prior = object$prior, dimen, method = c("plug-in", "predictive", "debiased"), ...)
x |
|
grp, pop
|
a |
n.pca |
an |
n.da |
an |
center |
a |
scale |
a |
var.contrib |
a |
var.loadings |
a |
pca.info |
a |
pca.select |
a |
perc.pca |
a |
... |
further arguments to be passed to other functions. For
|
glPca |
an optional |
object |
a |
truenames |
a |
dudi |
optionally, a multivariate analysis with the class
|
newdata |
an optional dataset of individuals whose membership is
seeked; can be a data.frame, a matrix, a genind or a
genlight object, but object class must match the
original ('training') data. In particular, variables must be exactly
the same as in the original data. For genind
objects, see |
prior, dimen, method
|
see |
The Discriminant Analysis of Principal Components (DAPC) is designed to investigate the genetic structure of biological populations. This multivariate method consists in a two-steps procedure. First, genetic data are transformed (centred, possibly scaled) and submitted to a Principal Component Analysis (PCA). Second, principal components of PCA are submitted to a Linear Discriminant Analysis (LDA). A trivial matrix operation allows to express discriminant functions as linear combination of alleles, therefore allowing one to compute allele contributions. More details about the computation of DAPC are to be found in the indicated reference.
DAPC does not infer genetic clusters ex nihilo; for this, see the
find.clusters function.
=== dapc objects ===
The class dapc is a list with the following
components:
call |
the matched call. |
n.pca |
number of PCA axes retained |
n.da |
number of DA axes retained |
var |
proportion of variance conserved by PCA principal components |
eig |
a numeric vector of eigenvalues. |
grp |
a factor giving prior group assignment |
prior |
a numeric vector giving prior group probabilities |
assign |
a factor giving posterior group assignment |
tab |
matrix of retained principal components of PCA |
loadings |
principal axes of DAPC, giving coefficients of the linear combination of retained PCA axes. |
ind.coord |
principal components of DAPC, giving the coordinates of individuals onto principal axes of DAPC; also called the discriminant functions. |
grp.coord |
coordinates of the groups onto the principal axes of DAPC. |
posterior |
a data.frame giving posterior membership probabilities for all individuals and all clusters. |
var.contr |
(optional) a data.frame giving the contributions of original variables (alleles in the case of genetic data) to the principal components of DAPC. |
var.load |
(optional) a data.frame giving the loadings of original variables (alleles in the case of genetic data) to the principal components of DAPC. |
match.prp |
a list, where each item is the proportion of individuals correctly matched to their original population in cross-validation. |
=== other outputs ===
Other functions have different outputs:
- summary.dapc returns a list with 6 components: n.dim (number
of retained DAPC axes), n.pop (number of groups/populations),
assign.prop (proportion of overall correct assignment),
assign.per.pop (proportion of correct assignment per group),
prior.grp.size (prior group sizes), and post.grp.size (posterior
group sizes), xval.dapc, xval.genind and xval
(all return a list of four lists, each one with as many items as
cross-validation runs. The first item is a list of assign
components, the secon is a list of posterior components, the
thirs is a list of ind.score components and the fourth is a
list of match.prp items, i.e. the prortion of the validation
set correctly matched to its original population)
Thibaut Jombart [email protected]
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
xvalDapc: selection of the optimal numbers of PCA axes
retained in DAPC using cross-validation.
scatter.dapc, assignplot,
compoplot: graphics for DAPC.
find.clusters: to identify clusters without prior.
dapcIllus: a set of simulated data illustrating
the DAPC
## data(dapcIllus), data(eHGDP), and data(H3N2) illustrate the dapc ## see ?dapcIllus, ?eHGDP, ?H3N2 ## ## Not run: example(dapcIllus) example(eHGDP) example(H3N2) ## End(Not run) ## H3N2 EXAMPLE ## data(H3N2) pop(H3N2) <- factor(H3N2$other$epid) dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5) ## remove internal segments and ellipses, different pch, add MStree scatter(dapc1, cell=0, pch=18:23, cstar=0, mstree=TRUE, lwd=2, lty=2) ## label individuals at the periphery # air = 2 is a measure of how much space each label needs # pch = NA suppresses plotting of points scatter(dapc1, label.inds = list(air = 2, pch = NA)) ## only ellipse, custom labels scatter(dapc1, cell=2, pch="", cstar=0, posi.da="top", label=paste("year\n",2001:2006), axesel=FALSE, col=terrain.colors(10)) ## SHOW COMPOPLOT ON MICROBOV DATA ## data(microbov) dapc1 <- dapc(microbov, n.pca=20, n.da=15) compoplot(dapc1, lab="") ## Not run: ## EXAMPLE USING GENLIGHT OBJECTS ## ## simulate data x <- glSim(50,4e3-50, 50, ploidy=2) x plot(x) ## perform DAPC dapc1 <- dapc(x, n.pca=10, n.da=1) dapc1 ## plot results scatter(dapc1, scree.da=FALSE) ## SNP contributions loadingplot(dapc1$var.contr) loadingplot(tail(dapc1$var.contr, 100), main="Loading plot - last 100 SNPs") ## USE "PREDICT" TO PREDICT GROUPS OF NEW INDIVIDUALS ## ## load data data(sim2pop) ## we make a dataset of: ## 30 individuals from pop A ## 30 individuals from pop B ## 30 hybrids ## separate populations and make F1 temp <- seppop(sim2pop) temp <- lapply(temp, function(e) hybridize(e,e,n=30)) # force equal popsizes ## make hybrids hyb <- hybridize(temp[[1]], temp[[2]], n=30) ## repool data - needed to ensure allele matching newdat <- repool(temp[[1]], temp[[2]], hyb) pop(newdat) <- rep(c("pop A", "popB", "hyb AB"), c(30,30,30)) ## perform the DAPC on the first 2 pop (60 first indiv) dapc1 <- dapc(newdat[1:60],n.pca=5,n.da=1) ## plot results scatter(dapc1, scree.da=FALSE) ## make prediction for the 30 hybrids hyb.pred <- predict(dapc1, newdat[61:90]) hyb.pred ## plot the inferred coordinates (circles are hybrids) points(hyb.pred$ind.scores, rep(.1, 30)) ## look at assignment using assignplot assignplot(dapc1, new.pred=hyb.pred) title("30 indiv popA, 30 indiv pop B, 30 hybrids") ## image using compoplot compoplot(dapc1, new.pred=hyb.pred, ncol=2) title("30 indiv popA, 30 indiv pop B, 30 hybrids") ## CROSS-VALIDATION ## data(sim2pop) xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=3) xval boxplot(xval$success~xval$n.pca, xlab="Number of PCA components", ylab="Classification succes", main="DAPC - cross-validation") ## End(Not run)## data(dapcIllus), data(eHGDP), and data(H3N2) illustrate the dapc ## see ?dapcIllus, ?eHGDP, ?H3N2 ## ## Not run: example(dapcIllus) example(eHGDP) example(H3N2) ## End(Not run) ## H3N2 EXAMPLE ## data(H3N2) pop(H3N2) <- factor(H3N2$other$epid) dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5) ## remove internal segments and ellipses, different pch, add MStree scatter(dapc1, cell=0, pch=18:23, cstar=0, mstree=TRUE, lwd=2, lty=2) ## label individuals at the periphery # air = 2 is a measure of how much space each label needs # pch = NA suppresses plotting of points scatter(dapc1, label.inds = list(air = 2, pch = NA)) ## only ellipse, custom labels scatter(dapc1, cell=2, pch="", cstar=0, posi.da="top", label=paste("year\n",2001:2006), axesel=FALSE, col=terrain.colors(10)) ## SHOW COMPOPLOT ON MICROBOV DATA ## data(microbov) dapc1 <- dapc(microbov, n.pca=20, n.da=15) compoplot(dapc1, lab="") ## Not run: ## EXAMPLE USING GENLIGHT OBJECTS ## ## simulate data x <- glSim(50,4e3-50, 50, ploidy=2) x plot(x) ## perform DAPC dapc1 <- dapc(x, n.pca=10, n.da=1) dapc1 ## plot results scatter(dapc1, scree.da=FALSE) ## SNP contributions loadingplot(dapc1$var.contr) loadingplot(tail(dapc1$var.contr, 100), main="Loading plot - last 100 SNPs") ## USE "PREDICT" TO PREDICT GROUPS OF NEW INDIVIDUALS ## ## load data data(sim2pop) ## we make a dataset of: ## 30 individuals from pop A ## 30 individuals from pop B ## 30 hybrids ## separate populations and make F1 temp <- seppop(sim2pop) temp <- lapply(temp, function(e) hybridize(e,e,n=30)) # force equal popsizes ## make hybrids hyb <- hybridize(temp[[1]], temp[[2]], n=30) ## repool data - needed to ensure allele matching newdat <- repool(temp[[1]], temp[[2]], hyb) pop(newdat) <- rep(c("pop A", "popB", "hyb AB"), c(30,30,30)) ## perform the DAPC on the first 2 pop (60 first indiv) dapc1 <- dapc(newdat[1:60],n.pca=5,n.da=1) ## plot results scatter(dapc1, scree.da=FALSE) ## make prediction for the 30 hybrids hyb.pred <- predict(dapc1, newdat[61:90]) hyb.pred ## plot the inferred coordinates (circles are hybrids) points(hyb.pred$ind.scores, rep(.1, 30)) ## look at assignment using assignplot assignplot(dapc1, new.pred=hyb.pred) title("30 indiv popA, 30 indiv pop B, 30 hybrids") ## image using compoplot compoplot(dapc1, new.pred=hyb.pred, ncol=2) title("30 indiv popA, 30 indiv pop B, 30 hybrids") ## CROSS-VALIDATION ## data(sim2pop) xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=3) xval boxplot(xval$success~xval$n.pca, xlab="Number of PCA components", ylab="Classification succes", main="DAPC - cross-validation") ## End(Not run)
The function xvalDapc performs stratified cross-validation of DAPC
using varying numbers of PCs (and keeping the number of discriminant
functions fixed); xvalDapc is a generic with methods for
data.frame and matrix.
xvalDapc(x, ...) ## Default S3 method: xvalDapc(x, grp, n.pca.max = 300, n.da = NULL, training.set = 0.9, result = c("groupMean", "overall"), center = TRUE, scale = FALSE, n.pca=NULL, n.rep = 30, xval.plot = TRUE, ...) ## S3 method for class 'data.frame' xvalDapc(x, grp, n.pca.max = 300, n.da = NULL, training.set = 0.9, result = c("groupMean", "overall"), center = TRUE, scale = FALSE, n.pca=NULL, n.rep = 30, xval.plot = TRUE, ...) ## S3 method for class 'matrix' xvalDapc(x, grp, n.pca.max = 300, n.da = NULL, training.set = 0.9, result = c("groupMean", "overall"), center = TRUE, scale = FALSE, n.pca=NULL, n.rep = 30, xval.plot = TRUE, ...) ## S3 method for class 'genlight' xvalDapc(x, ...) ## S3 method for class 'genind' xvalDapc(x, ...)xvalDapc(x, ...) ## Default S3 method: xvalDapc(x, grp, n.pca.max = 300, n.da = NULL, training.set = 0.9, result = c("groupMean", "overall"), center = TRUE, scale = FALSE, n.pca=NULL, n.rep = 30, xval.plot = TRUE, ...) ## S3 method for class 'data.frame' xvalDapc(x, grp, n.pca.max = 300, n.da = NULL, training.set = 0.9, result = c("groupMean", "overall"), center = TRUE, scale = FALSE, n.pca=NULL, n.rep = 30, xval.plot = TRUE, ...) ## S3 method for class 'matrix' xvalDapc(x, grp, n.pca.max = 300, n.da = NULL, training.set = 0.9, result = c("groupMean", "overall"), center = TRUE, scale = FALSE, n.pca=NULL, n.rep = 30, xval.plot = TRUE, ...) ## S3 method for class 'genlight' xvalDapc(x, ...) ## S3 method for class 'genind' xvalDapc(x, ...)
x |
|
grp |
a |
n.pca.max |
maximum number of PCA components to retain. |
n.da |
an |
training.set |
the proportion of data (individuals) to be used for the training set; defaults to 0.9 if all groups have >= 10 members; otherwise, training.set scales automatically to the largest proportion that still ensures all groups will be present in both training and validation sets. |
result |
a character string; "groupMean" for group-wise assignment sucess, or "overall" for an overall mean assignment success; see details. |
center |
a |
scale |
a |
n.pca |
an |
n.rep |
the number of replicates to be carried out at each level of PC retention; defaults to 30. |
xval.plot |
a logical indicating whether a plot of the cross-validation results should be generated. |
... |
further arguments to be passed to |
The Discriminant Analysis of Principal Components (DAPC) relies on dimension reduction of the data using PCA followed by a linear discriminant analysis. How many PCA axes to retain is often a non-trivial question. Cross validation provides an objective way to decide how many axes to retain: different numbers are tried and the quality of the corresponding DAPC is assessed by cross- validation: DAPC is performed on a training set, typically made of 90% of the observations (comprising 90% of the observations in each subpopulation) , and then used to predict the groups of the 10% of remaining observations. The current method uses the average prediction success per group (result="groupMean"), or the overall prediction success (result="overall"). The number of PCs associated with the lowest Mean Squared Error is then retained in the DAPC.
The permutation of the data for cross-validation is performed in part by the
functionboot. If you have a modern computer, it is
likely that you have multiple cores on your system. R by default utilizes
only one of these cores unless you tell it otherwise. For details, please
see the documentation of boot. Basically, if you want to
use multiple cores, you need two arguments:
parallel - what R parallel system to use (see below)
ncpus - number of cores you want to use
If you are on a unix system (Linux or OSX), you will want to specify
parallel = "multicore". If you are on Windows, you will want to
specify parallel = "snow".
A list containing seven items, and a plot of the results. The
first is a data.frame with two columns, the first giving the number of
PCs of PCA retained in the corresponding DAPC, and the second giving the
proportion of successful group assignment for each replicate. The second item
gives the mean and confidence interval for random chance. The third gives the
mean successful assignment at each level of PC retention. The fourth indicates
which number of PCs is associated with the highest mean success. The fifth
gives the Root Mean Squared Error at each level of PC retention. The sixth
indicates which number of PCs is associated with the lowest MSE. The seventh
item contains the DAPC carried out with the optimal number of PCs, determined
with reference to MSE.
If xval.plot=TRUE a scatterplot of the results of cross-validation
will be displayed.
Caitlin Collins [email protected], Thibaut Jombart [email protected], Zhian N. Kamvar [email protected]
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
## Not run: ## CROSS-VALIDATION ## data(sim2pop) xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=3) xval ## 100 replicates ## # Serial version (SLOW!) system.time(xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=100)) # Parallel version (faster!) system.time(xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=100, parallel = "multicore", ncpus = 2)) ## End(Not run)## Not run: ## CROSS-VALIDATION ## data(sim2pop) xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=3) xval ## 100 replicates ## # Serial version (SLOW!) system.time(xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=100)) # Parallel version (faster!) system.time(xval <- xvalDapc(sim2pop@tab, pop(sim2pop), n.pca.max=100, n.rep=100, parallel = "multicore", ncpus = 2)) ## End(Not run)
These functions provide graphic outputs for Discriminant Analysis of
Principal Components (DAPC, Jombart et al. 2010). See ?dapc for
details about this method. DAPC graphics are detailed in the DAPC tutorial
accessible using vignette("adegenet-dapc").
These functions all require an object of class dapc
(the ".dapc" can be ommitted when calling the functions):
- scatter.dapc: produces scatterplots of principal components (or
'discriminant functions'), with a screeplot of eigenvalues as inset.
- assignplot: plot showing the probabilities of assignment of
individuals to the different clusters.
## S3 method for class 'dapc' scatter(x, xax=1, yax=2, grp=x$grp, col=seasun(length(levels(grp))), pch=20, bg="white", solid=.7, scree.da=TRUE, scree.pca=FALSE, posi.da="bottomright", posi.pca="bottomleft", bg.inset="white", ratio.da=.25, ratio.pca=.25, inset.da=0.02, inset.pca=0.02, inset.solid=.5, onedim.filled=TRUE, mstree=FALSE, lwd=1, lty=1, segcol="black", legend=FALSE, posi.leg="topright", cleg=1, txt.leg=levels(grp), cstar = 1, cellipse = 1.5, axesell = FALSE, label = levels(grp), clabel = 1, xlim = NULL, ylim = NULL, grid = FALSE, addaxes = TRUE, origin = c(0,0), include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft", cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, label.inds = NULL, ...) assignplot(x, only.grp=NULL, subset=NULL, new.pred=NULL, cex.lab=.75,pch=3)## S3 method for class 'dapc' scatter(x, xax=1, yax=2, grp=x$grp, col=seasun(length(levels(grp))), pch=20, bg="white", solid=.7, scree.da=TRUE, scree.pca=FALSE, posi.da="bottomright", posi.pca="bottomleft", bg.inset="white", ratio.da=.25, ratio.pca=.25, inset.da=0.02, inset.pca=0.02, inset.solid=.5, onedim.filled=TRUE, mstree=FALSE, lwd=1, lty=1, segcol="black", legend=FALSE, posi.leg="topright", cleg=1, txt.leg=levels(grp), cstar = 1, cellipse = 1.5, axesell = FALSE, label = levels(grp), clabel = 1, xlim = NULL, ylim = NULL, grid = FALSE, addaxes = TRUE, origin = c(0,0), include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft", cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, label.inds = NULL, ...) assignplot(x, only.grp=NULL, subset=NULL, new.pred=NULL, cex.lab=.75,pch=3)
x |
a |
xax, yax
|
|
grp |
a factor defining group membership for the individuals. The scatterplot is optimal only for the default group, i.e. the one used in the DAPC analysis. |
col |
a suitable color to be used for groups. The specified vector should match the number of groups, not the number of individuals. |
pch |
a |
bg |
the color used for the background of the scatterplot. |
solid |
a value between 0 and 1 indicating the alpha level for the colors of the plot; 0=full transparency, 1=solid colours. |
scree.da |
a logical indicating whether a screeplot of Discriminant Analysis eigenvalues should be displayed in inset (TRUE) or not (FALSE). |
scree.pca |
a logical indicating whether a screeplot of Principal Component Analysis eigenvalues should be displayed in inset (TRUE) or not (FALSE); retained axes are displayed in black. |
posi.da |
the position of the inset of DA eigenvalues; can match any combination of "top/bottom" and "left/right". |
posi.pca |
the position of the inset of PCA eigenvalues; can match any combination of "top/bottom" and "left/right". |
bg.inset |
the color to be used as background for the inset plots. |
ratio.da |
the size of the inset of DA eigenvalues as a proportion of the current plotting region. |
ratio.pca |
the size of the inset of PCA eigenvalues as a proportion of the current plotting region. |
inset.da |
a vector with two numeric values (recycled if needed) indicating
the inset to be used for the screeplot of DA eigenvalues as a proportion of the
current plotting region; see |
inset.pca |
a vector with two numeric values (recycled if needed) indicating
the inset to be used for the screeplot of PCA eigenvalues as a proportion of the
current plotting region; see |
inset.solid |
a value between 0 and 1 indicating the alpha level for the colors of the inset plots; 0=full transparency, 1=solid colours. |
onedim.filled |
a logical indicating whether curves should be filled when plotting a single discriminant function (TRUE), or not (FALSE). |
mstree |
a logical indicating whether a minimum spanning tree linking the groups and based on the squared distances between the groups inside the entire space should added to the plot (TRUE), or not (FALSE). |
lwd, lty, segcol
|
the line width, line type, and segment colour to be used for the minimum spanning tree. |
legend |
a logical indicating whether a legend for group colours should added to the plot (TRUE), or not (FALSE). |
posi.leg |
the position of the legend for group colours; can match any
combination of "top/bottom" and "left/right", or a set of x/y coordinates stored
as a list ( |
cleg |
a size factor used for the legend. |
cstar, cellipse, axesell, label, clabel, xlim, ylim, grid, addaxes, origin, include.origin, sub, csub, possub, cgrid, pixmap, contour, area
|
arguments
passed to |
only.grp |
a |
subset |
|
new.pred |
an optional list, as returned by the |
cex.lab |
a |
txt.leg |
a character vector indicating the text to be used in
the legend; if not provided, group names stored in |
label.inds |
Named list of arguments passed to the
|
... |
further arguments to be passed to other functions. For
|
See the documentation of dapc for more information about the method.
All functions return the matched call.
Thibaut Jombart [email protected]
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
- dapc: implements the DAPC.
- find.clusters: to identify clusters without prior.
- dapcIllus: a set of simulated data illustrating the DAPC
- eHGDP, H3N2: empirical datasets illustrating
DAPC
## Not run: data(H3N2) dapc1 <- dapc(H3N2, pop=H3N2$other$epid, n.pca=30,n.da=6) ## defautl plot ## scatter(dapc1) ## label individuals at the periphery # air = 2 is a measure of how much space each label needs # pch = NA suppresses plotting of points scatter(dapc1, label.inds = list(air = 2, pch = NA)) ## showing different scatter options ## ## remove internal segments and ellipses, different pch, add MStree scatter(dapc1, pch=18:23, cstar=0, mstree=TRUE, lwd=2, lty=2, posi.da="topleft") ## only ellipse, custom labels, use insets scatter(dapc1, cell=2, pch="", cstar=0, posi.pca="topleft", posi.da="topleft", scree.pca=TRUE, inset.pca=c(.01,.3), label=paste("year\n",2001:2006), axesel=FALSE, col=terrain.colors(10)) ## without ellipses, use legend for groups scatter(dapc1, cell=0, cstar=0, scree.da=FALSE, clab=0, cex=3, solid=.4, bg="white", leg=TRUE, posi.leg="topleft") ## only one axis scatter(dapc1,1,1,scree.da=FALSE, legend=TRUE, solid=.4,bg="white") ## example using genlight objects ## ## simulate data x <- glSim(50,4e3-50, 50, ploidy=2) x plot(x) ## perform DAPC dapc2 <- dapc(x, n.pca=10, n.da=1) dapc2 ## plot results scatter(dapc2, scree.da=FALSE, leg=TRUE, txt.leg=paste("group", c('A','B')), col=c("red","blue")) ## SNP contributions loadingplot(dapc2$var.contr) loadingplot(tail(dapc2$var.contr, 100), main="Loading plot - last 100 SNPs") ## assignplot / compoplot ## assignplot(dapc1, only.grp=2006) data(microbov) dapc3 <- dapc(microbov, n.pca=20, n.da=15) compoplot(dapc3, lab="") ## End(Not run)## Not run: data(H3N2) dapc1 <- dapc(H3N2, pop=H3N2$other$epid, n.pca=30,n.da=6) ## defautl plot ## scatter(dapc1) ## label individuals at the periphery # air = 2 is a measure of how much space each label needs # pch = NA suppresses plotting of points scatter(dapc1, label.inds = list(air = 2, pch = NA)) ## showing different scatter options ## ## remove internal segments and ellipses, different pch, add MStree scatter(dapc1, pch=18:23, cstar=0, mstree=TRUE, lwd=2, lty=2, posi.da="topleft") ## only ellipse, custom labels, use insets scatter(dapc1, cell=2, pch="", cstar=0, posi.pca="topleft", posi.da="topleft", scree.pca=TRUE, inset.pca=c(.01,.3), label=paste("year\n",2001:2006), axesel=FALSE, col=terrain.colors(10)) ## without ellipses, use legend for groups scatter(dapc1, cell=0, cstar=0, scree.da=FALSE, clab=0, cex=3, solid=.4, bg="white", leg=TRUE, posi.leg="topleft") ## only one axis scatter(dapc1,1,1,scree.da=FALSE, legend=TRUE, solid=.4,bg="white") ## example using genlight objects ## ## simulate data x <- glSim(50,4e3-50, 50, ploidy=2) x plot(x) ## perform DAPC dapc2 <- dapc(x, n.pca=10, n.da=1) dapc2 ## plot results scatter(dapc2, scree.da=FALSE, leg=TRUE, txt.leg=paste("group", c('A','B')), col=c("red","blue")) ## SNP contributions loadingplot(dapc2$var.contr) loadingplot(tail(dapc2$var.contr, 100), main="Loading plot - last 100 SNPs") ## assignplot / compoplot ## assignplot(dapc1, only.grp=2006) data(microbov) dapc3 <- dapc(microbov, n.pca=20, n.da=15) compoplot(dapc3, lab="") ## End(Not run)
Datasets illustrating the Discriminant Analysis of Principal Components
(DAPC, Jombart et al. submitted).
dapcIllus is list of 4 components being all genind objects.
These data were simulated using various models using Easypop (2.0.1). The
dapcIllus is a list containing the following genind
objects:
- "a": island model with 6 populations
- "b": hierarchical
island model with 6 populations (3,2,1)
- "c": one-dimensional stepping
stone with 2x6 populations, and a boundary between the two sets of 6
populations
- "d": one-dimensional stepping stone with 24 populations
See "source" for a reference providing simulation details.
Thibaut Jombart [email protected]
Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Submitted to BMC genetics.
Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Submitted to Genetics.
- dapc: implements the DAPC.
- eHGDP: dataset illustrating the DAPC and
find.clusters.
- H3N2: dataset illustrating the DAPC.
- find.clusters: to identify clusters without prior.
## Not run: data(dapcIllus) attach(dapcIllus) a # this is a genind object, like b, c, and d. ## FINS CLUSTERS EX NIHILO clust.a <- find.clusters(a, n.pca=100, n.clust=6) clust.b <- find.clusters(b, n.pca=100, n.clust=6) clust.c <- find.clusters(c, n.pca=100, n.clust=12) clust.d <- find.clusters(d, n.pca=100, n.clust=24) ## examin outputs names(clust.a) lapply(clust.a, head) ## PERFORM DAPCs dapc.a <- dapc(a, pop=clust.a$grp, n.pca=100, n.da=5) dapc.b <- dapc(b, pop=clust.b$grp, n.pca=100, n.da=5) dapc.c <- dapc(c, pop=clust.c$grp, n.pca=100, n.da=11) dapc.d <- dapc(d, pop=clust.d$grp, n.pca=100, n.da=23) ## LOOK AT ONE RESULT dapc.a summary(dapc.a) ## FORM A LIST OF RESULTS FOR THE 4 DATASETS lres <- list(dapc.a, dapc.b, dapc.c, dapc.d) ## DRAW 4 SCATTERPLOTS par(mfrow=c(2,2)) lapply(lres, scatter) # detach data detach(dapcIllus) ## End(Not run)## Not run: data(dapcIllus) attach(dapcIllus) a # this is a genind object, like b, c, and d. ## FINS CLUSTERS EX NIHILO clust.a <- find.clusters(a, n.pca=100, n.clust=6) clust.b <- find.clusters(b, n.pca=100, n.clust=6) clust.c <- find.clusters(c, n.pca=100, n.clust=12) clust.d <- find.clusters(d, n.pca=100, n.clust=24) ## examin outputs names(clust.a) lapply(clust.a, head) ## PERFORM DAPCs dapc.a <- dapc(a, pop=clust.a$grp, n.pca=100, n.da=5) dapc.b <- dapc(b, pop=clust.b$grp, n.pca=100, n.da=5) dapc.c <- dapc(c, pop=clust.c$grp, n.pca=100, n.da=11) dapc.d <- dapc(d, pop=clust.d$grp, n.pca=100, n.da=23) ## LOOK AT ONE RESULT dapc.a summary(dapc.a) ## FORM A LIST OF RESULTS FOR THE 4 DATASETS lres <- list(dapc.a, dapc.b, dapc.c, dapc.d) ## DRAW 4 SCATTERPLOTS par(mfrow=c(2,2)) lapply(lres, scatter) # detach data detach(dapcIllus) ## End(Not run)
The function df2genind converts a data.frame (or a matrix) into a
genind object. The data.frame must meet the following
requirements:
genotypes are in row (one row per genotype)
markers/loci are in columns
each element is a string of characters coding alleles, ideally
separated by a character string (argument sep); if no separator is
used, the number of characters coding alleles must be indicated (argument
ncode).
df2genind( X, sep = NULL, ncode = NULL, ind.names = NULL, loc.names = NULL, pop = NULL, NA.char = "", ploidy = 2, type = c("codom", "PA"), strata = NULL, hierarchy = NULL, check.ploidy = getOption("adegenet.check.ploidy") )df2genind( X, sep = NULL, ncode = NULL, ind.names = NULL, loc.names = NULL, pop = NULL, NA.char = "", ploidy = 2, type = c("codom", "PA"), strata = NULL, hierarchy = NULL, check.ploidy = getOption("adegenet.check.ploidy") )
X |
a matrix or a data.frame containing allelle data only (see decription) |
sep |
a character string separating alleles. See details. |
ncode |
an optional integer giving the number of characters used for coding one genotype at one locus. If not provided, this is determined from data. |
ind.names |
optinal, a vector giving the individuals names; if NULL, taken from rownames of X. If factor or numeric, vector is converted to character. |
loc.names |
an optional character vector giving the markers names; if NULL, taken from colnames of X. |
pop |
an optional factor giving the population of each individual. |
NA.char |
a character string corresponding to missing allele (to be treated as NA) |
ploidy |
an integer indicating the degree of ploidy of the genotypes. |
type |
a character string indicating the type of marker: 'codom' stands for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for 'presence/absence' markers (e.g. AFLP, RAPD). |
strata |
an optional data frame that defines population stratifications for your samples. This is especially useful if you have a hierarchical or factorial sampling design. |
hierarchy |
a hierarchical formula that explicitely defines hierarchical
levels in your strata. see |
check.ploidy |
a boolean indicating if the ploidy should be checked (TRUE, default) or not (FALSE). Not checking the ploidy makes the import much faster, but might result in bugs/problems if the input file is misread or the ploidy is wrong. It is therefore advised to first import and check a subset of data to see if everything works as expected before setting this option to false. |
See genind2df to convert genind objects back to
such a data.frame.
=== Details for the sep argument ===
this character is directly
used in reguar expressions like gsub, and thus require some characters
to be preceeded by double backslashes. For instance, "/" works but "|" must
be coded as "\|".
an object of the class genind for df2genind; a
matrix of biallelic genotypes for genind2df
Thibaut Jombart [email protected], Zhian N. Kamvar [email protected]
genind2df, import2genind,
read.genetix, read.fstat,
read.structure
## simple example df <- data.frame(locusA=c("11","11","12","32"), locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22")) row.names(df) <- .genlab("genotype",4) df obj <- df2genind(df, ploidy=2, ncode=1) obj tab(obj) ## converting a genind as data.frame genind2df(obj) genind2df(obj, sep="/")## simple example df <- data.frame(locusA=c("11","11","12","32"), locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22")) row.names(df) <- .genlab("genotype",4) df obj <- df2genind(df, ploidy=2, ncode=1) obj tab(obj) ## converting a genind as data.frame genind2df(obj) genind2df(obj, sep="/")
This function computes measures of genetic distances
between populations using a genpop object.
Currently, five distances are available, some of which are euclidian
(see details).
A non-euclidian distance can be transformed into an Euclidean one
using cailliez in order to perform a
Principal Coordinate Analysis dudi.pco (both
functions in ade4).
The function dist.genpop is based on former dist.genet
function of ade4 package.
dist.genpop(x, method = 1, diag = FALSE, upper = FALSE)dist.genpop(x, method = 1, diag = FALSE, upper = FALSE)
x |
a list of class |
method |
an integer between 1 and 5. See details |
diag |
a logical value indicating whether the diagonal of the distance matrix should be printed by |
upper |
a logical value indicating whether the upper triangle of the distance matrix should be printed by |
Let A a table containing allelic frequencies with t populations (rows) and m alleles (columns).
Let the number of loci. The locus j gets m(j) alleles.
For the row i and the modality k of the variable j, notice the value (, ,
) the value of the initial table.
and
Let P the table of general term , ,
The option method computes the distance matrices between populations using the frequencies .
1. Nei's distance (not Euclidean):
2. Angular distance or Edwards' distance (Euclidean):
3. Coancestrality coefficient or Reynolds' distance (Eucledian):
4. Classical Euclidean distance or Rogers' distance (Eucledian):
5. Absolute genetics distance or Provesti 's distance (not Euclidean):
returns a distance matrix of class dist between the rows of the data frame
Thibaut Jombart [email protected]
Former dist.genet code by Daniel Chessel [email protected]
and documentation by Anne B. Dufour [email protected]
To complete informations about distances:
Distance 1:
Nei, M. (1972) Genetic distances between populations. American Naturalist, 106, 283–292.
Nei M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 23, 341–369.
Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.
Distance 2:
Edwards, A.W.F. (1971) Distance between populations on the basis of gene frequencies. Biometrics, 27, 873–881.
Cavalli-Sforza L.L. and Edwards A.W.F. (1967) Phylogenetic analysis: models and estimation procedures. Evolution, 32, 550–570.
Hartl, D.L. and Clark, A.G. (1989) Principles of population genetics. Sinauer Associates, Sunderland, Massachussetts (p. 303).
Distance 3:
Reynolds, J. B., B. S. Weir, and C. C. Cockerham. (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics, 105, 767–779.
Distance 4:
Rogers, J.S. (1972) Measures of genetic similarity and genetic distances. Studies in Genetics, Univ. Texas Publ., 7213, 145–153.
Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.
Distance 5:
Prevosti A. (1974) La distancia genetica entre poblaciones. Miscellanea Alcobe, 68, 109–118.
Prevosti A., Ocaña J. and Alonso G. (1975) Distances between populations of Drosophila subobscura, based on chromosome arrangements frequencies. Theoretical and Applied Genetics, 45, 231–241.
For more information on dissimilarity indexes:
Gower J. and Legendre P. (1986) Metric and Euclidean properties of
dissimilarity coefficients. Journal of Classification, 3,
5–48
Legendre P. and Legendre L. (1998) Numerical Ecology, Elsevier
Science B.V. 20, pp274–288.
## Not run: data(microsatt) obj <- as.genpop(microsatt$tab) listDist <- lapply(1:5, function(i) cailliez(dist.genpop(obj,met=i))) for(i in 1:5) {attr(listDist[[i]],"Labels") <- popNames(obj)} listPco <- lapply(listDist, dudi.pco,scannf=FALSE) par(mfrow=c(2,3)) for(i in 1:5) {scatter(listPco[[i]],sub=paste("Dist:", i))} ## End(Not run)## Not run: data(microsatt) obj <- as.genpop(microsatt$tab) listDist <- lapply(1:5, function(i) cailliez(dist.genpop(obj,met=i))) for(i in 1:5) {attr(listDist[[i]],"Labels") <- popNames(obj)} listPco <- lapply(listDist, dudi.pco,scannf=FALSE) par(mfrow=c(2,3)) for(i in 1:5) {scatter(listPco[[i]],sub=paste("Dist:", i))} ## End(Not run)
This dataset consists of 1350 individuals from native Human populations distributed worldwide typed at 678 microsatellite loci. The original HGDP-CEPH panel [1-3] has been extended by several native American populations [4]. This dataset was used to illustrate the Discriminant Analysis of Principal Components (DAPC, [5]).
eHGDP is a genind object with a data frame named
popInfo as supplementary component (eHGDP@other$popInfo),
which contains the following variables:
a character vector indicating populations.
a character vector indicating the geographic region of each population.
a
character vector indicating the correspondence with population labels used
in the genind object (i.e., as output by pop(eHGDP)).
geographic coordinates of the populations, indicated as north and east degrees.
Original panel by Human Genome Diversity Project (HGDP) and Centre d'Etude du Polymorphisme Humain (CEPH). See reference [4] for Native American populations.
This copy of the dataset was prepared by Francois Balloux.
[1] Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, et al. (2002) Genetic structure of human populations. Science 298: 2381-2385.
[2] Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, et al. (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A 102: 15942-15947.
[3] Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, et al. (2002) A human genome diversity cell line panel. Science 296: 261-262.
[4] Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, et al. (2007) Genetic Variation and Population Structure in Native Americans. PLoS Genetics 3: e185.
[5] Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Submitted to BMC genetics.
## Not run: ## LOAD DATA data(eHGDP) eHGDP ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS ## to reproduce exactly analyses from the paper, use "n.pca=1000" dapc1 <- dapc(eHGDP, all.contrib=TRUE, scale=FALSE, n.pca=200, n.da=80) # takes 2 minutes dapc1 ## (see ?dapc for details about the output) ## SCREEPLOT OF EIGENVALUES barplot(dapc1$eig, main="eHGDP - DAPC eigenvalues", col=c("red","green","blue", rep("grey", 1000))) ## SCATTERPLOTS ## (!) Note: colors may be inverted with respect to [5] ## as signs of principal components are arbitrary ## and change from one computer to another ## ## axes 1-2 s.label(dapc1$grp.coord[,1:2], clab=0, sub="Axes 1-2") par(xpd=T) colorplot(dapc1$grp.coord[,1:2], dapc1$grp.coord, cex=3, add=TRUE) add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25) ## axes 2-3 s.label(dapc1$grp.coord[,2:3], clab=0, sub="Axes 2-3") par(xpd=T) colorplot(dapc1$grp.coord[,2:3], dapc1$grp.coord, cex=3, add=TRUE) add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25) ## MAP DAPC1 RESULTS if(require(maps)){ xy <- cbind(eHGDP$other$popInfo$Longitude, eHGDP$other$popInfo$Latitude) par(mar=rep(.1,4)) map(fill=TRUE, col="lightgrey") colorplot(xy, -dapc1$grp.coord, cex=3, add=TRUE, trans=FALSE) } ## LOOK FOR OTHER CLUSTERS ## to reproduce results of the reference paper, use : ## grp <- find.clusters(eHGDP, max.n=50, n.pca=200, scale=FALSE) ## and then ## plot(grp$Kstat, type="b", col="blue") grp <- find.clusters(eHGDP, max.n=30, n.pca=200, scale=FALSE, n.clust=4) # takes about 2 minutes names(grp) ## (see ?find.clusters for details about the output) ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS ## to reproduce exactly analyses from the paper, use "n.pca=1000" dapc2 <- dapc(eHGDP, pop=grp$grp, all.contrib=TRUE, scale=FALSE, n.pca=200, n.da=80) # takes around a 1 minute dapc2 ## PRODUCE SCATTERPLOT scatter(dapc2) # axes 1-2 scatter(dapc2,2,3) # axes 2-3 ## MAP DAPC2 RESULTS if(require(maps)){ xy <- cbind(eHGDP$other$popInfo$Longitude, eHGDP$other$popInfo$Latitude) myCoords <- apply(dapc2$ind.coord, 2, tapply, pop(eHGDP), mean) par(mar=rep(.1,4)) map(fill=TRUE, col="lightgrey") colorplot(xy, myCoords, cex=3, add=TRUE, trans=FALSE) } ## End(Not run)## Not run: ## LOAD DATA data(eHGDP) eHGDP ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS ## to reproduce exactly analyses from the paper, use "n.pca=1000" dapc1 <- dapc(eHGDP, all.contrib=TRUE, scale=FALSE, n.pca=200, n.da=80) # takes 2 minutes dapc1 ## (see ?dapc for details about the output) ## SCREEPLOT OF EIGENVALUES barplot(dapc1$eig, main="eHGDP - DAPC eigenvalues", col=c("red","green","blue", rep("grey", 1000))) ## SCATTERPLOTS ## (!) Note: colors may be inverted with respect to [5] ## as signs of principal components are arbitrary ## and change from one computer to another ## ## axes 1-2 s.label(dapc1$grp.coord[,1:2], clab=0, sub="Axes 1-2") par(xpd=T) colorplot(dapc1$grp.coord[,1:2], dapc1$grp.coord, cex=3, add=TRUE) add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25) ## axes 2-3 s.label(dapc1$grp.coord[,2:3], clab=0, sub="Axes 2-3") par(xpd=T) colorplot(dapc1$grp.coord[,2:3], dapc1$grp.coord, cex=3, add=TRUE) add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25) ## MAP DAPC1 RESULTS if(require(maps)){ xy <- cbind(eHGDP$other$popInfo$Longitude, eHGDP$other$popInfo$Latitude) par(mar=rep(.1,4)) map(fill=TRUE, col="lightgrey") colorplot(xy, -dapc1$grp.coord, cex=3, add=TRUE, trans=FALSE) } ## LOOK FOR OTHER CLUSTERS ## to reproduce results of the reference paper, use : ## grp <- find.clusters(eHGDP, max.n=50, n.pca=200, scale=FALSE) ## and then ## plot(grp$Kstat, type="b", col="blue") grp <- find.clusters(eHGDP, max.n=30, n.pca=200, scale=FALSE, n.clust=4) # takes about 2 minutes names(grp) ## (see ?find.clusters for details about the output) ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS ## to reproduce exactly analyses from the paper, use "n.pca=1000" dapc2 <- dapc(eHGDP, pop=grp$grp, all.contrib=TRUE, scale=FALSE, n.pca=200, n.da=80) # takes around a 1 minute dapc2 ## PRODUCE SCATTERPLOT scatter(dapc2) # axes 1-2 scatter(dapc2,2,3) # axes 2-3 ## MAP DAPC2 RESULTS if(require(maps)){ xy <- cbind(eHGDP$other$popInfo$Longitude, eHGDP$other$popInfo$Latitude) myCoords <- apply(dapc2$ind.coord, 2, tapply, pop(eHGDP), mean) par(mar=rep(.1,4)) map(fill=TRUE, col="lightgrey") colorplot(xy, myCoords, cex=3, add=TRUE, trans=FALSE) } ## End(Not run)
mvmapper is an interactive tool for visualising outputs of a
multivariate analysis on a map from a web browser. The function
export_to_mvmapper is a generic with methods for several standard
classes of analyses in adegenet and ade4. Information on
individual locations, as well as any other relevant data, is passed through
the second argument info. By default, the function returns a formatted
data.frame and writes the output to a .csv file.
export_to_mvmapper(x, ...) ## Default S3 method: export_to_mvmapper(x, ...) ## S3 method for class 'dapc' export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...) ## S3 method for class 'dudi' export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...) ## S3 method for class 'spca' export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)export_to_mvmapper(x, ...) ## Default S3 method: export_to_mvmapper(x, ...) ## S3 method for class 'dapc' export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...) ## S3 method for class 'dudi' export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...) ## S3 method for class 'spca' export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)
x |
The analysis to be exported. Can be a |
... |
Further arguments to pass to other methods. |
info |
A |
write_file |
A |
out_file |
A character string indicating the file to which the output
should be written. If NULL, the file used will be named
|
mvmapper can be found at:
https://popphylotools.github.io/mvMapper/
A data.frame which can serve as input to mvmapper,
containing at least the following columns:
key: unique individual identifiers
PC1: first principal component; further principal components are
optional, but if provided will be numbered and follow PC1.
lat: latitude for each individual
lon: longitude for each individual
In addition, specific information is added for some analyses:
spca: Lag_PC columns contain the lag-vectors of the
principal components; the lag operator computes, for each individual, the
average score of neighbouring individuals; it is useful for clarifying
patches and clines.
dapc: grp is the group used in the analysis;
assigned_grp is the group assignment based on the discriminant
functions; support is the statistical support (i.e. assignment
probability) for assigned_grp.
Thibaut Jombart [email protected]
mvmapper is available at:
https://popphylotools.github.io/mvMapper/
# An example using the microsatellite dataset of Dupuis et al. 2016 (781 # individuals, 10 loci, doi: 10.1111/jeb.12931) # Reading input file from adegenet input_data <- system.file("data/swallowtails.rda", package="adegenet") data(swallowtails) # conducting a DAPC (n.pca determined using xvalDapc, see ??xvalDapc) dapc1 <- dapc(swallowtails, n.pca=40, n.da=200) # read in swallowtails_loc.csv, which contains "key", "lat", and "lon" # columns with column headers (this example contains additional columns # containing species identifications, locality descriptions, and COI # haplotype clades) input_locs <- system.file("files/swallowtails_loc.csv", package = "adegenet") loc <- read.csv(input_locs, header = TRUE) # generate mvmapper input file, automatically write the output to a csv, and # name the output csv "mvMapper_Data.csv" out_dir <- tempdir() out_file <- file.path(out_dir, "mvMapper_Data.csv") out <- export_to_mvmapper(dapc1, loc, write_file = TRUE, out_file = out_file)# An example using the microsatellite dataset of Dupuis et al. 2016 (781 # individuals, 10 loci, doi: 10.1111/jeb.12931) # Reading input file from adegenet input_data <- system.file("data/swallowtails.rda", package="adegenet") data(swallowtails) # conducting a DAPC (n.pca determined using xvalDapc, see ??xvalDapc) dapc1 <- dapc(swallowtails, n.pca=40, n.da=200) # read in swallowtails_loc.csv, which contains "key", "lat", and "lon" # columns with column headers (this example contains additional columns # containing species identifications, locality descriptions, and COI # haplotype clades) input_locs <- system.file("files/swallowtails_loc.csv", package = "adegenet") loc <- read.csv(input_locs, header = TRUE) # generate mvmapper input file, automatically write the output to a csv, and # name the output csv "mvMapper_Data.csv" out_dir <- tempdir() out_file <- file.path(out_dir, "mvMapper_Data.csv") out <- export_to_mvmapper(dapc1, loc, write_file = TRUE, out_file = out_file)
The function read.PLINK reads a data file exported by the PLINK
software with extension '.raw' and converts it into a "genlight"
object. Optionally, information about SNPs can be read from a ".map" file,
either by specifying the argument map.file in read.PLINK, or
using extract.PLINKmap to add information to an existing
"genlight" object.
extract.PLINKmap(file, x = NULL) read.PLINK( file, map.file = NULL, quiet = FALSE, chunkSize = 1000, parallel = FALSE, n.cores = NULL, ... )extract.PLINKmap(file, x = NULL) read.PLINK( file, map.file = NULL, quiet = FALSE, chunkSize = 1000, parallel = FALSE, n.cores = NULL, ... )
file |
for |
x |
an optional object of the class |
map.file |
an optional character string indicating the path to a ".map"
file, which contains information about the SNPs (chromosome, position). If
provided, this information is processed by |
quiet |
logical stating whether a conversion messages should be printed (TRUE,default) or not (FALSE). |
chunkSize |
an integer indicating the number of genomes to be read at a time; larger values require more RAM but decrease the time needed to read the data. |
parallel |
a logical indicating whether multiple cores -if available-
should be used for the computations (TRUE, default), or not (FALSE);
requires the package |
n.cores |
if |
... |
other arguments to be passed to other functions - currently not used. |
The function reads data by chunks of several genomes (minimum 1, no maximum)
at a time, which allows one to read massive datasets with negligible RAM
requirements (albeit at a cost of computational time). The argument
chunkSize indicates the number of genomes read at a time. Increasing
this value decreases the computational time required to read data in, while
increasing memory requirements.
See details for the documentation about how to export data using PLINK to the '.raw' format.
=== Exporting data from PLINK ===
Data need to be exported from PLINK using the option "–recodeA" (and NOT
"–recodeAD"). The PLINK command should therefore look like: plink
--file data --recodeA. For more information on this topic, please look at
this webpage: http://zzz.bwh.harvard.edu/plink/
- read.PLINK: an object of the class "genlight"
- extract.PLINKmap: if a "genlight" is provided as argument
x, this object incorporating the new information about SNPs in the
@other slot (with new components 'chromosome' and 'position');
otherwise, a list with two components containing chromosome and position
information.
Thibaut Jombart [email protected]
- ?genlight for a description of the class
"genlight".
- read.snp: read SNPs in adegenet's '.snp' format.
- fasta2genlight: extract SNPs from alignments with fasta
format.
- other import function in adegenet: import2genind,
df2genind, read.genetix
read.fstat, read.structure,
read.genepop.
- another function read.plink is available in the package
snpMatrix.
The function fasta2DNAbin reads alignments with the fasta
format (extensions ".fasta", ".fas", or ".fa"), and outputs a
DNAbin object (the efficient DNA representation from the
ape package). The output contains either the full alignments, or only
SNPs. This implementation is designed for memory-efficiency,
and can read in larger datasets than Ape's read.dna.
The function reads data by chunks of a few genomes (minimum 1, no
maximum) at a time, which allows one to read massive datasets with
negligible RAM requirements (albeit at a cost of computational
time). The argument chunkSize indicates the number of genomes
read at a time. Increasing this value decreases the computational time
required to read data in, while increasing memory requirements.
fasta2DNAbin(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE)fasta2DNAbin(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE)
file |
a character string giving the path to the file to convert, with the extension ".fa", ".fas", or ".fasta". Can also be a connection (which will be opened for reading if
necessary, and if so |
quiet |
a logical stating whether a conversion messages should be printed (FALSE, default) or not (TRUE). |
chunkSize |
an integer indicating the number of genomes to be read at a time; larger values require more RAM but decrease the time needed to read the data. |
snpOnly |
a logical indicating whether SNPs only should be returned. |
an object of the class DNAbin
Thibaut Jombart [email protected]
- ?DNAbin for a description of the class DNAbin.
- read.snp: read SNPs in adegenet's '.snp' format.
- read.PLINK: read SNPs in PLINK's '.raw' format.
- df2genind: convert any multiallelic markers into
adegenet genind.
- import2genind: read multiallelic markers from various
software into adegenet.
## Not run: ## show the example file ## ## this is the path to the file: myPath <- system.file("files/usflu.fasta",package="adegenet") myPath ## read the file obj <- fasta2DNAbin(myPath, chunk=10) # process 10 sequences at a time obj ## End(Not run)## Not run: ## show the example file ## ## this is the path to the file: myPath <- system.file("files/usflu.fasta",package="adegenet") myPath ## read the file obj <- fasta2DNAbin(myPath, chunk=10) # process 10 sequences at a time obj ## End(Not run)
The function fasta2genlight reads alignments with the fasta
format (extensions ".fasta", ".fas", or ".fa"), extracts the binary
SNPs, and converts the output into a genlight object.
The function reads data by chunks of a few genomes (minimum 1, no
maximum) at a time, which allows one to read massive datasets with
negligible RAM requirements (albeit at a cost of computational
time). The argument chunkSize indicates the number of genomes
read at a time. Increasing this value decreases the computational time
required to read data in, while increasing memory requirements.
Multiple cores can be used to decrease the overall computational time
on parallel architectures (needs the package parallel).
fasta2genlight(file, quiet = FALSE, chunkSize = 1000, saveNbAlleles = FALSE, parallel = FALSE, n.cores = NULL, ...)fasta2genlight(file, quiet = FALSE, chunkSize = 1000, saveNbAlleles = FALSE, parallel = FALSE, n.cores = NULL, ...)
file |
a character string giving the path to the file to convert, with the extension ".fa", ".fas", or ".fasta". |
quiet |
logical stating whether a conversion messages should be printed (FALSE,default) or not (TRUE). |
chunkSize |
an integer indicating the number of genomes to be read at a time; larger values require more RAM but decrease the time needed to read the data. |
saveNbAlleles |
a logical indicating whether the number of
alleles for each loci in the original alignment should be saved in the
|
parallel |
a logical indicating whether multiple cores -if
available- should be used for the computations (TRUE, default), or
not (FALSE); requires the package |
n.cores |
if |
... |
other arguments to be passed to other functions - currently not used. |
=== Using multiple cores ===
Most recent machines have one or several processors with multiple
cores. R processes usually use one single core. The package
parallel allows for parallelizing some computations on
multiple cores, which decreases drastically computational time.
To use this functionality, you need to have the last version of the
parallel package installed.
an object of the class genlight
Thibaut Jombart [email protected]
- ?genlight for a description of the class genlight.
- read.snp: read SNPs in adegenet's '.snp' format.
- read.PLINK: read SNPs in PLINK's '.raw' format.
- df2genind: convert any multiallelic markers into
adegenet genind.
- import2genind: read multiallelic markers from various
software into adegenet.
## Not run: ## show the example file ## ## this is the path to the file: myPath <- system.file("files/usflu.fasta",package="adegenet") myPath ## read the file obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time obj ## look at extracted information position(obj) alleles(obj) locNames(obj) ## plot positions of polymorphic sites temp <- density(position(obj), bw=10) plot(temp, xlab="Position in the alignment", lwd=2, main="Location of the SNPs") points(position(obj), rep(0, nLoc(obj)), pch="|", col="red") ## End(Not run)## Not run: ## show the example file ## ## this is the path to the file: myPath <- system.file("files/usflu.fasta",package="adegenet") myPath ## read the file obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time obj ## look at extracted information position(obj) alleles(obj) locNames(obj) ## plot positions of polymorphic sites temp <- density(position(obj), bw=10) plot(temp, xlab="Position in the alignment", lwd=2, main="Location of the SNPs") points(position(obj), rep(0, nLoc(obj)), pch="|", col="red") ## End(Not run)
These functions implement the clustering procedure used in Discriminant Analysis
of Principal Components (DAPC, Jombart et al. 2010). This procedure consists in
running successive K-means with an increasing number of clusters (k),
after transforming data using a principal component analysis (PCA). For each
model, a statistical measure of goodness of fit (by default, BIC) is computed,
which allows to choose the optimal k. See details for a
description of how to select the optimal k and
vignette("adegenet-dapc") for a tutorial.
Optionally, hierarchical clustering can be sought by providing a prior
clustering of individuals (argument clust). In such case, clusters will
be sought within each prior group.
The K-means procedure used in find.clusters is
kmeans function from the stats package. The PCA
function is dudi.pca from the ade4 package, except
for genlight objects which use the glPca procedure
from adegenet.
find.clusters is a generic function with methods for the
following types of objects:
data.frame (only numeric data)
matrix (only numeric data)
genind objects (genetic markers)
genlight objects (genome-wide SNPs)
## S3 method for class 'data.frame' find.clusters(x, clust = NULL, n.pca = NULL, n.clust = NULL, method = c("kmeans", "ward"), stat = c("BIC","AIC", "WSS"), choose.n.clust = TRUE, criterion = c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"), max.n.clust = round(nrow(x)/10), n.iter = 1e5, n.start = 10, center = TRUE, scale = TRUE, pca.select = c("nbEig","percVar"), perc.pca = NULL, ..., dudi = NULL) ## S3 method for class 'matrix' find.clusters(x, ...) ## S3 method for class 'genind' find.clusters(x, clust = NULL, n.pca = NULL, n.clust = NULL, method = c("kmeans", "ward"), stat = c("BIC","AIC", "WSS"), choose.n.clust = TRUE, criterion = c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"), max.n.clust = round(nrow(x@tab)/10), n.iter = 1e5, n.start = 10, scale = FALSE, truenames = TRUE, ...) ## S3 method for class 'genlight' find.clusters(x, clust = NULL, n.pca = NULL, n.clust = NULL, method = c("kmeans", "ward"), stat = c("BIC", "AIC", "WSS"), choose.n.clust = TRUE, criterion = c("diffNgroup", "min","goesup","smoothNgoesup", "goodfit"), max.n.clust = round(nInd(x)/10), n.iter = 1e5,n.start = 10, scale = FALSE, pca.select = c("nbEig","percVar"), perc.pca = NULL,glPca=NULL, ...)## S3 method for class 'data.frame' find.clusters(x, clust = NULL, n.pca = NULL, n.clust = NULL, method = c("kmeans", "ward"), stat = c("BIC","AIC", "WSS"), choose.n.clust = TRUE, criterion = c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"), max.n.clust = round(nrow(x)/10), n.iter = 1e5, n.start = 10, center = TRUE, scale = TRUE, pca.select = c("nbEig","percVar"), perc.pca = NULL, ..., dudi = NULL) ## S3 method for class 'matrix' find.clusters(x, ...) ## S3 method for class 'genind' find.clusters(x, clust = NULL, n.pca = NULL, n.clust = NULL, method = c("kmeans", "ward"), stat = c("BIC","AIC", "WSS"), choose.n.clust = TRUE, criterion = c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"), max.n.clust = round(nrow(x@tab)/10), n.iter = 1e5, n.start = 10, scale = FALSE, truenames = TRUE, ...) ## S3 method for class 'genlight' find.clusters(x, clust = NULL, n.pca = NULL, n.clust = NULL, method = c("kmeans", "ward"), stat = c("BIC", "AIC", "WSS"), choose.n.clust = TRUE, criterion = c("diffNgroup", "min","goesup","smoothNgoesup", "goodfit"), max.n.clust = round(nInd(x)/10), n.iter = 1e5,n.start = 10, scale = FALSE, pca.select = c("nbEig","percVar"), perc.pca = NULL,glPca=NULL, ...)
x |
|
clust |
an optional |
n.pca |
an |
n.clust |
an optinal |
method |
a |
stat |
a |
choose.n.clust |
a |
criterion |
a |
max.n.clust |
an |
n.iter |
an |
n.start |
an |
center |
a |
scale |
a |
pca.select |
a |
perc.pca |
a |
truenames |
a |
... |
further arguments to be passed to other functions. For
|
dudi |
optionally, a multivariate analysis with the class |
glPca |
an optional |
=== ON THE SELECTION OF K ===
(where K is the 'optimal' number of clusters)
So far, the analysis of data simulated under various population genetics models (see reference) suggested an ad hoc rule for the selection of the optimal number of clusters. First important result is that BIC seems more efficient than AIC and WSS to select the appropriate number of clusters (see example). The rule of thumb consists in increasing K until it no longer leads to an appreciable improvement of fit (i.e., to a decrease of BIC). In the most simple models (island models), BIC decreases until it reaches the optimal K, and then increases. In these cases, our rule amounts to choosing the lowest K. In other models such as stepping stones, the decrease of BIC often continues after the optimal K, but is much less steep.
An alternative approach is the automatic selection based on a fixed
criterion. Note that, in any case, it is highly recommended to look at
the graph of the BIC for different numbers of clusters as displayed
during the interactive cluster selection.
To use automated selection, set choose.n.clust to FALSE and specify
the criterion you want to use, from the following values:
- "diffNgroup": differences between successive values of the summary
statistics (by default, BIC) are splitted into two groups using a
Ward's clustering method (see ?hclust), to differentiate sharp
decrease from mild decreases or increases. The retained K is the one
before the first group switch. Appears to work well for
island/hierarchical models, and decently for isolation by distance
models, albeit with some unstability. Can be impacted by an initial,
very sharp decrease of the test statistics. IF UNSURE ABOUT THE
CRITERION TO USE, USE THIS ONE.
- "min": the model with the minimum summary statistics (as specified
by stat argument, BIC by default) is retained. Is likely to
work for simple island model, using BIC. It is likely to fail in
models relating to stepping stones, where the BIC always decreases
(albeit by a small amount) as K increases. In general, this approach
tends to over-estimate the number of clusters.
- "goesup": the selected model is the K after which increasing the number of clusters leads to increasing the summary statistics. Suffers from inaccuracy, since i) a steep decrease might follow a small 'bump' of increase of the statistics, and ii) increase might never happen, or happen after negligible decreases. Is likely to work only for clear-cut island models.
- "smoothNgoesup": a variant of "goesup", in which the summary statistics is first smoothed using a lowess approach. Is meant to be more accurate than "goesup" as it is less prone to stopping to small 'bumps' in the decrease of the statistics.
- "goodfit": another criterion seeking a good fit with a minimum number of clusters. This approach does not rely on differences between successive statistics, but on absolute fit. It selects the model with the smallest K so that the overall fit is above a given threshold.
The class find.clusters is a list with the following
components:
Kstat |
a |
stat |
a |
grp |
a |
size |
an |
Thibaut Jombart [email protected]
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11:94. doi:10.1186/1471-2156-11-94
- dapc: implements the DAPC.
- scatter.dapc: graphics for DAPC.
- dapcIllus: dataset illustrating the DAPC and find.clusters.
- eHGDP: dataset illustrating the DAPC and find.clusters.
- kmeans: implementation of K-means in the stat package.
- dudi.pca: implementation of PCA in the ade4 package.
## Not run: ## THIS ONE TAKES A FEW MINUTES TO RUN ## data(eHGDP) ## here, n.clust is specified, so that only on K value is used grp <- find.clusters(eHGDP, max.n=30, n.pca=200, scale=FALSE, n.clust=4) # takes about 2 minutes names(grp) grp$Kstat grp$stat ## to try different values of k (interactive) grp <- find.clusters(eHGDP, max.n=50, n.pca=200, scale=FALSE) ## and then, to plot BIC values: plot(grp$Kstat, type="b", col="blue") ## ANOTHER SIMPLE EXAMPLE ## data(sim2pop) # this actually contains 2 pop ## DETECTION WITH BIC (clear result) foo.BIC <- find.clusters(sim2pop, n.pca=100, choose=FALSE) plot(foo.BIC$Kstat, type="o", xlab="number of clusters (K)", ylab="BIC", col="blue", main="Detection based on BIC") points(2, foo.BIC$Kstat[2], pch="x", cex=3) mtext(3, tex="'X' indicates the actual number of clusters") ## DETECTION WITH AIC (less clear-cut) foo.AIC <- find.clusters(sim2pop, n.pca=100, choose=FALSE, stat="AIC") plot(foo.AIC$Kstat, type="o", xlab="number of clusters (K)", ylab="AIC", col="purple", main="Detection based on AIC") points(2, foo.AIC$Kstat[2], pch="x", cex=3) mtext(3, tex="'X' indicates the actual number of clusters") ## DETECTION WITH WSS (less clear-cut) foo.WSS <- find.clusters(sim2pop, n.pca=100, choose=FALSE, stat="WSS") plot(foo.WSS$Kstat, type="o", xlab="number of clusters (K)", ylab="WSS (residual variance)", col="red", main="Detection based on WSS") points(2, foo.WSS$Kstat[2], pch="x", cex=3) mtext(3, tex="'X' indicates the actual number of clusters") ## TOY EXAMPLE FOR GENLIGHT OBJECTS ## x <- glSim(100,500,500) x plot(x) grp <- find.clusters(x, n.pca = 100, choose = FALSE, stat = "BIC") plot(grp$Kstat, type = "o", xlab = "number of clusters (K)", ylab = "BIC", main = "find.clusters on a genlight object\n(two groups)") ## End(Not run)## Not run: ## THIS ONE TAKES A FEW MINUTES TO RUN ## data(eHGDP) ## here, n.clust is specified, so that only on K value is used grp <- find.clusters(eHGDP, max.n=30, n.pca=200, scale=FALSE, n.clust=4) # takes about 2 minutes names(grp) grp$Kstat grp$stat ## to try different values of k (interactive) grp <- find.clusters(eHGDP, max.n=50, n.pca=200, scale=FALSE) ## and then, to plot BIC values: plot(grp$Kstat, type="b", col="blue") ## ANOTHER SIMPLE EXAMPLE ## data(sim2pop) # this actually contains 2 pop ## DETECTION WITH BIC (clear result) foo.BIC <- find.clusters(sim2pop, n.pca=100, choose=FALSE) plot(foo.BIC$Kstat, type="o", xlab="number of clusters (K)", ylab="BIC", col="blue", main="Detection based on BIC") points(2, foo.BIC$Kstat[2], pch="x", cex=3) mtext(3, tex="'X' indicates the actual number of clusters") ## DETECTION WITH AIC (less clear-cut) foo.AIC <- find.clusters(sim2pop, n.pca=100, choose=FALSE, stat="AIC") plot(foo.AIC$Kstat, type="o", xlab="number of clusters (K)", ylab="AIC", col="purple", main="Detection based on AIC") points(2, foo.AIC$Kstat[2], pch="x", cex=3) mtext(3, tex="'X' indicates the actual number of clusters") ## DETECTION WITH WSS (less clear-cut) foo.WSS <- find.clusters(sim2pop, n.pca=100, choose=FALSE, stat="WSS") plot(foo.WSS$Kstat, type="o", xlab="number of clusters (K)", ylab="WSS (residual variance)", col="red", main="Detection based on WSS") points(2, foo.WSS$Kstat[2], pch="x", cex=3) mtext(3, tex="'X' indicates the actual number of clusters") ## TOY EXAMPLE FOR GENLIGHT OBJECTS ## x <- glSim(100,500,500) x plot(x) grp <- find.clusters(x, n.pca = 100, choose = FALSE, stat = "BIC") plot(grp$Kstat, type = "o", xlab = "number of clusters (K)", ylab = "BIC", main = "find.clusters on a genlight object\n(two groups)") ## End(Not run)
The function findMutations identifies mutations (position and
nature) of pairs of aligned DNA sequences. The function
graphMutations does the same thing but plotting mutations on a
directed graph.
Both functions are generics, but the only methods implemented in
adegenet so far is for DNAbin objects.
findMutations(...) ## S3 method for class 'DNAbin' findMutations(x, from=NULL, to=NULL, allcomb=TRUE, ...) graphMutations(...) ## S3 method for class 'DNAbin' graphMutations(x, from=NULL, to=NULL, allcomb=TRUE, plot=TRUE, curved.edges=TRUE, ...)findMutations(...) ## S3 method for class 'DNAbin' findMutations(x, from=NULL, to=NULL, allcomb=TRUE, ...) graphMutations(...) ## S3 method for class 'DNAbin' graphMutations(x, from=NULL, to=NULL, allcomb=TRUE, plot=TRUE, curved.edges=TRUE, ...)
x |
a |
from |
a vector indicating the DNA sequences from which mutations
should be found. If |
to |
a vector indicating the DNA sequences to which mutations
should be found. If |
allcomb |
a logical indicating whether all combinations of sequences (from and to) should be considered (TRUE, default), or not (FALSE). |
plot |
a logical indicating whether the graph should be plotted. |
curved.edges |
a logical indicating whether the edges of the graph should be curved. |
... |
further arguments to be passed to other methods. Used in
|
For findMutations, a named list indicating the mutations from
one sequence to another. For each comparison, a three-column matrix is
provided, corresponding to the nucleotides in first and second
sequence, and a summary of the mutation provided as:
[position]:[nucleotide in first sequence]->[nucleotide in second
sequence].
For graphMutations, a graph with the class igraph.
Thibaut Jombart [email protected].
The fasta2DNAbin to read fasta alignments with minimum
RAM use.
## Not run: data(woodmouse) ## mutations between first 3 sequences findMutations(woodmouse[1:3,]) ## mutations from the first to sequences 2 and 3 findMutations(woodmouse[1:3,], from=1) ## same, graphical display g <- graphMutations(woodmouse[1:3,], from=1) ## some manual checks as.character(woodmouse)[1:3,35] as.character(woodmouse)[1:3,36] as.character(woodmouse)[1:3,106] ## End(Not run)## Not run: data(woodmouse) ## mutations between first 3 sequences findMutations(woodmouse[1:3,]) ## mutations from the first to sequences 2 and 3 findMutations(woodmouse[1:3,], from=1) ## same, graphical display g <- graphMutations(woodmouse[1:3,], from=1) ## some manual checks as.character(woodmouse)[1:3,35] as.character(woodmouse)[1:3,36] as.character(woodmouse)[1:3,106] ## End(Not run)
These functions are under development. Please email the author before
using them for published work.
The function gengraph generates graphs based on genetic
distances, so that pairs of entities (individuals or populations) are
connected if and only if they are distant by less than a given
threshold distance. Graph algorithms and classes from the
igraph package are used.
gengraph is a generic function with methods for the
following types of objects:
- matrix (only numeric data)
- dist
- genind objects (genetic markers, individuals)
- genpop objects (genetic markers, populations)
- DNAbin objects (DNA sequences)
gengraph(x, ...) ## S3 method for class 'matrix' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'dist' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'genind' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'genpop' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, method=1, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'DNAbin' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...)gengraph(x, ...) ## S3 method for class 'matrix' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'dist' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'genind' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'genpop' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, method=1, truenames=TRUE, nbreaks=10, ...) ## S3 method for class 'DNAbin' gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...)
x |
a |
cutoff |
a |
ngrp |
an |
computeAll |
a |
plot |
a |
show.graph |
a |
col.pal |
a color palette used to define group colors. |
method |
an |
truenames |
a logical indicating whether original labels should be used for plotting (TRUE), as opposed to indices of sequences (FALSE). |
nbreaks |
an integer indicating the number of breaks used by the heuristic when seeking an exact number of groups. |
... |
further arguments to be used by other functions; currently not used. |
The class gengraph is a list with the following
components:
graph |
a graph of class |
clust |
a list containing group information: |
cutoff |
the value used as a cutoff point |
col |
the color used to plot each group. |
Original idea by Anne Cori and Christophe Fraser. Implementation by Thibaut Jombart [email protected].
The igraph package.
if(require(ape)){ data(woodmouse) g <- gengraph(woodmouse, cutoff=5) g plot(g$graph) }if(require(ape)){ data(woodmouse) g <- gengraph(woodmouse, cutoff=5) g plot(g$graph) }
The S4 class genind is used to store individual genotypes.
It contains several components described in the 'slots' section).
The summary of a genind object invisibly returns a list of component.
The function .valid.genind is for internal use.
The function genind creates a genind object from a valid table
of alleles corresponding to the @tab slot.
Note that as in other S4 classes, slots are accessed using @ instead
of $.
tab:(accessor: tab)
matrix integers containing genotypes data for
individuals (in rows) for all alleles (in columns). The table
differs depending on the @type slot:
- 'codom': values
are numbers of alleles, summing up to the
individuals' ploidies.
- 'PA': values are presence/absence of alleles.
In all cases, rows and columns are given generic names.
loc.fac:(accessor: locFac) locus
factor for the columns of tab
loc.n.all:(accessor: nAll) integer
vector giving the number of observed alleles per locus (see note)
all.names:(accessor: alleles) list
having one component per locus, each containing a character vector of allele
names
ploidy:(accessor: ploidy) an integer
vector indicating the degree of ploidy of the genotypes. Beware: 2 is not
an integer, but 2L or as.integer(2) is.
type:a character string indicating the type of marker: 'codom' stands for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP).
call:the matched call
strata:(accessor: strata) (optional)
data frame giving levels of population stratification for each individual
hierarchy:(accessor: hier) (optional,
currently unused) a hierarchical formula defining the
hierarchical levels in the @@strata slot.
pop:(accessor: pop) (optional) factor
giving the population of each individual
other:(accessor: other) (optional) a
list containing other information
The loc.n.all slot will reflect the number of columns per locus that
contain at least one observation. This means that the sum of the this vector
will not necessarily equal the number of columns in the data unless you use
drop = TRUE when subsetting.
Class "gen", directly.
Class "indInfo", directly.
signature(x = "genind"): give the names of the
components of a genind object
signature(x = "genind"): prints a genind object
signature(object = "genind"): shows a genind
object (same as print)
signature(object = "genind"): summarizes a
genind object, invisibly returning its content or suppress printing of auxiliary information by specifying verbose = FALSE
Thibaut Jombart [email protected]
as.genind, genind2genpop,
genpop, import2genind,
read.genetix, read.genepop,
read.fstat
Related classes:
- genpop for storing data per populations
- genlight for an efficient storage of binary SNPs genotypes
showClass("genind") obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet")) obj validObject(obj) summary(obj) ## Not run: # test inter-colonies structuration if(require(hierfstat)){ gtest <- gstat.randtest(obj,nsim=99) gtest plot(gtest) } # perform a between-class PCA pca1 <- dudi.pca(scaleGen(obj, NA.method="mean"),scannf=FALSE,scale=FALSE) pcabet1 <- between(pca1,obj@pop,scannf=FALSE) pcabet1 s.class(pcabet1$ls,obj@pop,sub="Inter-class PCA",possub="topleft",csub=2) add.scatter.eig(pcabet1$eig,2,xax=1,yax=2) ## End(Not run)showClass("genind") obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet")) obj validObject(obj) summary(obj) ## Not run: # test inter-colonies structuration if(require(hierfstat)){ gtest <- gstat.randtest(obj,nsim=99) gtest plot(gtest) } # perform a between-class PCA pca1 <- dudi.pca(scaleGen(obj, NA.method="mean"),scannf=FALSE,scale=FALSE) pcabet1 <- between(pca1,obj@pop,scannf=FALSE) pcabet1 s.class(pcabet1$ls,obj@pop,sub="Inter-class PCA",possub="topleft",csub=2) add.scatter.eig(pcabet1$eig,2,xax=1,yax=2) ## End(Not run)
The function genind2df converts a genind back to a
data.frame of raw allelic data.
genind2df(x, pop = NULL, sep = "", usepop = TRUE, oneColPerAll = FALSE)genind2df(x, pop = NULL, sep = "", usepop = TRUE, oneColPerAll = FALSE)
x |
a genind object |
pop |
an optional factor giving the population of each individual. |
sep |
a character string separating alleles. See details. |
usepop |
a logical stating whether the population (argument |
oneColPerAll |
a logical stating whether or not alleles should be split
into columns (defaults to |
a data.frame of raw allelic data, with individuals in rows and loci in column
Thibaut Jombart [email protected]
df2genind, import2genind, read.genetix,
read.fstat, read.structure
## simple example df <- data.frame(locusA=c("11","11","12","32"), locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22")) row.names(df) <- .genlab("genotype",4) df obj <- df2genind(df, ploidy=2, ncode=1) obj obj@tab ## converting a genind as data.frame genind2df(obj) genind2df(obj, sep="/")## simple example df <- data.frame(locusA=c("11","11","12","32"), locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22")) row.names(df) <- .genlab("genotype",4) df obj <- df2genind(df, ploidy=2, ncode=1) obj obj@tab ## converting a genind as data.frame genind2df(obj) genind2df(obj, sep="/")
The function genind2genpop converts genotypes data (genind) into
alleles counts per population (genpop).
genind2genpop( x, pop = NULL, quiet = FALSE, process.other = FALSE, other.action = mean )genind2genpop( x, pop = NULL, quiet = FALSE, process.other = FALSE, other.action = mean )
x |
an object of class |
pop |
a factor giving the population of each genotype in 'x' OR a formula specifying which strata are to be used when converting to a genpop object. If none provided, population factors are sought in x@pop, but if given, the argument prevails on x@pop. |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
process.other |
a logical indicating whether the |
other.action |
a function to be used when processing the |
=== 'missing' argument ===
The values of the 'missing' argument in
genind2genpop have the following effects:
- "NA": if all genotypes
of a population for a given allele are missing, count value will be NA
- "0": if all genotypes of a population for a given allele are missing, count
value will be 0
- "chi2": if all genotypes of a population for a given allele are missing,
count value will be that of a theoretical count in of a Chi-squared test.
This is obtained by the product of the margins sums divided by the total
number of alleles.
=== processing the @other slot ===
Essentially,
genind2genpop is about aggregating data per population. The function
can do the same for all numeric items in the @other slot provided
they have the same length (for vectors) or the same number of rows
(matrix-like objects) as the number of genotypes. When the case is
encountered and if process.other is TRUE, then these objects are
processed using the function defined in other.action per population.
For instance, spatial coordinates of genotypes would be averaged to obtain
population coordinates.
A genpop object. The component @other in 'x' is passed to the created genpop object.
Thibaut Jombart [email protected]
## simple conversion data(nancycats) nancycats catpop <- genind2genpop(nancycats) catpop summary(catpop) ## processing the @other slot data(sim2pop) sim2pop$other$foo <- letters sim2pop dim(sim2pop$other$xy) # matches the number of genotypes sim2pop$other$foo # does not match the number of genotypes obj <- genind2genpop(sim2pop, process.other=TRUE) obj$other # the new xy is the populations' centre pch <- as.numeric(pop(sim2pop)) col <- pop(sim2pop) levels(col) <- c("blue","red") col <- as.character(col) plot(sim2pop$other$xy, pch=pch, col=col) text(obj$other$xy, lab=row.names(obj$other$xy), col=c("blue","red"), cex=2, font=2) ## Not run: data(microbov) strata(microbov) <- data.frame(other(microbov)) summary(genind2genpop(microbov)) # Conversion based on population factor summary(genind2genpop(microbov, ~coun)) # Conversion based on country summary(genind2genpop(microbov, ~coun/spe)) # Conversion based on country and species ## End(Not run)## simple conversion data(nancycats) nancycats catpop <- genind2genpop(nancycats) catpop summary(catpop) ## processing the @other slot data(sim2pop) sim2pop$other$foo <- letters sim2pop dim(sim2pop$other$xy) # matches the number of genotypes sim2pop$other$foo # does not match the number of genotypes obj <- genind2genpop(sim2pop, process.other=TRUE) obj$other # the new xy is the populations' centre pch <- as.numeric(pop(sim2pop)) col <- pop(sim2pop) levels(col) <- c("blue","red") col <- as.character(col) plot(sim2pop$other$xy, pch=pch, col=col) text(obj$other$xy, lab=row.names(obj$other$xy), col=c("blue","red"), cex=2, font=2) ## Not run: data(microbov) strata(microbov) <- data.frame(other(microbov)) summary(genind2genpop(microbov)) # Conversion based on population factor summary(genind2genpop(microbov, ~coun)) # Conversion based on country summary(genind2genpop(microbov, ~coun/spe)) # Conversion based on country and species ## End(Not run)
These functions provide facilities for usual computations using genlight objects. When ploidy varies across individuals, the outputs of these functions depend on whether the information units are individuals, or alleles within individuals (see details).
These functions are:
- glSum: computes the sum of the number of second allele in each SNP.
- glNA: computes the number of missing values in each SNP.
- glMean: computes the mean number of second allele in each SNP.
- glVar: computes the variance of the number of second allele in each SNP.
- glDotProd: computes dot products between (possibly
centred/scaled) vectors of individuals - uses compiled C code - used
by glPca.
glSum(x, alleleAsUnit = TRUE, useC = FALSE) glNA(x, alleleAsUnit = TRUE) glMean(x, alleleAsUnit = TRUE) glVar(x, alleleAsUnit = TRUE) glDotProd(x, center = FALSE, scale = FALSE, alleleAsUnit = FALSE, parallel = FALSE, n.cores = NULL)glSum(x, alleleAsUnit = TRUE, useC = FALSE) glNA(x, alleleAsUnit = TRUE) glMean(x, alleleAsUnit = TRUE) glVar(x, alleleAsUnit = TRUE) glDotProd(x, center = FALSE, scale = FALSE, alleleAsUnit = FALSE, parallel = FALSE, n.cores = NULL)
x |
a genlight object |
alleleAsUnit |
a logical indicating whether alleles are considered as units (i.e., a diploid genotype equals two samples, a triploid, three, etc.) or whether individuals are considered as units of information. |
center |
a logical indicating whether SNPs should be centred to mean zero. |
scale |
a logical indicating whether SNPs should be scaled to unit variance. |
useC |
a logical indicating whether compiled C code should be used (TRUE) or not (FALSE, default). |
parallel |
a logical indicating whether multiple cores -if
available- should be used for the computations (TRUE, default), or
not (FALSE); requires the package |
n.cores |
if |
=== On the unit of information ===
In the cases where individuals can have different ploidy, computation of sums, means, etc. of allelic data depends on what we consider as a unit of information.
To estimate e.g. allele frequencies, unit of information can be
considered as the allele, so that a diploid genotype contains two
samples, a triploid individual, three samples, etc. In such a case,
all computations are done directly on the number of alleles. This
corresponds to alleleAsUnit = TRUE.
However, when the focus is put on studying differences/similarities
between individuals, the unit of information is the individual, and
all genotypes possess the same information no matter what their ploidy
is. In this case, computations are made after standardizing
individual genotypes to relative allele frequencies. This
corresponds to alleleAsUnit = FALSE.
Note that when all individuals have the same ploidy, this distinction does not hold any more.
A numeric vector containing the requested information.
Thibaut Jombart [email protected]
- genlight: class of object for storing massive binary
SNP data.
- dapc: Discriminant Analysis of Principal Components.
- glPca: PCA for genlight objects.
- glSim: a simple simulator for genlight objects.
- glPlot: plotting genlight objects.
## Not run: x <- new("genlight", list(c(0,0,1,1,0), c(1,1,1,0,0,1), c(2,1,1,1,1,NA))) x as.matrix(x) ploidy(x) ## compute statistics - allele as unit ## glNA(x) glSum(x) glMean(x) ## compute statistics - individual as unit ## glNA(x, FALSE) glSum(x, FALSE) glMean(x, FALSE) ## explanation: data are taken as relative frequencies temp <- as.matrix(x)/ploidy(x) apply(temp,2, function(e) sum(is.na(e))) # NAs apply(temp,2,sum, na.rm=TRUE) # sum apply(temp,2,mean, na.rm=TRUE) # mean ## End(Not run)## Not run: x <- new("genlight", list(c(0,0,1,1,0), c(1,1,1,0,0,1), c(2,1,1,1,1,NA))) x as.matrix(x) ploidy(x) ## compute statistics - allele as unit ## glNA(x) glSum(x) glMean(x) ## compute statistics - individual as unit ## glNA(x, FALSE) glSum(x, FALSE) glMean(x, FALSE) ## explanation: data are taken as relative frequencies temp <- as.matrix(x)/ploidy(x) apply(temp,2, function(e) sum(is.na(e))) # NAs apply(temp,2,sum, na.rm=TRUE) # sum apply(temp,2,mean, na.rm=TRUE) # mean ## End(Not run)
The class genlight is a formal (S4) class for storing a genotypes
of binary SNPs in a compact way, using a bit-level coding scheme.
This storage is most efficient with haploid data, where the memory
taken to represent data can be reduced more than 50 times. However,
genlight can be used for any level of ploidy, and still remain an
efficient storage mode.
A genlight object can be constructed from vectors of integers
giving the number of the second allele for each locus and each
individual (see 'Objects of the class genlight' below).
genlight stores multiple genotypes. Each genotype is stored
as a SNPbin object.
=== On the subsetting using [ ===
The function [ accepts the following extra arguments:
a logical stating whether elements of the
@other slot should be treated as well (TRUE), or not
(FALSE). If treated, elements of the list are examined for a
possible match of length (vectors, lists) or number of rows
(matrices, data frames) with the number of individuals. Those who
match are subsetted accordingly. Others are left as is, issuing a
warning unless the argument quiet is set to TRUE.
a logical indicating whether warnings should be issued
when trying to subset components of the @other slot which
do not match the number of individuals (TRUE), or not (FALSE,
default).
further arguments passed to the genlight constructor.
genlight objects can be created by calls to new("genlight",
...), where '...' can be the following arguments:
geninput genotypes, where each genotype is coded as a vector of numbers of the second allele. If a list, each slot of the list correspond to an individual; if a matrix or a data.frame, rows correspond to individuals and columns to SNPs. If individuals or loci are named in the input, these names will we stored in the produced object. All individuals are expected to have the same number of SNPs. Shorter genotypes are completed with NAs, issuing a warning.
ploidyan optional vector of integers indicating the ploidy of the genotypes. Genotypes can therefore have different ploidy. If not provided, ploidy will be guessed from the data (as the maximum number of second alleles in each individual).
ind.namesan optional vector of characters giving the labels of the genotypes.
loc.namesan optional vector of characters giving the labels of the SNPs.
loc.allan optional vector of characters indicating the alleles of each SNP; for each SNP, alleles must be coded by two letters separated by '/', e.g. 'a/t' is valid, but 'a t' or 'a |t' are not.
chromosomean optional factor indicating the chromosome to which each SNP belongs.
positionan optional vector of integers indicating the position of the SNPs.
otheran optional list storing miscellaneous information.
The following slots are the content of instances of the class
genlight; note that in most cases, it is better to retrieve
information via accessors (see below), rather than by accessing the
slots manually.
gen:a list of genotypes stored as SNPbin objects.
n.loc:an integer indicating the number of SNPs of the genotype.
ind.names:a vector of characters indicating the names of genotypes.
loc.names:a vector of characters indicating the names of SNPs.
loc.all:a vector of characters indicating the alleles of each SNP.
chromosome:an optional factor indicating the chromosome to which each SNP belongs.
position:an optional vector of integers indicating the position of the SNPs.
ploidy:a vector of integers indicating the ploidy of each individual.
pop:a factor indicating the population of each individual.
strata:a data frame containing different levels of population definition. (For methods, see addStrata and setPop)
hierarchy:a hierarchical formula defining the hierarchical levels in the @@strata slot.
other:a list containing other miscellaneous information.
Here is a list of methods available for genlight objects. Most of
these methods are accessors, that is, functions which are used to
retrieve the content of the object. Specific manpages can exist for
accessors with more than one argument. These are indicated by a '*'
symbol next to the method's name. This list also contains methods
for conversion from genlight to other classes.
signature(x = "genlight"): usual method to subset
objects in R. Is to be applied as if the object was a matrix where
genotypes were rows and SNPs were columns. Indexing can be done via
vectors of signed integers or of logicals. See details for extra
supported arguments.
signature(x = "genlight"): printing of the
object.
signature(x = "genlight"): similar to the @ operator;
used to access the content of slots of the object.
signature(x = "genlight"): similar to the @ operator;
used to replace the content of slots of the object.
signature(x = "genlight"): returns a table of
allele counts (see tab; additional arguments are
freq, a logical stating if relative frequencies should be
returned (use for varying ploidy), and NA.method, a character
indicating if missing values should be replaced by the mean
frequency("mean"), or left as is ("asis").
signature(x = "genlight"): returns the number of
individuals in the object.
signature(x = "genlight"): returns the number of
populations in the object.
signature(x = "genlight"): returns the number of
SNPs in the object.
signature(x = "genlight"): returns the number of
individuals and SNPs in the object, respectively.
signature(x = "genlight"): returns the names of
the slots of the object.
signature(x = "genlight"): returns the names of
the individuals, if provided when the object was constructed.
signature(x = "genlight"): sets the names of
the individuals using a character vector of length
nInd(x).
signature(x = "genlight"): returns the names of
the populations, if provided when the object was constructed.
signature(x = "genlight"): sets the names of
the populations using a character vector of length
nPop(x).
signature(x = "genlight"): returns the names of
the loci, if provided when the object was constructed.
signature(x = "genlight"): sets the names of
the SNPs using a character vector of length nLoc(x).
signature(x = "genlight"): returns the ploidy of
the genotypes.
signature(x = "genlight"): sets the ploidy of
the individuals using a vector of integers of size nInd(x);
if a single value is provided, the same ploidy is assumed for all
individuals.
signature(x = "genlight"): returns the indices
of missing values (NAs) as a list with one vector of integer for each individual.
signature(x = "genlight"): returns the names
of the alleles of each SNPs, if provided when the object was
constructed.
signature(x = "genlight"): sets the names
of the alleles of each SNPs using a character vector of length
nLoc(x); for each SNP, two alleles must be provided,
separated by a "/", e.g. 'a/t', 'c/a', etc.
signature(x = "genlight"): returns a factor
indicating the chromosome of each SNPs, or NULL if the information
is missing.
signature(x = "genlight"): sets the
chromosome to which SNPs belong using a factor of length
nLoc(x).
signature(x = "genlight"): shortcut for
chromosome.
signature(x = "genlight"): shortcut for
chromosome<-.
signature(x = "genlight"): returns an integer
vector indicating the position of each SNPs, or NULL if the
information is missing.
signature(x = "genlight"): sets the
positions of the SNPs using an integer vector of length
nLoc(x).
signature(x = "genlight"): returns a factor
indicating the population of each individual, if provided when the
object was constructed.
signature(x = "genlight"): sets the population
of each individual using a factor of length nInd(x).
signature(x = "genlight"): returns the content of
the slot @other.
signature(x = "genlight"): sets the content of
the slot @other.
signature(x = "genlight"): converts a
genlight object into a matrix of integers, with individuals
in rows and SNPs in columns. The S4 method 'as' can be used as
well (e.g. as(x, "matrix")).
signature(x = "genlight"): same as as.matrix.
signature(x = "genlight"): converts a
genlight object into a list of genotypes coded as vector of
integers (numbers of second allele). The S4 method 'as' can be
used as well (e.g. as(x, "list")).
signature(x = "genlight"): merges several
genlight objects by column, i.e. regroups data of
identical individuals genotyped for different SNPs.
signature(x = "genlight"): merges several
genlight objects by row, i.e. regroups data of
different individuals genotyped for the same SNPs.
Thibaut Jombart ([email protected])
Zhian N. Kamvar ([email protected])
Related class:
- SNPbin, for storing individual genotypes of
binary SNPs
- genind, for storing other types of genetic markers.
## Not run: ## TOY EXAMPLE ## ## create and convert data dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA)) x <- new("genlight", dat) x ## examine the content of the object names(x) x@gen x@gen[[1]]@snp # bit-level coding for first individual ## conversions as.list(x) as.matrix(x) ## round trips - must return TRUE identical(x, new("genlight", as.list(x))) # list identical(x, new("genlight", as.matrix(x))) # matrix identical(x, new("genlight", as.data.frame(x))) # data.frame ## test subsetting x[c(1,3)] # keep individuals 1 and 3 as.list(x[c(1,3)]) x[c(1,3), 1:2] # keep individuals 1 and 3, loci 1 and 2 as.list(x[c(1,3), 1:2]) x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)] # same, using logicals as.list(x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)]) ## REAL-SIZE EXAMPLE ## ## 50 genotypes of 1,000,000 SNPs dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE)) names(dat) <- paste("indiv", 1:length(dat)) print(object.size(dat), unit="aut") # size of the original data x <- new("genlight", dat) # conversion x print(object.size(x), unit="au") # size of the genlight object object.size(dat)/object.size(x) # conversion efficiency #### cbind, rbind #### a <- new("genlight", list(toto=rep(1,10), tata=rep(c(0,1), each=5), titi=c(NA, rep(1,9)) )) ara <- rbind(a,a) ara as.matrix(ara) aca <- cbind(a,a) aca as.matrix(aca) #### subsetting @other #### x <- new("genlight", list(a=1,b=0,c=1), other=list(1:3, letters,data.frame(2:4))) x other(x) x[2:3] other(x[2:3]) other(x[2:3, treatOther=FALSE]) #### seppop #### pop(x) # no population info pop(x) <- c("pop1","pop1", "pop2") # set population memberships pop(x) seppop(x) ## End(Not run)## Not run: ## TOY EXAMPLE ## ## create and convert data dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA)) x <- new("genlight", dat) x ## examine the content of the object names(x) x@gen x@gen[[1]]@snp # bit-level coding for first individual ## conversions as.list(x) as.matrix(x) ## round trips - must return TRUE identical(x, new("genlight", as.list(x))) # list identical(x, new("genlight", as.matrix(x))) # matrix identical(x, new("genlight", as.data.frame(x))) # data.frame ## test subsetting x[c(1,3)] # keep individuals 1 and 3 as.list(x[c(1,3)]) x[c(1,3), 1:2] # keep individuals 1 and 3, loci 1 and 2 as.list(x[c(1,3), 1:2]) x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)] # same, using logicals as.list(x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)]) ## REAL-SIZE EXAMPLE ## ## 50 genotypes of 1,000,000 SNPs dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE)) names(dat) <- paste("indiv", 1:length(dat)) print(object.size(dat), unit="aut") # size of the original data x <- new("genlight", dat) # conversion x print(object.size(x), unit="au") # size of the genlight object object.size(dat)/object.size(x) # conversion efficiency #### cbind, rbind #### a <- new("genlight", list(toto=rep(1,10), tata=rep(c(0,1), each=5), titi=c(NA, rep(1,9)) )) ara <- rbind(a,a) ara as.matrix(ara) aca <- cbind(a,a) aca as.matrix(aca) #### subsetting @other #### x <- new("genlight", list(a=1,b=0,c=1), other=list(1:3, letters,data.frame(2:4))) x other(x) x[2:3] other(x[2:3]) other(x[2:3, treatOther=FALSE]) #### seppop #### pop(x) # no population info pop(x) <- c("pop1","pop1", "pop2") # set population memberships pop(x) seppop(x) ## End(Not run)
An object of class genpop contain alleles counts
for several loci.
It contains several components (see 'slots' section).
Such object is obtained using genind2genpop which converts
individuals genotypes of known population into a genpop object.
Note that the function summary of a genpop object
returns a list of components.
Note that as in other S4 classes, slots are accessed using @ instead
of $.
tab:matrix of alleles counts for each combinaison of population (in rows) and alleles (in columns).
loc.fac:locus factor for the columns of tab
loc.n.all:integer vector giving the number of alleles per locus
all.names:list having one component per locus, each containing a character vector of alleles names
call:the matched call
ploidy:an integer indicating the degree of ploidy of the genotypes. Beware: 2 is not an integer, but as.integer(2) is.
type:a character string indicating the type of marker: 'codom' stands for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP).
other:(optional) a list containing other information
Class "gen", directly.
Class "popInfo", directly.
signature(x = "genpop"): give the names of the
components of a genpop object
signature(x = "genpop"): prints a genpop object
signature(object = "genpop"): shows a genpop
object (same as print)
signature(object = "genpop"): summarizes a
genpop object, invisibly returning its content or suppress printing of auxiliary information by specifying verbose = FALSE
Thibaut Jombart [email protected]
as.genpop, is.genpop,makefreq, genind, import2genind, read.genetix, read.genepop, read.fstat
obj1 <- import2genind(system.file("files/nancycats.gen", package="adegenet")) obj1 obj2 <- genind2genpop(obj1) obj2 ## Not run: data(microsatt) # use as.genpop to convert convenient count tab to genpop obj3 <- as.genpop(microsatt$tab) obj3 all(obj3@tab==microsatt$tab) # perform a correspondance analysis obj4 <- genind2genpop(obj1,missing="chi2") ca1 <- dudi.coa(as.data.frame(obj4@tab),scannf=FALSE) s.label(ca1$li,sub="Correspondance Analysis",csub=2) add.scatter.eig(ca1$eig,2,xax=1,yax=2,posi="top") ## End(Not run)obj1 <- import2genind(system.file("files/nancycats.gen", package="adegenet")) obj1 obj2 <- genind2genpop(obj1) obj2 ## Not run: data(microsatt) # use as.genpop to convert convenient count tab to genpop obj3 <- as.genpop(microsatt$tab) obj3 all(obj3@tab==microsatt$tab) # perform a correspondance analysis obj4 <- genind2genpop(obj1,missing="chi2") ca1 <- dudi.coa(as.data.frame(obj4@tab),scannf=FALSE) s.label(ca1$li,sub="Correspondance Analysis",csub=2) add.scatter.eig(ca1$eig,2,xax=1,yax=2,posi="top") ## End(Not run)
These two Monte Carlo tests are used to assess the existence of global
and local spatial structures. They can be used as an aid to interprete
global and local components of spatial Principal Component Analysis
(sPCA).
They rely on the decomposition of a data matrix X into global and local
components using multiple regression on Moran's Eigenvector Maps (MEMs).
They require a data matrix (X) and a list of weights derived from a
connection network. X is regressed onto global MEMs (U+) in the global
test and on local ones (U-) in the local test. One mean
is obtained for each MEM, the k highest being summed to form the test
statistic.
The reference distribution of these statistics are obtained by randomly permuting the rows of X.
global.rtest(X, listw, k = 1, nperm = 499) local.rtest(X, listw, k = 1, nperm = 499)global.rtest(X, listw, k = 1, nperm = 499) local.rtest(X, listw, k = 1, nperm = 499)
X |
a data matrix, with variables in columns |
listw |
a list of weights of class |
k |
integer: the number of highest |
nperm |
integer: the number of randomisations to be performed. |
This test is purely R code. A C or C++ version will be developped soon.
An object of class randtest.
Thibaut Jombart [email protected]
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity, 101, 92–103.
## Not run: data(sim2pop) if(require(spdep)){ cn <- chooseCN(sim2pop@other$xy,ask=FALSE,type=1,plot=FALSE,res="listw") # global test Gtest <- global.rtest(sim2pop@tab,cn) Gtest # local test Ltest <- local.rtest(sim2pop@tab,cn) Ltest } ## End(Not run)## Not run: data(sim2pop) if(require(spdep)){ cn <- chooseCN(sim2pop@other$xy,ask=FALSE,type=1,plot=FALSE,res="listw") # global test Gtest <- global.rtest(sim2pop@tab,cn) Gtest # local test Ltest <- local.rtest(sim2pop@tab,cn) Ltest } ## End(Not run)
These functions implement Principal Component Analysis (PCA) for
massive SNP datasets stored as genlight object. This
implementation has the advantage of never representing to complete data
matrix, therefore making huge economies in terms of rapid access
memory (RAM). When the parallel package is available,
glPca uses multiple-core ressources for more efficient
computations. glPca returns lists with the class glPca
(see 'value').
Other functions are defined for objects of this class:
- print: prints the content of a glPca object.
- scatter: produces scatterplots of principal components,
with a screeplot of eigenvalues as inset.
- loadingplot: plots the loadings of the analysis for one given
axis, using an adapted version of the generic function loadingplot.
glPca(x, center = TRUE, scale = FALSE, nf = NULL, loadings = TRUE, alleleAsUnit = FALSE, useC = TRUE, parallel = FALSE, n.cores = NULL, returnDotProd=FALSE, matDotProd=NULL) ## S3 method for class 'glPca' print(x, ...) ## S3 method for class 'glPca' scatter(x, xax = 1, yax = 2, posi = "bottomleft", bg = "white", ratio = 0.3, label = rownames(x$scores), clabel = 1, xlim = NULL, ylim = NULL, grid = TRUE, addaxes = TRUE, origin = c(0, 0), include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft", cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, ...) ## S3 method for class 'glPca' loadingplot(x, at=NULL, threshold=NULL, axis=1, fac=NULL, byfac=FALSE, lab=rownames(x$loadings), cex.lab=0.7, cex.fac=1, lab.jitter=0, main="Loading plot", xlab="SNP positions", ylab="Contributions", srt = 90, adj = c(0, 0.5), ...)glPca(x, center = TRUE, scale = FALSE, nf = NULL, loadings = TRUE, alleleAsUnit = FALSE, useC = TRUE, parallel = FALSE, n.cores = NULL, returnDotProd=FALSE, matDotProd=NULL) ## S3 method for class 'glPca' print(x, ...) ## S3 method for class 'glPca' scatter(x, xax = 1, yax = 2, posi = "bottomleft", bg = "white", ratio = 0.3, label = rownames(x$scores), clabel = 1, xlim = NULL, ylim = NULL, grid = TRUE, addaxes = TRUE, origin = c(0, 0), include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft", cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, ...) ## S3 method for class 'glPca' loadingplot(x, at=NULL, threshold=NULL, axis=1, fac=NULL, byfac=FALSE, lab=rownames(x$loadings), cex.lab=0.7, cex.fac=1, lab.jitter=0, main="Loading plot", xlab="SNP positions", ylab="Contributions", srt = 90, adj = c(0, 0.5), ...)
x |
for |
center |
a logical indicating whether the numbers of alleles should be centered; defaults to TRUE |
scale |
a logical indicating whether the numbers of alleles should be scaled; defaults to FALSE |
nf |
an integer indicating the number of principal components to be retained; if NULL, a screeplot of eigenvalues will be displayed and the user will be asked for a number of retained axes. |
loadings |
a logical indicating whether loadings of the alleles should be computed (TRUE, default), or not (FALSE). Vectors of loadings are not always useful, and can take a large amount of RAM when millions of SNPs are considered. |
alleleAsUnit |
a logical indicating whether alleles are considered as units (i.e., a diploid genotype equals two samples, a triploid, three, etc.) or whether individuals are considered as units of information. |
useC |
a logical indicating whether compiled C code should be used for faster computations; this option cannot be used alongside parallel option. |
parallel |
a logical indicating whether multiple cores -if
available- should be used for the computations (TRUE), or
not (FALSE, default); requires the package |
n.cores |
if |
returnDotProd |
a logical indicating whether the matrix of dot products between individuals should be returned (TRUE) or not (FALSE, default). |
matDotProd |
an optional matrix of dot products between individuals, NULL by default. This option is used internally to speed up computation time when re-running the same PCA several times. Leave this argument as NULL unless you really know what you are doing. |
... |
further arguments to be passed to other functions. |
xax, yax
|
|
posi, bg, ratio
|
arguments used to customize the inset in scatterplots
of |
label, clabel, xlim, ylim, grid, addaxes, origin, include.origin, sub, csub, possub, cgrid, pixmap, contour, area
|
arguments passed to |
at |
an optional numeric vector giving the abscissa at which loadings are plotted. Useful when variates are SNPs with a known position in an alignement. |
threshold |
a threshold value above which values of x are identified. By default, this is the third quartile of x. |
axis |
an integer indicating the column of x to be plotted; used only if x is a matrix-like object. |
fac |
a factor defining groups of SNPs. |
byfac |
a logical stating whether loadings should be averaged by
groups of SNPs, as defined by |
lab |
a character vector giving the labels used to annotate values above the threshold. |
cex.lab |
a numeric value indicating the size of annotations. |
cex.fac |
a numeric value indicating the size of annotations for groups of observations. |
lab.jitter |
a numeric value indicating the factor of randomisation for the position of annotations. Set to 0 (by default) implies no randomisation. |
main |
the main title of the figure. |
xlab |
the title of the x axis. |
ylab |
the title of the y axis. |
srt |
rotation of the labels; see ?text. |
adj |
adjustment of the labels; see ?text. |
=== Using multiple cores ===
Most recent machines have one or several processors with multiple
cores. R processes usually use one single core. The package
parallel allows for parallelizing some computations on
multiple cores, which can decrease drastically computational time.
Lastly, note that using compiled C code (useC=TRUE)is an
alternative for speeding up computations, but cannot be used together
with the parallel option.
=== glPca objects ===
The class glPca is a list with the following
components:
call |
the matched call. |
eig |
a numeric vector of eigenvalues. |
scores |
a matrix of principal components, containing the coordinates of each individual (in row) on each principal axis (in column). |
loadings |
(optional) a matrix of loadings, containing the loadings of each SNP (in row) for each principal axis (in column). |
-
=== other outputs ===
Other functions have different outputs:
- scatter return the matched call.
- loadingplot returns information about the most contributing
SNPs (see loadingplot.default)
Thibaut Jombart [email protected]
- genlight: class of object for storing massive binary
SNP data.
- glSim: a simple simulator for genlight objects.
- glPlot: plotting genlight objects.
- dapc: Discriminant Analysis of Principal Components.
## Not run: ## simulate a toy dataset x <- glSim(50,4e3, 50, ploidy=2) x plot(x) ## perform PCA pca1 <- glPca(x, nf=2) ## plot eigenvalues barplot(pca1$eig, main="eigenvalues", col=heat.colors(length(pca1$eig))) ## basic plot scatter(pca1, ratio=.2) ## plot showing groups s.class(pca1$scores, pop(x), col=colors()[c(131,134)]) add.scatter.eig(pca1$eig,2,1,2) ## End(Not run)## Not run: ## simulate a toy dataset x <- glSim(50,4e3, 50, ploidy=2) x plot(x) ## perform PCA pca1 <- glPca(x, nf=2) ## plot eigenvalues barplot(pca1$eig, main="eigenvalues", col=heat.colors(length(pca1$eig))) ## basic plot scatter(pca1, ratio=.2) ## plot showing groups s.class(pca1$scores, pop(x), col=colors()[c(131,134)]) add.scatter.eig(pca1$eig,2,1,2) ## End(Not run)
genlight object can be plotted using the function
glPlot, which is also used as the dedicated plot
method. These functions relie on image to represent SNPs
data. More specifically, colors are used to represent the number of
second allele for each locus and individual.
glPlot(x, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),...) ## S4 method for signature 'genlight' plot(x, y=NULL, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),...)glPlot(x, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),...) ## S4 method for signature 'genlight' plot(x, y=NULL, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),...)
x |
a genlight object. |
col |
an optional color vector; the first value corresponds to 0
alleles, the last value corresponds to the ploidy level of the
data. Therefore, the vector should have a length of ( |
legend |
a logical indicating whether a legend should be added to the plot. |
posi |
a character string indicating where the legend should be positioned. Can be any concatenation of "bottom"/"top" and "left"/"right". |
bg |
a color used as a background for the legend; by default,
transparent white is used; this may not be supported on some
devices, and therefore background should be specified
(e.g. |
... |
further arguments to be passed to |
y |
ununsed argument, present for compatibility with the
|
Thibaut Jombart [email protected]
- genlight: class of object for storing massive binary
SNP data.
- glSim: a simple simulator for genlight
objects.
- glPca: PCA for genlight objects.
## Not run: ## simulate data x <- glSim(100, 1e3, n.snp.struc=100, ploid=2) ## default plot glPlot(x) plot(x) # identical plot ## disable legend plot(x, leg=FALSE) ## use other colors plot(x, col=heat.colors(3), bg="white") ## End(Not run)## Not run: ## simulate data x <- glSim(100, 1e3, n.snp.struc=100, ploid=2) ## default plot glPlot(x) plot(x) # identical plot ## disable legend plot(x, leg=FALSE) ## use other colors plot(x, col=heat.colors(3), bg="white") ## End(Not run)
The function glSim simulates simple SNP data with the
possibility of contrasted structures between two groups
as well as background ancestral population structure.
Returned objects are instances of the class genlight.
glSim(n.ind, n.snp.nonstruc, n.snp.struc = 0, grp.size = c(0.5, 0.5), k = NULL, pop.freq = NULL, ploidy = 1, alpha = 0, parallel = FALSE, LD = TRUE, block.minsize = 10, block.maxsize = 1000, theta = NULL, sort.pop = FALSE, ...)glSim(n.ind, n.snp.nonstruc, n.snp.struc = 0, grp.size = c(0.5, 0.5), k = NULL, pop.freq = NULL, ploidy = 1, alpha = 0, parallel = FALSE, LD = TRUE, block.minsize = 10, block.maxsize = 1000, theta = NULL, sort.pop = FALSE, ...)
n.ind |
an integer indicating the number of individuals to be simulated. |
n.snp.nonstruc |
an integer indicating the number of non-structured SNPs to be simulated; for these SNPs, all individuals are drawn from the same binomial distribution. |
n.snp.struc |
an integer indicating the number of structured SNPs to be simulated; for these SNPs, different binomial distributions are used for the two simulated groups; frequencies of the derived alleles in groups A and B are built to differ (see details). |
grp.size |
a vector of length 2 specifying the proportions of the two phenotypic groups (must sum to 1). By default, both groups have the same size. |
k |
an integer specifying the number of ancestral populations to be generated. |
pop.freq |
a vector of length |
ploidy |
an integer indicating the ploidy of the simulated genotypes. |
alpha |
asymmetry parameter: a numeric value between 0 and 0.5, used to enforce allelic differences between the groups. Differences between groups are strongest when alpha = 0.5 and weakest when alpha = 0 (see details). |
parallel |
a logical indicating whether multiple cores should be used in generating the simulated data (TRUE). This option can reduce the amount of computational time required to simulate the data, but is not supported on Windows. |
LD |
a logical indicating whether loci should be displaying linkage disequilibrium (TRUE) or be generated independently (FALSE, default). When set to TRUE, data are generated by blocks of correlated SNPs (see details). |
block.minsize |
an optional integer indicating the minimum number of
SNPs to be handled at a time during the simulation of linked SNPs (when
|
block.maxsize |
an optional integer indicating the maximum number of SNPs to be handled at a time during the simulation of linked SNPs. Note: if LD blocks of equal size are desired, set block.minsize = block.maxsize. |
theta |
an optional numeric value between 0 and 0.5 specifying the extent to which linkage should be diluted. Linkage is strongest when theta = 0 and weakest when theta = 0.5. |
sort.pop |
a logical specifying whether individuals should be ordered by
ancestral population ( |
... |
arguments to be passed to the genlight constructor. |
=== Allele frequencies in contrasted groups ===
When n.snp.struc is greater than 0, some SNPs are simulated in
order to differ between groups (noted 'A' and 'B'). Different patterns
between groups are achieved by using different
frequencies of the second allele for A and B, denoted and
. For a given SNP, is drawn from a uniform
distribution between 0 and (0.5 - alpha). is then computed
as 1 - . Therefore, differences between groups are mild for
alpha=0, and total for alpha = 0.5.
=== Linked or independent loci ===
Independent loci (LD=FALSE) are simulated using the standard
binomial distribution, with randomly generated allele
frequencies. Linked loci (LD=FALSE) are trickier towe need to
simulate discrete variables with pre-defined correlation structure.
Here, we first generate deviates from multivariate normal distributions with randomly generated correlation structures. These variables are then discretized using the quantiles of the distribution. Further improvement of the procedure will aim at i) specifying the strength of the correlations between blocks of alleles and ii) enforce contrasted structures between groups.
A genlight object.
Caitlin Collins [email protected], Thibaut Jombart [email protected]
- genlight: class of object for storing massive binary
SNP data.
- glPlot: plotting genlight objects.
- glPca: PCA for genlight objects.
## Not run: ## no structure x <- glSim(100, 1e3, ploid=2) plot(x) ## 1,000 non structured SNPs, 100 structured SNPs x <- glSim(100, 1e3, n.snp.struc=100, ploid=2) plot(x) ## 1,000 non structured SNPs, 100 structured SNPs, ploidy=4 x <- glSim(100, 1e3, n.snp.struc=100, ploid=4) plot(x) ## same thing, stronger differences between groups x <- glSim(100, 1e3, n.snp.struc=100, ploid=2, alpha=0.4) plot(x) ## same thing, loci with LD structures x <- glSim(100, 1e3, n.snp.struc=100, ploid=2, alpha=0.4, LD=TRUE, block.minsize=100) plot(x) ## End(Not run)## Not run: ## no structure x <- glSim(100, 1e3, ploid=2) plot(x) ## 1,000 non structured SNPs, 100 structured SNPs x <- glSim(100, 1e3, n.snp.struc=100, ploid=2) plot(x) ## 1,000 non structured SNPs, 100 structured SNPs, ploidy=4 x <- glSim(100, 1e3, n.snp.struc=100, ploid=4) plot(x) ## same thing, stronger differences between groups x <- glSim(100, 1e3, n.snp.struc=100, ploid=2, alpha=0.4) plot(x) ## same thing, loci with LD structures x <- glSim(100, 1e3, n.snp.struc=100, ploid=2, alpha=0.4, LD=TRUE, block.minsize=100) plot(x) ## End(Not run)
The dataset H3N2 consists of 1903 strains of seasonal influenza
(H3N2) distributed worldwide, and typed at 125 SNPs located in the
hemagglutinin (HA) segment. It is stored as an R object with class
genind and can be accessed as usual using data(H3N2)
(see example). These data were gathered from DNA sequences available from
Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).
H3N2 is a genind object with several data frame as
supplementary components (H3N2@other) slort, which contains the
following items:
a data.frame containing
miscellaneous annotations of the sequences.
a matrix with two columns indicating the geographic coordinates of the strains, as longitudes and latitudes.
a character vector indicating the epidemic of the strains.
The data file usflu.fasta is a toy dataset also gathered from
Genbank, consisting of the aligned sequences of 80 seasonal influenza
isolates (HA segment) sampled in the US, in fasta format. This file
is installed alongside the package; the path to this file is automatically
determined by R using system.file (see example in this manpage and in
?fasta2genlight) as well.
This dataset was prepared by Thibaut Jombart ([email protected]), from annotated sequences available on Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).
Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Submitted to BMC genetics.
## Not run: #### H3N2 #### ## LOAD DATA data(H3N2) H3N2 ## set population to yearly epidemics pop(H3N2) <- factor(H3N2$other$epid) ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS ## to reproduce exactly analyses from the paper, use "n.pca=1000" dapc1 <- dapc(H3N2, all.contrib=TRUE, scale=FALSE, n.pca=150, n.da=5) dapc1 ## (see ?dapc for details about the output) ## SCREEPLOT OF EIGENVALUES barplot(dapc1$eig, main="H3N2 - DAPC eigenvalues") ## SCATTERPLOT (axes 1-2) scatter(dapc1, posi.da="topleft", cstar=FALSE, cex=2, pch=17:22, solid=.5, bg="white") #### usflu.fasta #### myPath <- system.file("files/usflu.fasta",package="adegenet") myPath ## extract SNPs from alignments using fasta2genlight ## see ?fasta2genlight for more details obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time obj ## End(Not run)## Not run: #### H3N2 #### ## LOAD DATA data(H3N2) H3N2 ## set population to yearly epidemics pop(H3N2) <- factor(H3N2$other$epid) ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS ## to reproduce exactly analyses from the paper, use "n.pca=1000" dapc1 <- dapc(H3N2, all.contrib=TRUE, scale=FALSE, n.pca=150, n.da=5) dapc1 ## (see ?dapc for details about the output) ## SCREEPLOT OF EIGENVALUES barplot(dapc1$eig, main="H3N2 - DAPC eigenvalues") ## SCATTERPLOT (axes 1-2) scatter(dapc1, posi.da="topleft", cstar=FALSE, cex=2, pch=17:22, solid=.5, bg="white") #### usflu.fasta #### myPath <- system.file("files/usflu.fasta",package="adegenet") myPath ## extract SNPs from alignments using fasta2genlight ## see ?fasta2genlight for more details obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time obj ## End(Not run)
The function haploGen implements simulations of genealogies of
haplotypes. This forward-time, individual-based simulation tool allows
haplotypes to replicate and mutate according to specified parameters,
and keeps track of their genealogy.
Simulations can be spatially explicit or not (see geo.sim
argument). In the first case, haplotypes are assigned to locations on
a regular grip. New haplotypes disperse from their ancestor's location
according to a random Poisson diffusion, or alternatively according to
a pre-specified migration scheme. This tool does not allow for
simulating selection or linkage disequilibrium.
Produced objects are lists with the class haploGen; see 'value'
section for more information on this class. Other functions are
available to print, plot, subset, sample or convert haploGen
objects. A seqTrack method is also provided for analysing
haploGen objects.
Note that for simulation of outbreaks, the new tool simOutbreak
in the outbreaker package should be used.
haploGen(seq.length=1e4, mu.transi=1e-4, mu.transv=mu.transi/2, t.max=20, gen.time=function(){1+rpois(1,0.5)}, repro=function(){rpois(1,1.5)}, max.nb.haplo=200, geo.sim=FALSE, grid.size=10, lambda.xy=0.5, mat.connect=NULL, ini.n=1, ini.xy=NULL) ## S3 method for class 'haploGen' print(x, ...) ## S3 method for class 'haploGen' as.igraph(x, col.pal=redpal, ...) ## S3 method for class 'haploGen' plot(x, y=NULL, col.pal=redpal, ...) ## S3 method for class 'haploGen' x[i, j, drop=FALSE] ## S3 method for class 'haploGen' labels(object, ...) ## S3 method for class 'haploGen' as.POSIXct(x, tz="", origin=as.POSIXct("2000/01/01"), ...) ## S3 method for class 'haploGen' seqTrack(x, best=c("min","max"), prox.mat=NULL, ...) as.seqTrack.haploGen(x) plotHaploGen(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", add=FALSE, ...) sample.haploGen(x, n)haploGen(seq.length=1e4, mu.transi=1e-4, mu.transv=mu.transi/2, t.max=20, gen.time=function(){1+rpois(1,0.5)}, repro=function(){rpois(1,1.5)}, max.nb.haplo=200, geo.sim=FALSE, grid.size=10, lambda.xy=0.5, mat.connect=NULL, ini.n=1, ini.xy=NULL) ## S3 method for class 'haploGen' print(x, ...) ## S3 method for class 'haploGen' as.igraph(x, col.pal=redpal, ...) ## S3 method for class 'haploGen' plot(x, y=NULL, col.pal=redpal, ...) ## S3 method for class 'haploGen' x[i, j, drop=FALSE] ## S3 method for class 'haploGen' labels(object, ...) ## S3 method for class 'haploGen' as.POSIXct(x, tz="", origin=as.POSIXct("2000/01/01"), ...) ## S3 method for class 'haploGen' seqTrack(x, best=c("min","max"), prox.mat=NULL, ...) as.seqTrack.haploGen(x) plotHaploGen(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", add=FALSE, ...) sample.haploGen(x, n)
seq.length |
an integer indicating the length of the simulated haplotypes, in number of nucleotides. |
mu.transi |
the rate of transitions, in number of mutation per site and per time unit. |
mu.transv |
the rate of transversions, in number of mutation per site and per time unit. |
t.max |
an integer indicating the maximum number of time units to run the simulation for. |
gen.time |
an integer indicating the generation time, in number of time units. Can be a (fixed) number or a function returning a number (then called for each reproduction event). |
repro |
an integer indicating the number of descendents per haplotype. Can be a (fixed) number or a function returning a number (then called for each reproduction event). |
max.nb.haplo |
an integer indicating the maximum number of haplotypes handled at any time of the simulation, used to control the size of the produced object. Larger number will lead to slower simulations. If this number is exceeded, the genealogy is prunded to as to keep this number of haplotypes. |
geo.sim |
a logical stating whether simulations should be spatially explicit (TRUE) or not (FALSE, default). Spatially-explicit simulations are slightly slower than their non-spatial counterpart. |
grid.size |
the size of the square grid of possible locations for spatial simulations. The total number of locations will be this number squared. |
lambda.xy |
the parameter of the Poisson distribution used to determine dispersion in x and y axes. |
mat.connect |
a matrix of connectivity describing migration
amongts all pairs of locations. |
ini.n |
an integer specifying the number of (identical) haplotypes to initiate the simulation |
ini.xy |
a vector of two integers giving the x/y coordinates of the initial haplotype. |
x, object
|
|
y |
unused argument, for compatibility with 'plot'. |
col.pal |
a color palette to be used to represent weights using
colors on the edges of the graph. See |
i, j, drop
|
|
best, prox.mat
|
arguments to be passed to the
|
annot, date.range, col, bg, add
|
arguments to be passed to |
n |
an integer indicating the number of haplotypes to be retained in the sample |
tz, origin
|
aguments to be passed to |
... |
further arguments to be passed to other methods; for
'plot', arguments are passed to |
=== Dependencies with other packages ===
- ape package is required as it implements efficient handling of DNA
sequences used in haploGen objects. To install this package,
simply type:install.packages("ape")
- for various purposes including plotting, converting genealogies to
graphs can be useful. From adegenet version 1.3-5 onwards, this is
achieved using the package igraph. See below.
=== Converting haploGen objects to graphs ===haploGen objects can be converted to igraph
objects (package igraph), which can in turn be plotted and manipulated using classical
graph tools. Simply use 'as.igraph(x)' where 'x' is a
haploGen object. This functionality requires the igraph
package. Graphs are time oriented (top=old, bottom=recent).
=== haploGen class ===haploGen objects are lists containing the following slots:
- seq: DNA sequences in the DNAbin matrix format
- dates: dates of appearance of the haplotypes
- ances: a vector of integers giving the index of each haplotype's
ancestor
- id: a vector of integers giving the index of each haplotype
- xy: (optional) a matrix of spatial coordinates of haplotypes
- call: the matched call
=== misc functions ===
- as.POSIXct: returns a vector of dates with POSIXct format
- labels: returns the labels of the haplotypes
- as.seqTrack: returns a seqTrack object. Note that this object is not a
proper seqTrack analysis, but just a format conversion convenient for
plotting haploGen objects.
Thibaut Jombart [email protected]
Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease outbreaks from genetic data: a graph approach. Heredity. doi: 10.1038/hdy.2010.78.
simOutbreak in the package 'outbreaker' for simulating disease
outbreaks under a realistic epidemiological model.
## Not run: if(require(ape) && require(igraph)){ ## PERFORM SIMULATIONS x <- haploGen(geo.sim=TRUE) x ## PLOT DATA plot(x) ## PLOT SPATIAL SPREAD plotHaploGen(x, bg="white") title("Spatial dispersion") ## USE SEQTRACK RECONSTRUCTION x.recons <- seqTrack(x) mean(x.recons$ances==x$ances, na.rm=TRUE) # proportion of correct reconstructions g <- as.igraph(x) g plot(g) plot(g, vertex.size=0) } ## End(Not run)## Not run: if(require(ape) && require(igraph)){ ## PERFORM SIMULATIONS x <- haploGen(geo.sim=TRUE) x ## PLOT DATA plot(x) ## PLOT SPATIAL SPREAD plotHaploGen(x, bg="white") title("Spatial dispersion") ## USE SEQTRACK RECONSTRUCTION x.recons <- seqTrack(x) mean(x.recons$ances==x$ances, na.rm=TRUE) # proportion of correct reconstructions g <- as.igraph(x) g plot(g) plot(g, vertex.size=0) } ## End(Not run)
The following methods allow the user to quickly change the hierarchy or population of a genind or genlight object.
hier(x, formula = NULL, combine = TRUE, value) hier(x) <- valuehier(x, formula = NULL, combine = TRUE, value) hier(x) <- value
x |
a genind or genlight object |
formula |
a nested formula indicating the order of the population hierarchy to be returned. |
combine |
if |
value |
a formula specifying the full hierarchy of columns in the strata slot. (See Details below) |
You must first specify your strata before you can specify your hierarchies. Hierarchies are special cases of strata in that the levels must be nested within each other. An error will occur if you specify a hierarchy that is not truly hierarchical.
The preferred use of these functions is with a formula
object. Specifically, a hierarchical formula argument is used to name which
strata are hierarchical. An example of a hierarchical formula would
be:
~Country/City/Neighborhood
|
This convention was
chosen as it becomes easier to type and makes intuitive sense when defining
a hierarchy. Note: it is important to use hierarchical formulas when
specifying hierarchies as other types of formulas (eg.
~Country*City*Neighborhood) will give incorrect results.
Zhian N. Kamvar
# let's look at the microbov data set: data(microbov) microbov # We see that we have three vectors of different names in the 'other' slot. ?microbov # These are Country, Breed, and Species names(other(microbov)) # Let's set the hierarchy strata(microbov) <- data.frame(other(microbov)) microbov # And change the names so we know what they are nameStrata(microbov) <- ~Country/Breed/Species # let's see what the hierarchy looks like by Species and Breed: hier(microbov) <- ~Species/Breed head(hier(microbov, ~Species/Breed))# let's look at the microbov data set: data(microbov) microbov # We see that we have three vectors of different names in the 'other' slot. ?microbov # These are Country, Breed, and Species names(other(microbov)) # Let's set the hierarchy strata(microbov) <- data.frame(other(microbov)) microbov # And change the names so we know what they are nameStrata(microbov) <- ~Country/Breed/Species # let's see what the hierarchy looks like by Species and Breed: hier(microbov) <- ~Species/Breed head(hier(microbov, ~Species/Breed))
This function computes the expected heterozygosity (Hs) within
populations of a genpop object. This function is
available for codominant markers (@type="codom") only. Hs is
commonly used for measuring within population genetic diversity (and
as such, it still has sense when computed from haploid data).
Hs(x, pop = NULL)Hs(x, pop = NULL)
x |
|
pop |
only used if x is a genind; an optional factor to be used as population; if not provided, pop(x) is used. |
Let m(k) be the number of alleles of locus k, with a
total of K loci. We note the allele frequency of
allele i in a given population. Then, is given for a
given population by:
a vector of Hs values (one value per population)
Thibaut Jombart [email protected]
Hs.test to test differences in Hs between two groups
## Not run: data(nancycats) Hs(genind2genpop(nancycats)) ## End(Not run)## Not run: data(nancycats) Hs(genind2genpop(nancycats)) ## End(Not run)
This procedure permits to test if two groups have significant differences in expected heterozygosity (Hs). The test statistic used is simply the difference in Hs between the two groups 'x' and 'y':
Hs.test(x, y, n.sim = 999, alter = c("two-sided", "greater", "less"))Hs.test(x, y, n.sim = 999, alter = c("two-sided", "greater", "less"))
x |
a genind object. |
y |
a genind object. |
n.sim |
the number of permutations to be used to generate the reference distribution. |
alter |
a character string indicating the alternative hypothesis |
Individuals are randomly permuted between groups to obtain a reference distribution of the test statistics.
an object of the class randtest
Thibaut Jombart [email protected]
Hs to compute Hs for different populations;
as.randtest for the class of Monte Carlo tests.
## Not run: data(microbov) Hs(microbov) test <- Hs.test(microbov[pop="Borgou"], microbov[pop="Lagunaire"], n.sim=499) test plot(test) ## End(Not run)## Not run: data(microbov) Hs(microbov) test <- Hs.test(microbov[pop="Borgou"], microbov[pop="Lagunaire"], n.sim=499) test plot(test) ## End(Not run)
The function HWE.test is a generic function to
perform Hardy-Weinberg Equilibrium tests defined by the
genetics package. adegenet proposes a method for genind
objects.
The output can be of two forms:
- a list of tests (class htest) for each locus-population
combinaison
- a population x locus matrix containing p-values of the tests
## S3 method for class 'genind' HWE.test(x,pop=NULL,permut=FALSE,nsim=1999,hide.NA=TRUE,res.type=c("full","matrix"))## S3 method for class 'genind' HWE.test(x,pop=NULL,permut=FALSE,nsim=1999,hide.NA=TRUE,res.type=c("full","matrix"))
x |
an object of class |
pop |
a factor giving the population of each individual. If NULL, pop is seeked from x$pop. |
permut |
a logical passed to |
nsim |
number of simulations if Monte Carlo is used (passed to |
hide.NA |
a logical stating whether non-tested loci (e.g., when an allele is fixed) should be hidden in the results (TRUE, default) or not (FALSE). |
res.type |
a character or a character vector whose only first argument is considered giving the type of result to display. If "full", then a list of complete tests is returned. If "matrix", then a matrix of p-values is returned. |
Monte Carlo procedure is quiet computer-intensive when large
datasets are involved. For more precision on the performed test, read
HWE.test documentation (genetics package).
Returns either a list of tests or a matrix of p-values. In the
first case, each test is designated by locus first and then by
population. For instance if res is the "full" output of the
function, then the test for population "PopA" at locus "Myloc" is
given by res$Myloc$PopA. If res is a matrix of p-values,
populations are in rows and loci in columns. P-values are given for
the upper-tail: they correspond to the probability that an oberved
chi-square statistic as high as or higher than the one observed
occured under H0 (HWE).
In all cases, NA values are likely to appear in fixed loci, or entirely non-typed loci.
Thibaut Jombart [email protected]
HWE.test in the genetics package, chisq.test
## Not run: data(nancycats) obj <- nancycats if(require(genetics)){ obj.test <- HWE.test(obj) # pvalues matrix to have a preview HWE.test(obj,res.type="matrix") #more precise view to... obj.test$fca90$P10 } ## End(Not run)## Not run: data(nancycats) obj <- nancycats if(require(genetics)){ obj.test <- HWE.test(obj) # pvalues matrix to have a preview HWE.test(obj,res.type="matrix") #more precise view to... obj.test$fca90$P10 } ## End(Not run)
The function hybridize performs hybridization between two set
of genotypes stored in genind objects (referred as the "2
populations"). Allelic frequencies are derived for each population,
and then gametes are sampled following a multinomial distribution.
hybridize( x1, x2, n, pop = "hybrid", res.type = c("genind", "df", "STRUCTURE"), file = NULL, quiet = FALSE, sep = "/", hyb.label = "h" )hybridize( x1, x2, n, pop = "hybrid", res.type = c("genind", "df", "STRUCTURE"), file = NULL, quiet = FALSE, sep = "/", hyb.label = "h" )
x1 |
a genind object |
x2 |
a genind object |
n |
an integer giving the number of hybrids requested |
pop |
a character string giving naming the population of the created hybrids. |
res.type |
a character giving the type of output requested. Must
be "genind" (default), "df" (i.e. data.frame like in
|
file |
a character giving the name of the file to be written when 'res.type' is "STRUCTURE"; if NULL, a the created file is of the form "hybrids_[the current date].str". |
quiet |
a logical specifying whether the writing to a file (when 'res.type' is "STRUCTURE") should be announced (FALSE, default) or not (TRUE). |
sep |
a character used to separate two alleles |
hyb.label |
a character string used to construct the hybrids labels; by default, "h", which gives labels: "h01", "h02", "h03",... |
The result consists in a set of 'n' genotypes, with different possible outputs (see 'res.type' argument).
If the output is a STRUCTURE file, this file will have the following
caracteristics:
- file contains the genotypes of the parents, and then the genotypes
of hybrids
- the first column identifies genotypes
- the second column identifies the population (1 and 2 for parents x1 and x2;
3 for hybrids)
- the first line contains the names of the markers
- one row = one genotype (onerowperind will be true)
- missing values coded by "-9" (the software's default)
A genind object (by default), or a data.frame of alleles (res.type="df"). No R output if res.type="STRUCTURE" (results written to the specified file).
Thibaut Jombart [email protected]
## Not run: ## Let's make some cattle hybrids data(microbov) ## first, isolate each breed temp <- seppop(microbov) names(temp) salers <- temp$Salers zebu <- temp$Zebu ## let's make some... Zeblers zebler <- hybridize(salers, zebu, n=40, pop="Zebler") ## now let's merge all data into a single genind newDat <- repool(microbov, zebler) ## make a correspondance analysis ## and see where hybrids are placed X <- genind2genpop(newDat, quiet=TRUE) coa1 <- dudi.coa(tab(X),scannf=FALSE,nf=3) s.label(coa1$li) add.scatter.eig(coa1$eig,2,1,2) ## End(Not run)## Not run: ## Let's make some cattle hybrids data(microbov) ## first, isolate each breed temp <- seppop(microbov) names(temp) salers <- temp$Salers zebu <- temp$Zebu ## let's make some... Zeblers zebler <- hybridize(salers, zebu, n=40, pop="Zebler") ## now let's merge all data into a single genind newDat <- repool(microbov, zebler) ## make a correspondance analysis ## and see where hybrids are placed X <- genind2genpop(newDat, quiet=TRUE) coa1 <- dudi.coa(tab(X),scannf=FALSE,nf=3) s.label(coa1$li) add.scatter.eig(coa1$eig,2,1,2) ## End(Not run)
Toy hybrid dataset
a genind object
Data simulated by Marie-Pauline Beugin. Example by Thibaut Jombart.
data(hybridtoy) x <- hybridtoy pca1 <- dudi.pca(tab(x), scannf=FALSE, scale=FALSE) s.class(pca1$li, pop(x)) if(require(ggplot2)) { p <- ggplot(pca1$li, aes(x=Axis1)) + geom_density(aes(fill=pop(x)), alpha=.4, adjust=1) + geom_point(aes(y=0, color=pop(x)), pch="|", size=10, alpha=.5) p } ## kmeans km <- find.clusters(x, n.pca=10, n.clust=2) table(pop(x), km$grp) ## dapc dapc1 <- dapc(x, pop=km$grp, n.pca=10, n.da=1) scatter(dapc1) scatter(dapc1, grp=pop(x)) compoplot(dapc1, col.pal=spectral, n.col=2) ## ML-EM with hybrids res <- snapclust(x, k=2, hybrids=TRUE, detailed=TRUE) compoplot(res, n.col=3) table(res$group, pop(x))data(hybridtoy) x <- hybridtoy pca1 <- dudi.pca(tab(x), scannf=FALSE, scale=FALSE) s.class(pca1$li, pop(x)) if(require(ggplot2)) { p <- ggplot(pca1$li, aes(x=Axis1)) + geom_density(aes(fill=pop(x)), alpha=.4, adjust=1) + geom_point(aes(y=0, color=pop(x)), pch="|", size=10, alpha=.5) p } ## kmeans km <- find.clusters(x, n.pca=10, n.clust=2) table(pop(x), km$grp) ## dapc dapc1 <- dapc(x, pop=km$grp, n.pca=10, n.da=1) scatter(dapc1) scatter(dapc1, grp=pop(x)) compoplot(dapc1, col.pal=spectral, n.col=2) ## ML-EM with hybrids res <- snapclust(x, k=2, hybrids=TRUE, detailed=TRUE) compoplot(res, n.col=3) table(res$group, pop(x))
Their are several ways to import genotype data to a genind
object: i) from a data.frame with a given format (see
df2genind), ii) from a file with a recognized extension, or
iii) from an alignement of sequences (see DNAbin2genind).
import2genind(file, quiet = FALSE, ...)import2genind(file, quiet = FALSE, ...)
file |
a character string giving the path to the file to convert, with the appropriate extension. |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
... |
other arguments passed to the appropriate 'read' function
(currently passed to |
The function import2genind detects the extension of the file given in
argument and seeks for an appropriate import function to create a
genind object.
Current recognized formats are :
- GENETIX files
(.gtx)
- Genepop files (.gen)
- Fstat files (.dat)
- STRUCTURE
files (.str or .stru)
Beware: same data in different formats are not expected to produce exactly
the same genind objects.
For instance, conversions made by GENETIX
to Fstat may change the the sorting of the genotypes; GENETIX stores
individual names whereas Fstat does not; Genepop chooses a sample's name
from the name of its last genotype; etc.
an object of the class genind
Thibaut Jombart [email protected]
Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F.
(1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la genetique des
populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000,
Universite de Montpellier II, Montpellier (France).
Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155: 945-959
Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population genetics
software for exact tests and ecumenicism. J. Heredity,
86:248-249
Fstat (version 2.9.3). Software by Jerome Goudet.
http://www2.unil.ch/popgen/softwares/fstat.htm
Excoffier L. & Heckel G.(2006) Computer programs for population genetics data analysis: a survival guide Nature, 7: 745-758
import2genind, read.genetix,
read.fstat, read.structure,
read.genepop
import2genind(system.file("files/nancycats.gtx", package="adegenet")) import2genind(system.file("files/nancycats.dat", package="adegenet")) import2genind(system.file("files/nancycats.gen", package="adegenet")) import2genind(system.file("files/nancycats.str", package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)import2genind(system.file("files/nancycats.gtx", package="adegenet")) import2genind(system.file("files/nancycats.dat", package="adegenet")) import2genind(system.file("files/nancycats.gen", package="adegenet")) import2genind(system.file("files/nancycats.str", package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)
The function inbreeding estimates the inbreeding coefficient
of an individuals (F) by computing its likelihood function. It can
return either the density of probability of F, or a sample of F values
from this distribution. This operation is performed for all the
individuals of a genind object. Any ploidy greater than
1 is acceptable.
inbreeding(x, pop = NULL, truenames = TRUE, res.type = c("sample", "function", "estimate"), N = 200, M = N * 10)inbreeding(x, pop = NULL, truenames = TRUE, res.type = c("sample", "function", "estimate"), N = 200, M = N * 10)
x |
an object of class genind. |
pop |
a factor giving the 'population' of each individual. If NULL,
pop is seeked from |
truenames |
a logical indicating whether true names should be used (TRUE, default) instead of generic labels (FALSE); used if res.type is "matrix". |
res.type |
a character string matching "sample", "function", or "estimate" specifying whether the output should be a function giving the density of probability of F values ("function"), the maximum likelihood estimate of F from this distribution ("estimate"), or a sample of F values taken from this distribution ("sample", default). |
N |
an integer indicating the size of the sample to be taken from the distribution of F values. |
M |
an integer indicating the number of different F values to be used to generate the sample. Values larger than N are recommended to avoid poor sampling of the distribution. |
Let denote the inbreeding coefficient, defined as the
probability for an individual to inherit two identical alleles from a
single ancestor.
Let refer to the frequency of allele in the
population. Let be an variable which equates 1 if the
individual is homozygote, and 0 otherwise. For one locus, the
probability of being homozygote is computed as:
The probability of being heterozygote is:
The likelihood of a genotype is defined as the probability of being the observed state (homozygote or heterozygote). In the case of multilocus genotypes, log-likelihood are summed over the loci.
A named list with one component for each individual, each of which is
a function or a vector of sampled F values (see res.type argument).
Thibaut Jombart [email protected]
Zhian N. Kamvar
Hs: computation of expected heterozygosity.
## Not run: ## cattle breed microsatellite data data(microbov) ## isolate Lagunaire breed lagun <- seppop(microbov)$Lagunaire ## estimate inbreeding - return sample of F values Fsamp <- inbreeding(lagun, N=30) ## plot the first 10 results invisible(sapply(Fsamp[1:10], function(e) plot(density(e), xlab="F", xlim=c(0,1), main="Density of the sampled F values"))) ## compute means for all individuals Fmean=sapply(Fsamp, mean) hist(Fmean, col="orange", xlab="mean value of F", main="Distribution of mean F across individuals") ## estimate inbreeding - return proba density functions Fdens <- inbreeding(lagun, res.type="function") ## view function for the first individual Fdens[[1]] ## plot the first 10 functions invisible(sapply(Fdens[1:10], plot, ylab="Density", main="Density of probability of F values")) ## estimate inbreeding - return maximum likelihood estimates Fest <- inbreeding(lagun, res.type = "estimate") mostInbred <- which.max(Fest) plot(Fdens[[mostInbred]], ylab = "Density", xlab = "F", main = paste("Probability density of F values\nfor", names(mostInbred))) abline(v = Fest[mostInbred], col = "red", lty = 2) legend("topright", legend = "MLE", col = "red", lty = 2) ## note that estimates and average samples are likely to be different. plot(Fest, ylab = "F", col = "blue", main = "comparison of MLE and average sample estimates of F") points(Fmean, pch = 2, col = "red") arrows(x0 = 1:length(Fest), y0 = Fest, y1 = Fmean, x1 = 1:length(Fest), length = 0.125) legend("topleft", legend = c("estimate", "sample"), col = c("blue", "red"), pch = c(1, 2), title = "res.type") ## End(Not run)## Not run: ## cattle breed microsatellite data data(microbov) ## isolate Lagunaire breed lagun <- seppop(microbov)$Lagunaire ## estimate inbreeding - return sample of F values Fsamp <- inbreeding(lagun, N=30) ## plot the first 10 results invisible(sapply(Fsamp[1:10], function(e) plot(density(e), xlab="F", xlim=c(0,1), main="Density of the sampled F values"))) ## compute means for all individuals Fmean=sapply(Fsamp, mean) hist(Fmean, col="orange", xlab="mean value of F", main="Distribution of mean F across individuals") ## estimate inbreeding - return proba density functions Fdens <- inbreeding(lagun, res.type="function") ## view function for the first individual Fdens[[1]] ## plot the first 10 functions invisible(sapply(Fdens[1:10], plot, ylab="Density", main="Density of probability of F values")) ## estimate inbreeding - return maximum likelihood estimates Fest <- inbreeding(lagun, res.type = "estimate") mostInbred <- which.max(Fest) plot(Fdens[[mostInbred]], ylab = "Density", xlab = "F", main = paste("Probability density of F values\nfor", names(mostInbred))) abline(v = Fest[mostInbred], col = "red", lty = 2) legend("topright", legend = "MLE", col = "red", lty = 2) ## note that estimates and average samples are likely to be different. plot(Fest, ylab = "F", col = "blue", main = "comparison of MLE and average sample estimates of F") points(Fmean, pch = 2, col = "red") arrows(x0 = 1:length(Fest), y0 = Fest, y1 = Fmean, x1 = 1:length(Fest), length = 0.125) legend("topleft", legend = c("estimate", "sample"), col = c("blue", "red"), pch = c(1, 2), title = "res.type") ## End(Not run)
The function new has a method for building genind objects.
See the class description of genind for more information on this data structure.
The functions genind and as.genind are aliases for new("genind", ...).
## S4 method for signature 'genind' initialize( .Object, tab, pop = NULL, prevcall = NULL, ploidy = 2L, type = c("codom", "PA"), strata = NULL, hierarchy = NULL, ... ) genind(...) as.genind(...)## S4 method for signature 'genind' initialize( .Object, tab, pop = NULL, prevcall = NULL, ploidy = 2L, type = c("codom", "PA"), strata = NULL, hierarchy = NULL, ... ) genind(...) as.genind(...)
.Object |
prototyped object (generated automatically when calling 'new') |
tab |
A matrix of integers corresponding to the @tab slot of a genind object, with individuals in rows and alleles in columns, and containing either allele counts (if type="codom") or allele presence/absence (if type="PA") |
pop |
an optional factor with one value per row in |
prevcall |
an optional call to be stored in the object |
ploidy |
an integer vector indicating the ploidy of the individual; each individual can have a different value; if only one value is provided, it is recycled to generate a vector of the right length. |
type |
a character string indicating the type of marker: codominant ("codom") or presence/absence ("PA") |
strata |
a data frame containing population hierarchies or stratifications in columns. This must be the same length as the number of individuals in the data set. |
hierarchy |
a hierarchical formula defining the columns of the strata slot that are hierarchical. Defaults to NULL. |
... |
further arguments passed to other methods (currently not used) |
Most users do not need using the constructor, but merely to convert raw allele data using df2genind and related functions.
a genind object
the description of the genind class; df2genind
The function new has a method for building genpop objects.
See the class description of genpop for more information on this data structure.
The functions genpop and as.genpop are aliases for new("genpop", ...).
## S4 method for signature 'genpop' initialize( .Object, tab, prevcall = NULL, ploidy = 2L, type = c("codom", "PA"), ... ) genpop(...) as.genpop(...)## S4 method for signature 'genpop' initialize( .Object, tab, prevcall = NULL, ploidy = 2L, type = c("codom", "PA"), ... ) genpop(...) as.genpop(...)
.Object |
prototyped object (generated automatically when calling 'new') |
tab |
A matrix of integers corresponding to the @tab slot of a genpop object, with individuals in rows and alleles in columns, and containing either allele counts |
prevcall |
an optional call to be stored in the object |
ploidy |
an integer vector indicating the ploidy of the individual; each individual can have a different value; if only one value is provided, it is recycled to generate a vector of the right length. |
type |
a character string indicating the type of marker: codominant ("codom") or presence/absence ("PA") |
... |
further arguments passed to other methods (currently not used) |
Most users do not need using the constructor, but merely to convert raw allele data using genind2genpop.
a genpop object
the description of the genpop class; df2genind and related functions for reading raw allele data
The simple function isPoly can be used to check which loci are
polymorphic, or alternatively to check which alleles give rise to polymorphism.
## S4 method for signature 'genind' isPoly(x, by=c("locus","allele"), thres=1/100) ## S4 method for signature 'genpop' isPoly(x, by=c("locus","allele"), thres=1/100)## S4 method for signature 'genind' isPoly(x, by=c("locus","allele"), thres=1/100) ## S4 method for signature 'genpop' isPoly(x, by=c("locus","allele"), thres=1/100)
x |
|
by |
a character being "locus" or "allele", indicating whether results should indicate polymorphic loci ("locus"), or alleles giving rise to polymorphism ("allele"). |
thres |
a numeric value giving the minimum frequency of an allele giving rise to polymorphism (defaults to 0.01). |
A vector of logicals.
Thibaut Jombart [email protected]
## Not run: data(nancycats) isPoly(nancycats,by="loc", thres=0.1) isPoly(nancycats[1:3],by="loc", thres=0.1) genind2df(nancycats[1:3]) ## End(Not run)## Not run: data(nancycats) isPoly(nancycats,by="loc", thres=0.1) isPoly(nancycats[1:3],by="loc", thres=0.1) genind2df(nancycats[1:3]) ## End(Not run)
Do not use. We work on that stuff. Contact us if interested.
KIC(object, ...) ## S3 method for class 'snapclust' KIC(object, ...)KIC(object, ...) ## S3 method for class 'snapclust' KIC(object, ...)
object |
An object returned by the function |
... |
Further arguments for compatibility with the |
Thibaut Jombart [email protected]
snapclust to generate clustering solutions.
The loadingplot function represents positive values of a vector
and identifies the values above a given threshold. It can also
indicate groups of observations provided as a factor.
Such graphics can be used, for instance, to assess the weight of each variable (loadings) in a given analysis.
loadingplot(x, ...) ## Default S3 method: loadingplot(x, at=NULL, threshold=quantile(x,0.75), axis=1, fac=NULL, byfac=FALSE, lab=NULL, cex.lab=0.7, cex.fac=1, lab.jitter=0, main="Loading plot", xlab="Variables", ylab="Loadings", srt = 0, adj = NULL, ...)loadingplot(x, ...) ## Default S3 method: loadingplot(x, at=NULL, threshold=quantile(x,0.75), axis=1, fac=NULL, byfac=FALSE, lab=NULL, cex.lab=0.7, cex.fac=1, lab.jitter=0, main="Loading plot", xlab="Variables", ylab="Loadings", srt = 0, adj = NULL, ...)
x |
either a vector with numeric values to be plotted, or a
matrix-like object containing numeric values. In such case, the
|
at |
an optional numeric vector giving the abscissa at which loadings are plotted. Useful when variates are SNPs with a known position in an alignement. |
threshold |
a threshold value above which values of x are identified. By default, this is the third quartile of x. |
axis |
an integer indicating the column of x to be plotted; used only if x is a matrix-like object. |
fac |
a factor defining groups of observations. |
byfac |
a logical stating whether loadings should be averaged by
groups of observations, as defined by |
lab |
a character vector giving the labels used to annotate values above the threshold; if NULL, names are taken from the object. |
cex.lab |
a numeric value indicating the size of annotations. |
cex.fac |
a numeric value indicating the size of annotations for groups of observations. |
lab.jitter |
a numeric value indicating the factor of randomisation for the position of annotations. Set to 0 (by default) implies no randomisation. |
main |
the main title of the figure. |
xlab |
the title of the x axis. |
ylab |
the title of the y axis. |
srt |
rotation of the labels; see ?text. |
adj |
adjustment of the labels; see ?text. |
... |
further arguments to be passed to the plot function. |
Invisibly returns a list with the following components:
- threshold: the threshold used
- var.names: the names of observations above the threshold
- var.idx: the indices of observations above the threshold
- var.values: the values above the threshold
Thibaut Jombart [email protected]
x <- runif(20) names(x) <- letters[1:20] grp <- factor(paste("group", rep(1:4,each=5))) ## basic plot loadingplot(x) ## adding groups loadingplot(x,fac=grp,main="My title",cex.lab=1)x <- runif(20) names(x) <- letters[1:20] grp <- factor(paste("group", rep(1:4,each=5))) ## basic plot loadingplot(x) ## adding groups loadingplot(x,fac=grp,main="My title",cex.lab=1)
The function makefreq is a generic to compute allele frequencies.
These can be derived for genind or genpop objects.
In the case of genind objects, data are kept at the individual level, but standardised so that allele frequencies sum up to 1.
makefreq(x, ...) ## S4 method for signature 'genind' makefreq(x, quiet = FALSE, missing = NA, truenames = TRUE, ...) ## S4 method for signature 'genpop' makefreq(x, quiet = FALSE, missing = NA, truenames = TRUE, ...)makefreq(x, ...) ## S4 method for signature 'genind' makefreq(x, quiet = FALSE, missing = NA, truenames = TRUE, ...) ## S4 method for signature 'genpop' makefreq(x, quiet = FALSE, missing = NA, truenames = TRUE, ...)
x |
|
... |
further arguments (curently unused) |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
missing |
treatment for missing values. Can be NA, 0 or "mean" (see details) |
truenames |
deprecated; there for backward compatibility |
There are 3 treatments for missing values:
- NA: kept as NA.
- 0:
missing values are considered as zero. Recommended for a PCA on
compositionnal data.
- "mean": missing values are given the mean
frequency of the corresponding allele. Recommended for a centred PCA.
Note that this function is now a simple wrapper for the accessor tab.
Returns a list with the following components:
tab |
matrix of allelic frequencies (rows: populations; columns: alleles). |
nobs |
number of observations (i.e. alleles) for each population x locus combinaison. |
call |
the matched call |
Thibaut Jombart [email protected]
## Not run: data(microbov) obj1 <- microbov obj2 <- genind2genpop(obj1) # perform a correspondance analysis on counts data Xcount <- tab(obj2, NA.method="zero") ca1 <- dudi.coa(Xcount,scannf=FALSE) s.label(ca1$li,sub="Correspondance Analysis",csub=1.2) add.scatter.eig(ca1$eig,nf=2,xax=1,yax=2,posi="topleft") # perform a principal component analysis on frequency data Xfreq <- makefreq(obj2, missing="mean") Xfreq <- tab(obj2, NA.method="mean") # equivalent to line above pca1 <- dudi.pca(Xfreq,scale=FALSE,scannf=FALSE) s.label(pca1$li,sub="Principal Component Analysis",csub=1.2) add.scatter.eig(pca1$eig,nf=2,xax=1,yax=2,posi="top") ## End(Not run)## Not run: data(microbov) obj1 <- microbov obj2 <- genind2genpop(obj1) # perform a correspondance analysis on counts data Xcount <- tab(obj2, NA.method="zero") ca1 <- dudi.coa(Xcount,scannf=FALSE) s.label(ca1$li,sub="Correspondance Analysis",csub=1.2) add.scatter.eig(ca1$eig,nf=2,xax=1,yax=2,posi="topleft") # perform a principal component analysis on frequency data Xfreq <- makefreq(obj2, missing="mean") Xfreq <- tab(obj2, NA.method="mean") # equivalent to line above pca1 <- dudi.pca(Xfreq,scale=FALSE,scannf=FALSE) s.label(pca1$li,sub="Principal Component Analysis",csub=1.2) add.scatter.eig(pca1$eig,nf=2,xax=1,yax=2,posi="top") ## End(Not run)
This data set gives the genotypes of 704 cattle individuals for 30 microsatellites recommended by the FAO. The individuals are divided into two countries (Afric, France), two species (Bos taurus, Bos indicus) and 15 breeds. Individuals were chosen in order to avoid pseudoreplication according to their exact genealogy.
microbov is a genind object with 3 supplementary components:
a factor giving the country of each individual (AF: Afric; FR: France).
a factor giving the breed of each individual.
is a factor giving the species of each individual (BT: Bos taurus; BI: Bos indicus).
Data prepared by Katayoun Moazami-Goudarzi and Denis Lalo\"e (INRA, Jouy-en-Josas, France)
Lalo\"e D., Jombart T., Dufour A.-B. and Moazami-Goudarzi K. (2007) Consensus genetic structuring and typological value of markers using Multiple Co-Inertia Analysis. Genetics Selection Evolution. 39: 545–567.
## Not run: data(microbov) microbov summary(microbov) # make Y, a genpop object Y <- genind2genpop(microbov) # make allelic frequency table temp <- makefreq(Y,missing="mean") X <- temp$tab nsamp <- temp$nobs # perform 1 PCA per marker kX <- ktab.data.frame(data.frame(X),[email protected]) kpca <- list() for(i in 1:30) {kpca[[i]] <- dudi.pca(kX[[i]],scannf=FALSE,nf=2,center=TRUE,scale=FALSE)} sel <- sample(1:30,4) col = rep('red',15) col[c(2,10)] = 'darkred' col[c(4,12,14)] = 'deepskyblue4' col[c(8,15)] = 'darkblue' # display %PCA par(mfrow=c(2,2)) for(i in sel) { s.multinom(kpca[[i]]$c1,kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i]) add.scatter.eig(kpca[[i]]$eig,3,xax=1,yax=2,posi="top") } # perform a Multiple Coinertia Analysis kXcent <- kX for(i in 1:30) kXcent[[i]] <- as.data.frame(scalewt(kX[[i]],center=TRUE,scale=FALSE)) mcoa1 <- mcoa(kXcent,scannf=FALSE,nf=3, option="uniform") # coordinated %PCA mcoa.axes <- split(mcoa1$axis, [email protected]) mcoa.coord <- split(mcoa1$Tli,mcoa1$TL[,1]) var.coord <- lapply(mcoa.coord,function(e) apply(e,2,var)) par(mfrow=c(2,2)) for(i in sel) { s.multinom(mcoa.axes[[i]][,1:2],kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i]) add.scatter.eig(var.coord[[i]],2,xax=1,yax=2,posi="top") } # reference typology par(mfrow=c(1,1)) s.label(mcoa1$SynVar,lab=popNames(microbov),sub="Reference typology",csub=1.5) add.scatter.eig(mcoa1$pseudoeig,nf=3,xax=1,yax=2,posi="top") # typologial values tv <- mcoa1$cov2 tv <- apply(tv,2,function(c) c/sum(c))*100 rownames(tv) <- locNames(Y) tv <- tv[order(locNames(Y)),] par(mfrow=c(3,1),mar=c(5,3,3,4),las=3) for(i in 1:3){ barplot(round(tv[,i],3),ylim=c(0,12),yaxt="n",main=paste("Typological value - structure",i)) axis(side=2,at=seq(0,12,by=2),labels=paste(seq(0,12,by=2),"%"),cex=3) abline(h=seq(0,12,by=2),col="grey",lty=2) } ## End(Not run)## Not run: data(microbov) microbov summary(microbov) # make Y, a genpop object Y <- genind2genpop(microbov) # make allelic frequency table temp <- makefreq(Y,missing="mean") X <- temp$tab nsamp <- temp$nobs # perform 1 PCA per marker kX <- ktab.data.frame(data.frame(X),Y@loc.n.all) kpca <- list() for(i in 1:30) {kpca[[i]] <- dudi.pca(kX[[i]],scannf=FALSE,nf=2,center=TRUE,scale=FALSE)} sel <- sample(1:30,4) col = rep('red',15) col[c(2,10)] = 'darkred' col[c(4,12,14)] = 'deepskyblue4' col[c(8,15)] = 'darkblue' # display %PCA par(mfrow=c(2,2)) for(i in sel) { s.multinom(kpca[[i]]$c1,kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i]) add.scatter.eig(kpca[[i]]$eig,3,xax=1,yax=2,posi="top") } # perform a Multiple Coinertia Analysis kXcent <- kX for(i in 1:30) kXcent[[i]] <- as.data.frame(scalewt(kX[[i]],center=TRUE,scale=FALSE)) mcoa1 <- mcoa(kXcent,scannf=FALSE,nf=3, option="uniform") # coordinated %PCA mcoa.axes <- split(mcoa1$axis, Y@loc.fac) mcoa.coord <- split(mcoa1$Tli,mcoa1$TL[,1]) var.coord <- lapply(mcoa.coord,function(e) apply(e,2,var)) par(mfrow=c(2,2)) for(i in sel) { s.multinom(mcoa.axes[[i]][,1:2],kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i]) add.scatter.eig(var.coord[[i]],2,xax=1,yax=2,posi="top") } # reference typology par(mfrow=c(1,1)) s.label(mcoa1$SynVar,lab=popNames(microbov),sub="Reference typology",csub=1.5) add.scatter.eig(mcoa1$pseudoeig,nf=3,xax=1,yax=2,posi="top") # typologial values tv <- mcoa1$cov2 tv <- apply(tv,2,function(c) c/sum(c))*100 rownames(tv) <- locNames(Y) tv <- tv[order(locNames(Y)),] par(mfrow=c(3,1),mar=c(5,3,3,4),las=3) for(i in 1:3){ barplot(round(tv[,i],3),ylim=c(0,12),yaxt="n",main=paste("Typological value - structure",i)) axis(side=2,at=seq(0,12,by=2),labels=paste(seq(0,12,by=2),"%"),cex=3) abline(h=seq(0,12,by=2),col="grey",lty=2) } ## End(Not run)
This function computes the minor allele frequency for each locus in a genind object. To test if loci are polymorphic, see the function isPoly.
minorAllele(x)minorAllele(x)
x |
a genind object |
Thibaut Jombart [email protected]
## Not run: ## LOAD DATA data(nancycats) ## COMPUTE ALLELE FREQUENCIES x <- nancycats apply(tab(x, freq=TRUE),2,mean, na.rm=TRUE) ## GET MINOR ALLELE FREQUENCY m.freq <- minorAllele(x) m.freq ## End(Not run)## Not run: ## LOAD DATA data(nancycats) ## COMPUTE ALLELE FREQUENCIES x <- nancycats apply(tab(x, freq=TRUE),2,mean, na.rm=TRUE) ## GET MINOR ALLELE FREQUENCY m.freq <- minorAllele(x) m.freq ## End(Not run)
The Monmonier's algorithm detects boundaries among vertices of a
valuated graph. This is achieved by finding the path
exhibiting the largest distances between connected vertices.
The highest distance between two connected vertices (i.e. neighbours) is
found, giving the starting point of the path. Then, the algorithm
seeks the highest distance between immediate neighbours, and so on
until a threshold value is attained.
This threshold can be chosen from the plot of sorted distances between
connected vertices: a boundary will likely result in an abrupt decrease
of these values.
When several paths are looked for, the previous paths are taken into
account, and cannot be either crossed or redrawn. Monmonier's
algorithm can be used to assess the boundaries between patches of
homogeneous observations.
Although Monmonier algorithm was initially designed for Voronoi
tesselation, this implementation generalizes this algorithm to different
connection networks. The optimize.monmonier function produces a
monmonier object by trying several starting points, and
returning the best boundary (i.e. largest sum of local distances). This
is designed to avoid the algorithm to be trapped by a single strong
local difference inside an homogeneous patch.
monmonier(xy, dist, cn, threshold=NULL, bd.length=NULL, nrun=1, skip.local.diff=rep(0,nrun),scanthres=is.null(threshold), allowLoop=TRUE) optimize.monmonier(xy, dist, cn, ntry=10, bd.length=NULL, return.best=TRUE, display.graph=TRUE, threshold=NULL, scanthres=is.null(threshold), allowLoop=TRUE) ## S3 method for class 'monmonier' plot(x, variable=NULL, displayed.runs=1:x$nrun, add.arrows=TRUE, col='blue', lty=1, bwd=4, clegend=1, csize=0.7, method=c('squaresize','greylevel'), sub='', csub=1, possub='topleft', cneig=1, pixmap=NULL, contour=NULL, area=NULL, add.plot=FALSE, ...) ## S3 method for class 'monmonier' print(x, ...)monmonier(xy, dist, cn, threshold=NULL, bd.length=NULL, nrun=1, skip.local.diff=rep(0,nrun),scanthres=is.null(threshold), allowLoop=TRUE) optimize.monmonier(xy, dist, cn, ntry=10, bd.length=NULL, return.best=TRUE, display.graph=TRUE, threshold=NULL, scanthres=is.null(threshold), allowLoop=TRUE) ## S3 method for class 'monmonier' plot(x, variable=NULL, displayed.runs=1:x$nrun, add.arrows=TRUE, col='blue', lty=1, bwd=4, clegend=1, csize=0.7, method=c('squaresize','greylevel'), sub='', csub=1, possub='topleft', cneig=1, pixmap=NULL, contour=NULL, area=NULL, add.plot=FALSE, ...) ## S3 method for class 'monmonier' print(x, ...)
xy |
a matrix yielding the spatial coordinates of the objects, with two columns respectively giving X and Y |
dist |
an object of class |
cn |
a connection network of class |
threshold |
a number giving the minimal distance between two neighbours crossed by the path; by default, this is the third quartile of all the distances between neighbours |
bd.length |
an optional integer giving the requested length of the boundaries (in number of local differences) |
nrun |
is a integer giving the number of runs of the algorithm, that is, the number of paths to search, being one by default |
skip.local.diff |
is a vector of integers, whose length is the number of paths ( |
scanthres |
a logical stating whether the threshold sould be chosen from the barplot of sorted distances between neighbours |
allowLoop |
a logical specifying whether the boundary can loop (TRUE, default) or not (FALSE) |
ntry |
an integer giving the number of different starting points tried. |
return.best |
a logical stating whether the best monmonier object should be returned (TRUE, default) or not (FALSE) |
display.graph |
a logical whether the scores of each try should be plotted (TRUE, default) or not |
x |
a monmonier object |
variable |
a variable to be plotted using |
displayed.runs |
an integer vector giving the rank of the paths to represent |
add.arrows |
a logical, stating whether arrows should indicate the direction of the path (TRUE) or not (FALSE, used by default) |
col |
a characters vector giving the colors to be used for each boundary; recycled is needed; 'blue' is used by default |
lty |
a characters vector giving the type of line to be used for each boundary; 1 is used by default |
bwd |
a number giving the boundary width factor, applying to every segments of the paths; 4 is used by default |
clegend |
like in |
csize |
like in |
method |
like in |
sub |
a string of characters giving the subtitle of the plot |
csub |
the size factor of the subtitle |
possub |
the position of the subtitle; available choices are 'topleft' (by default), 'topright', 'bottomleft', and 'bottomright' |
cneig |
the size factor of the connection network |
pixmap |
an object of the class |
contour |
a data frame with 4 columns to plot the contour of the map: each row gives a segment (x1,y1,x2,y2) |
area |
a data frame of class 'area' to plot a set of surface units in contour |
add.plot |
a logical stating whether the plot should be added to the current one (TRUE), or displayed in a new window (FALSE, by default) |
... |
further arguments passed to other methods |
The function monmonier returns a list of the class monmonier, which contains the general informations about the algorithm, and about each run.
When displayed, the width of the boundaries reflects their 'strength'.
Let a segment MN be part of the path, M being the middle of AB, N of CD.
Then the boundary width for MN is proportionnal to (d(AB)+d(CD))/2.
As there is no perfect method to display graphically a quantitative
variable (see for instance the differences between the two methods of
s.value), the boundaries provided by this algorithm seem
sometimes more reliable than the boundaries our eyes perceive (or miss).
Returns an object of class monmonier, which contains the following elements :
run1 (run2, ...)
|
for each run, a list containing a dataframe giving the path coordinates, and a vector of the distances between neighbours of the path |
nrun |
the number of runs performed, i.e. the number of boundaries in the monmonier object |
threshold |
the threshold value, minimal distance between neighbours accounted for by the algorithm |
xy |
the matrix of spatial coordinates |
cn |
the connection network of class |
call |
the call of the function |
Thibaut Jombart [email protected]
Monmonier, M. (1973) Maximum-difference barriers: an alternative numerical regionalization method. Geographic Analysis, 3, 245–261.
Manni, F., Guerard, E. and Heyer, E. (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by "Monmonier's algorithm". Human Biology, 76, 173–190
if(require(spdep)){ ### non-interactive example # est-west separation load(system.file("files/mondata1.rda",package="adegenet")) cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE) mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2) plot(mon1,mondata1$x1) plot(mon1,mondata1$x1,met="greylevel",add.arr=FALSE,col="red",bwd=6,lty=2) # square in the middle load(system.file("files/mondata2.rda",package="adegenet")) cn2 <- chooseCN(mondata2$xy,type=1,ask=FALSE) mon2 <- monmonier(mondata2$xy,dist(mondata2$x2),cn2,threshold=2) plot(mon2,mondata2$x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5) ### genetic data example ## Not run: data(sim2pop) if(require(hierfstat)){ ## try and find the Fst fstat(sim2pop,fst=TRUE) # Fst = 0.038 } ## run monmonier algorithm # build connection network gab <- chooseCN(sim2pop@other$xy,ask=FALSE,type=2) # filter random noise pca1 <- dudi.pca(sim2pop@tab,scale=FALSE, scannf=FALSE, nf=1) # run the algorithm mon1 <- monmonier(sim2pop@other$xy,dist(pca1$l1[,1]),gab,scanthres=FALSE) # graphical display plot(mon1,var=pca1$l1[,1]) temp <- sim2pop@pop levels(temp) <- c(17,19) temp <- as.numeric(as.character(temp)) plot(mon1) points(sim2pop@other$xy,pch=temp,cex=2) legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19)) ### interactive example # north-south separation xy <- matrix(runif(120,0,10), ncol=2) x1 <- rnorm(60) x1[xy[,2] > 5] <- x1[xy[,2] > 5]+3 cn1 <- chooseCN(xy,type=1,ask=FALSE) mon1 <- optimize.monmonier(xy,dist(x1)^2,cn1,ntry=10) # graphics plot(mon1,x1,met="greylevel",csize=.6) # island in the middle x2 <- rnorm(60) sel <- (xy[,1]>3.5 & xy[,2]>3.5 & xy[,1]<6.5 & xy[,2]<6.5) x2[sel] <- x2[sel]+4 cn2 <- chooseCN(xy,type=1,ask=FALSE) mon2 <- optimize.monmonier(xy,dist(x2)^2,cn2,ntry=10) # graphics plot(mon2,x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5) ## End(Not run) }if(require(spdep)){ ### non-interactive example # est-west separation load(system.file("files/mondata1.rda",package="adegenet")) cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE) mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2) plot(mon1,mondata1$x1) plot(mon1,mondata1$x1,met="greylevel",add.arr=FALSE,col="red",bwd=6,lty=2) # square in the middle load(system.file("files/mondata2.rda",package="adegenet")) cn2 <- chooseCN(mondata2$xy,type=1,ask=FALSE) mon2 <- monmonier(mondata2$xy,dist(mondata2$x2),cn2,threshold=2) plot(mon2,mondata2$x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5) ### genetic data example ## Not run: data(sim2pop) if(require(hierfstat)){ ## try and find the Fst fstat(sim2pop,fst=TRUE) # Fst = 0.038 } ## run monmonier algorithm # build connection network gab <- chooseCN(sim2pop@other$xy,ask=FALSE,type=2) # filter random noise pca1 <- dudi.pca(sim2pop@tab,scale=FALSE, scannf=FALSE, nf=1) # run the algorithm mon1 <- monmonier(sim2pop@other$xy,dist(pca1$l1[,1]),gab,scanthres=FALSE) # graphical display plot(mon1,var=pca1$l1[,1]) temp <- sim2pop@pop levels(temp) <- c(17,19) temp <- as.numeric(as.character(temp)) plot(mon1) points(sim2pop@other$xy,pch=temp,cex=2) legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19)) ### interactive example # north-south separation xy <- matrix(runif(120,0,10), ncol=2) x1 <- rnorm(60) x1[xy[,2] > 5] <- x1[xy[,2] > 5]+3 cn1 <- chooseCN(xy,type=1,ask=FALSE) mon1 <- optimize.monmonier(xy,dist(x1)^2,cn1,ntry=10) # graphics plot(mon1,x1,met="greylevel",csize=.6) # island in the middle x2 <- rnorm(60) sel <- (xy[,1]>3.5 & xy[,2]>3.5 & xy[,1]<6.5 & xy[,2]<6.5) x2[sel] <- x2[sel]+4 cn2 <- chooseCN(xy,type=1,ask=FALSE) mon2 <- optimize.monmonier(xy,dist(x2)^2,cn2,ntry=10) # graphics plot(mon2,x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5) ## End(Not run) }
This data set gives the genotypes of 237 cats (Felis catus L.) for 9 microsatellites markers. The individuals are divided into 17 colonies whose spatial coordinates are also provided.
nancycats is a genind object with spatial coordinates of the
colonies as a supplementary components (@xy).
Dominique Pontier (UMR CNRS 5558, University Lyon1, France)
Devillard, S.; Jombart, T. & Pontier, D. Disentangling spatial and genetic structure of stray cat (Felis catus L.) colonies in urban habitat using: not all colonies are equal. submitted to Molecular Ecology
## Not run: data(nancycats) nancycats # summary's results are stored in x x <- summary(nancycats) # some useful graphics barplot(x$loc.n.all,ylab="Alleles numbers",main="Alleles numbers per locus") plot(x$pop.eff,x$pop.nall,type="n",xlab="Sample size",ylab="Number of alleles") text(x$pop.eff,y=x$pop.nall,lab=names(x$pop.nall)) par(las=3) barplot(table(nancycats@pop),ylab="Number of genotypes",main="Number of genotypes per colony") # are cats structured among colonies ? if(require(hierfstat)){ gtest <- gstat.randtest(nancycats,nsim=99) gtest plot(gtest) dat <- genind2hierfstat(nancycats) Fstat <- varcomp.glob(dat$pop,dat[,-1]) Fstat } ## End(Not run)## Not run: data(nancycats) nancycats # summary's results are stored in x x <- summary(nancycats) # some useful graphics barplot(x$loc.n.all,ylab="Alleles numbers",main="Alleles numbers per locus") plot(x$pop.eff,x$pop.nall,type="n",xlab="Sample size",ylab="Number of alleles") text(x$pop.eff,y=x$pop.nall,lab=names(x$pop.nall)) par(las=3) barplot(table(nancycats@pop),ylab="Number of genotypes",main="Number of genotypes per colony") # are cats structured among colonies ? if(require(hierfstat)){ gtest <- gstat.randtest(nancycats,nsim=99) gtest plot(gtest) dat <- genind2hierfstat(nancycats) Fstat <- varcomp.glob(dat$pop,dat[,-1]) Fstat } ## End(Not run)
The genind and genlight objects have changed in Adegenet version 2.0. They have each gained strata and hierarchy slots. What's more is that the genind objects have been optimized for storage and now store the tab slot as integers instead of numerics. This function will convert old genind or genlight objects to new ones seamlessly.
old2new_genind(object, donor = new("genind")) old2new_genlight(object, donor = new("genlight")) old2new_genpop(object, donor = new("genpop"))old2new_genind(object, donor = new("genind")) old2new_genlight(object, donor = new("genlight")) old2new_genpop(object, donor = new("genpop"))
object |
a genind or genlight object from version 1.4 or earlier. |
donor |
a new object to place all the data into. |
Thibaut Jombart [email protected]
Zhian N. Kamvar [email protected]
The function pairDistPlot extracts and plots pairwise distances
between different groups (graphs use ggplot2). The function
pairDistPlot does the same, without the graphs.
pairDistPlot is a generic function with methods for the
following types of objects:
- dist
- matrix (only numeric data)
- genind objects (genetic markers, individuals)
- DNAbin objects (DNA sequences)
pairDist(x, ...) pairDistPlot(x, ...) ## S3 method for class 'dist' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...) ## S3 method for class 'matrix' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...) ## S3 method for class 'genind' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...) ## S3 method for class 'DNAbin' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...)pairDist(x, ...) pairDistPlot(x, ...) ## S3 method for class 'dist' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...) ## S3 method for class 'matrix' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...) ## S3 method for class 'genind' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...) ## S3 method for class 'DNAbin' pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE, jitter=TRUE, ...)
x |
pairwise distances provided as a |
grp |
a factor defining a grouping of individuals. |
within |
a logical indicating whether to keep within-group comparisons. |
sep |
a character used as separator between group names |
data |
a logical indicating whether data of the plot should be returned. |
violin |
a logical indicating whether a violinplot should be generated. |
boxplot |
a logical indicating whether a boxplot should be generated. |
jitter |
a logical indicating whether a jitter-plot should be generated. |
... |
further arguments to be used by other functions; used for
|
A list with different components, depending on the values of the
arguments. Plots are returned as ggplot2 objects.
Thibaut Jombart [email protected].
gengraph to identify connectivity based on distances.
## Not run: ## use a subset of influenza data data(H3N2) set.seed(1) dat <- H3N2[sample(1:nInd(H3N2), 100)] ## get pairwise distances temp <- pairDistPlot(dat, other(dat)$epid) ## see raw data head(temp$data) ## see plots temp$boxplot temp$violin temp$jitter ## End(Not run)## Not run: ## use a subset of influenza data data(H3N2) set.seed(1) dat <- H3N2[sample(1:nInd(H3N2), 100)] ## get pairwise distances temp <- pairDistPlot(dat, other(dat)$epid) ## see raw data head(temp$data) ## see plots temp$boxplot temp$violin temp$jitter ## End(Not run)
The generic function propTyped is devoted to investigating the
structure of missing data in adegenet objects.
Methods are defined for genind and genpop objects. They can return the proportion of available (i.e. non-missing) data per individual/population, locus, or the combination of both in with case the matrix indicates which entity (individual or population) was typed on which locus.
## S4 method for signature 'genind' propTyped(x, by=c("ind","loc","both")) ## S4 method for signature 'genpop' propTyped(x, by=c("pop","loc","both"))## S4 method for signature 'genind' propTyped(x, by=c("ind","loc","both")) ## S4 method for signature 'genpop' propTyped(x, by=c("pop","loc","both"))
x |
|
by |
a character being "ind","loc", or "both" for genind object and "pop","loc", or "both" for genpop object. It specifies whether proportion of typed data are provided by entity ("ind"/"pop"), by locus ("loc") or both ("both"). See details. |
When by is set to "both", the result is a matrix of binary data
with entities in rows (individuals or populations) and markers in
columns. The values of the matrix are 1 for typed data, and 0 for NA.
A vector of proportion (when by equals "ind", "pop", or
"loc"), or a matrix of binary data (when by equals "both")
Thibaut Jombart [email protected]
## Not run: data(nancycats) propTyped(nancycats,by="loc") propTyped(genind2genpop(nancycats),by="both") ## End(Not run)## Not run: data(nancycats) propTyped(nancycats,by="loc") propTyped(genind2genpop(nancycats),by="both") ## End(Not run)
The function read.fstat reads Fstat data files (.dat) and convert
them into a genind object.
read.fstat(file, quiet = FALSE)read.fstat(file, quiet = FALSE)
file |
a character string giving the path to the file to convert, with the appropriate extension. |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
Note: read.fstat is meant for DIPLOID DATA ONLY. Haploid data with
the Hierfstat format can be read into R using read.table or
read.csv after removing headers and 'POP' lines, and then converted
using df2genind.
an object of the class genind
Thibaut Jombart [email protected]
Fstat (version 2.9.3). Software by Jerome Goudet.
http://www2.unil.ch/popgen/softwares/fstat.htm
import2genind, df2genind,
read.genetix, read.structure,
read.genepop
obj <- read.fstat(system.file("files/nancycats.dat",package="adegenet")) objobj <- read.fstat(system.file("files/nancycats.dat",package="adegenet")) obj
The function read.genepop reads Genepop data files (.gen) and convert
them into a genind object.
read.genepop(file, ncode = 2L, quiet = FALSE)read.genepop(file, ncode = 2L, quiet = FALSE)
file |
a character string giving the path to the file to convert, with the appropriate extension. |
ncode |
an integer indicating the number of characters used to code an allele. |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
Note: read.genepop is meant for DIPLOID DATA ONLY. Haploid data with
the Genepop format can be read into R using read.table or
read.csv after removing headers and 'POP' lines, and then converted
using df2genind.
an object of the class genind
Thibaut Jombart [email protected]
Raymond M. & Rousset F, (1995). GENEPOP (version 1.2):
population genetics software for exact tests and ecumenicism. J.
Heredity, 86:248-249
import2genind, df2genind,
read.fstat, read.structure,
read.genetix
obj <- read.genepop(system.file("files/nancycats.gen",package="adegenet")) objobj <- read.genepop(system.file("files/nancycats.gen",package="adegenet")) obj
The function read.genetix reads GENETIX data files (.gtx) and convert
them into a genind object.
read.genetix(file = NULL, quiet = FALSE)read.genetix(file = NULL, quiet = FALSE)
file |
a character string giving the path to the file to convert, with the appropriate extension. |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
Note: read.genetix is meant for DIPLOID DATA ONLY. Haploid data with
the GENETIX format can be read into R using read.table or
read.csv after removing headers and 'POP' lines, and then converted
using df2genind.
an object of the class genind
Thibaut Jombart [email protected]
Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F.
(1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la genetique des
populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000,
Universite de Montpellier II, Montpellier (France).
import2genind, df2genind,
read.fstat, read.structure,
read.genepop
obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet")) objobj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet")) obj
The function read.snp reads a SNP data file with extension '.snp' and
converts it into a genlight object. This format is devoted to
handle biallelic SNP only, but can accommodate massive datasets such as
complete genomes with considerably less memory than other formats.
read.snp( file, quiet = FALSE, chunkSize = 1000, parallel = FALSE, n.cores = NULL, ... )read.snp( file, quiet = FALSE, chunkSize = 1000, parallel = FALSE, n.cores = NULL, ... )
file |
a character string giving the path to the file to convert, with the extension ".snp". |
quiet |
logical stating whether a conversion messages should be printed (TRUE,default) or not (FALSE). |
chunkSize |
an integer indicating the number of genomes to be read at a time; larger values require more RAM but decrease the time needed to read the data. |
parallel |
a logical indicating whether multiple cores -if available-
should be used for the computations (TRUE, default), or not (FALSE);
requires the package |
n.cores |
if |
... |
other arguments to be passed to other functions - currently not used. |
The function reads data by chunks of a few genomes (minimum 1, no maximum)
at a time, which allows one to read massive datasets with negligible RAM
requirements (albeit at a cost of computational time). The argument
chunkSize indicates the number of genomes read at a time. Increasing
this value decreases the computational time required to read data in, while
increasing memory requirements.
A description of the .snp format is provided in an example file distributed with adegenet (see example below).
=== The .snp format ===
Details of the .snp format can be found in the example file distributed with
adegenet (see below), or on the adegenet website (type adegenetWeb()
in R).
an object of the class "genlight"
Thibaut Jombart [email protected]
- ?genlight for a description of the class
"genlight".
- read.PLINK: read SNPs in PLINK's '.raw' format.
- fasta2genlight: extract SNPs from alignments with fasta
format.
- df2genind: convert any multiallelic markers into adegenet
"genlight".
- import2genind: read multiallelic markers from various
software into adegenet.
## Not run: ## show the example file ## ## this is the path to the file: system.file("files/exampleSnpDat.snp",package="adegenet") ## show its content: file.show(system.file("files/exampleSnpDat.snp",package="adegenet")) ## read the file obj <- read.snp(system.file("files/exampleSnpDat.snp",package="adegenet"), chunk=2) obj as.matrix(obj) ploidy(obj) alleles(obj) locNames(obj) ## End(Not run)## Not run: ## show the example file ## ## this is the path to the file: system.file("files/exampleSnpDat.snp",package="adegenet") ## show its content: file.show(system.file("files/exampleSnpDat.snp",package="adegenet")) ## read the file obj <- read.snp(system.file("files/exampleSnpDat.snp",package="adegenet"), chunk=2) obj as.matrix(obj) ploidy(obj) alleles(obj) locNames(obj) ## End(Not run)
The function read.structure reads STRUCTURE data files (.str ou
.stru) and convert them into a genind object. By default, this
function is interactive and asks a few questions about data content. This
can be disabled (for optional questions) by turning the 'ask' argument to
FALSE. However, one has to know the number of genotypes, of markers and if
genotypes are coded on a single or on two rows before importing data.
read.structure( file, n.ind = NULL, n.loc = NULL, onerowperind = NULL, col.lab = NULL, col.pop = NULL, col.others = NULL, row.marknames = NULL, NA.char = "-9", pop = NULL, sep = NULL, ask = TRUE, quiet = FALSE )read.structure( file, n.ind = NULL, n.loc = NULL, onerowperind = NULL, col.lab = NULL, col.pop = NULL, col.others = NULL, row.marknames = NULL, NA.char = "-9", pop = NULL, sep = NULL, ask = TRUE, quiet = FALSE )
file |
a character string giving the path to the file to convert, with the appropriate extension. |
n.ind |
an integer giving the number of genotypes (or 'individuals') in the dataset |
n.loc |
an integer giving the number of markers in the dataset |
onerowperind |
a STRUCTURE coding option: are genotypes coded on a single row (TRUE), or on two rows (FALSE, default) |
col.lab |
an integer giving the index of the column containing labels of genotypes. '0' if absent. |
col.pop |
an integer giving the index of the column containing population to which genotypes belong. '0' if absent. |
col.others |
an vector of integers giving the indexes of the columns containing other informations to be read. Will be available in @other of the created object. |
row.marknames |
an integer giving the index of the row containing the names of the markers. '0' if absent. |
NA.char |
the character string coding missing data. "-9" by default. Note that in any case, series of zero (like "000") are interpreted as NA too. |
pop |
an optional factor giving the population of each individual. |
sep |
a character string used as separator between alleles. |
ask |
a logical specifying if the function should ask for optional informations about the dataset (TRUE, default), or try to be as quiet as possible (FALSE). |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
Note: read.structure is meant for DIPLOID DATA ONLY. Haploid data
with the STRUCTURE format can easily be read into R using read.table
or read.csv and then converted using df2genind.
an object of the class genind
Thibaut Jombart [email protected]
Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155: 945-959
import2genind, df2genind,
read.fstat, read.genetix,
read.genepop
obj <- read.structure(system.file("files/nancycats.str",package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE) objobj <- read.structure(system.file("files/nancycats.str",package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE) obj
The function repool allows to merge genotypes from different
genind objects into a single 'pool' (i.e. a new genind).
The markers have to be the same for all objects to be merged, but
there is no constraint on alleles.
repool(..., list = FALSE)repool(..., list = FALSE)
... |
a list of genind objects, or a series of genind objects separated by commas |
list |
a logical indicating whether a list of objects with matched alleles shall be returned (TRUE), or a single genind object (FALSE, default). |
This function can be useful, for instance, when hybrids are created
using hybridize, to merge hybrids with their parent
population for further analyses. Note that repool can also
reverse the action of seppop.
Thibaut Jombart [email protected]
## Not run: ## use the cattle breeds dataset data(microbov) temp <- seppop(microbov) names(temp) ## hybridize salers and zebu -- nasty cattle zebler <- hybridize(temp$Salers, temp$Zebu, n=40) zebler ## now merge zebler with other cattle breeds nastyCattle <- repool(microbov, zebler) nastyCattle ## End(Not run)## Not run: ## use the cattle breeds dataset data(microbov) temp <- seppop(microbov) names(temp) ## hybridize salers and zebu -- nasty cattle zebler <- hybridize(temp$Salers, temp$Zebu, n=40) zebler ## now merge zebler with other cattle breeds nastyCattle <- repool(microbov, zebler) nastyCattle ## End(Not run)
This data set contains the genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains, in France. No prior clustering about individuals is known. Each genotype is georeferenced. These data also contain a raster map of elevation of the sampling area.
rupica is a genind object with 3 supplementary components
inside the @other slot:
a matrix containing the spatial coordinates of the genotypes.
a raster map of elevation,
with the asc format from the adehabitat package.
a function to display the map of elevation with an
appropriate legend (use showBauges()).
Daniel Maillard, 'Office National de la Chasse et de la Faune Sauvage' (ONCFS), France.
Cassar S (2008) Organisation spatiale de la variabilité
génétique et phénotypique a l'échelle du paysage: le cas du chamois et du
chevreuil, en milieu de montagne. PhD Thesis. University Claude Bernard -
Lyon 1, France.
Cassar S, Jombart T, Loison A, Pontier D, Dufour A-B, Jullien J-M, Chevrier T, Maillard D. Spatial genetic structure of Alpine chamois (Rupicapra rupicapra): a consequence of landscape features and social factors? submitted to Molecular Ecology.
data(rupica) rupica ## Not run: required_packages <- require(adehabitat) && require(adespatial) && require(spdep) if (required_packages) { ## see the sampling area showBauges <- rupica$other$showBauges showBauges() points(rupica$other$xy,col="red") ## perform a sPCA spca1 <- spca(rupica,type=5,d1=0,d2=2300,plot=FALSE,scannf=FALSE,nfposi=2,nfnega=0) barplot(spca1$eig,col=rep(c("black","grey"),c(2,100)),main="sPCA eigenvalues") screeplot(spca1,main="sPCA eigenvalues: decomposition") ## data visualization showBauges(,labcex=1) s.value(spca1$xy,spca1$ls[,1],add.p=TRUE,csize=.5) add.scatter.eig(spca1$eig,1,1,1,posi="topleft",sub="Eigenvalues") showBauges(,labcex=1) s.value(spca1$xy,spca1$ls[,2],add.p=TRUE,csize=.5) add.scatter.eig(spca1$eig,2,2,2,posi="topleft",sub="Eigenvalues") rupica$other$showBauges() colorplot(spca1$xy,spca1$li,cex=1.5,add.plot=TRUE) ## global and local tests Gtest <- global.rtest(rupica@tab,spca1$lw,nperm=999) Gtest plot(Gtest) Ltest <- local.rtest(rupica@tab,spca1$lw,nperm=999) Ltest plot(Ltest) } ## End(Not run)data(rupica) rupica ## Not run: required_packages <- require(adehabitat) && require(adespatial) && require(spdep) if (required_packages) { ## see the sampling area showBauges <- rupica$other$showBauges showBauges() points(rupica$other$xy,col="red") ## perform a sPCA spca1 <- spca(rupica,type=5,d1=0,d2=2300,plot=FALSE,scannf=FALSE,nfposi=2,nfnega=0) barplot(spca1$eig,col=rep(c("black","grey"),c(2,100)),main="sPCA eigenvalues") screeplot(spca1,main="sPCA eigenvalues: decomposition") ## data visualization showBauges(,labcex=1) s.value(spca1$xy,spca1$ls[,1],add.p=TRUE,csize=.5) add.scatter.eig(spca1$eig,1,1,1,posi="topleft",sub="Eigenvalues") showBauges(,labcex=1) s.value(spca1$xy,spca1$ls[,2],add.p=TRUE,csize=.5) add.scatter.eig(spca1$eig,2,2,2,posi="topleft",sub="Eigenvalues") rupica$other$showBauges() colorplot(spca1$xy,spca1$li,cex=1.5,add.plot=TRUE) ## global and local tests Gtest <- global.rtest(rupica@tab,spca1$lw,nperm=999) Gtest plot(Gtest) Ltest <- local.rtest(rupica@tab,spca1$lw,nperm=999) Ltest plot(Ltest) } ## End(Not run)
The generic function scaleGen is an analogue to the scale
function, but is designed with further arguments giving scaling options.
scaleGen(x, ...) ## S4 method for signature 'genind' scaleGen( x, center = TRUE, scale = TRUE, NA.method = c("asis", "mean", "zero"), truenames = TRUE ) ## S4 method for signature 'genpop' scaleGen( x, center = TRUE, scale = TRUE, NA.method = c("asis", "mean", "zero"), truenames = TRUE )scaleGen(x, ...) ## S4 method for signature 'genind' scaleGen( x, center = TRUE, scale = TRUE, NA.method = c("asis", "mean", "zero"), truenames = TRUE ) ## S4 method for signature 'genpop' scaleGen( x, center = TRUE, scale = TRUE, NA.method = c("asis", "mean", "zero"), truenames = TRUE )
x |
|
... |
further arguments passed to other methods. |
center |
a logical stating whether alleles frequencies should be centred to mean zero (default to TRUE). Alternatively, a vector of numeric values, one per allele, can be supplied: these values will be substracted from the allele frequencies. |
scale |
a logical stating whether alleles frequencies should be scaled (default to TRUE). Alternatively, a vector of numeric values, one per allele, can be supplied: these values will be substracted from the allele frequencies. |
NA.method |
a method to replace NA; asis: leave NAs as is; mean: replace by the mean allele frequencies; zero: replace by zero |
truenames |
no longer used; kept for backward compatibility |
Methods are defined for genind and genpop objects. Both return data.frames of scaled allele frequencies.
A matrix of scaled allele frequencies with genotypes (genind) or populations in (genpop) in rows and alleles in columns.
Thibaut Jombart [email protected]
## Not run: ## load data data(microbov) obj <- genind2genpop(microbov) ## apply scaling X1 <- scaleGen(obj) ## compute PCAs with and without scaling pcaObj <- dudi.pca(obj, scale = FALSE, scannf = FALSE) # pca with no scaling pcaX1 <- dudi.pca(X1, scale = FALSE, scannf = FALSE, nf = 100) # pca scaled using scaleGen() pcaX2 <- dudi.pca(obj, scale = TRUE, scannf = FALSE, nf = 100) # pca scaled in-PCA ## get the loadings of alleles for the two scalings U1 <- pcaObj$c1 U2 <- pcaX1$c1 U3 <- pcaX2$c1 ## find an optimal plane to compare loadings ## use a procustean rotation of loadings tables pro1 <- procuste(U1, U2, nf = 2) pro2 <- procuste(U2, U3, nf = 2) pro3 <- procuste(U1, U3, nf = 2) ## graphics par(mfrow=c(2, 3)) # eigenvalues barplot(pcaObj$eig, main = "Eigenvalues\n no scaling") barplot(pcaX1$eig, main = "Eigenvalues\n scaleGen scaling") barplot(pcaX2$eig, main = "Eigenvalues\n in-PCA scaling") # differences between loadings of alleles s.match(pro1$scorX, pro1$scorY, clab = 0, sub = "no scaling -> scaling (procustean rotation)") s.match(pro2$scorX, pro2$scorY, clab = 0, sub = "scaling scaleGen -> in-PCA scaling") s.match(pro3$scorX, pro3$scorY, clab = 0, sub = "no scaling -> in-PCA scaling") ## End(Not run)## Not run: ## load data data(microbov) obj <- genind2genpop(microbov) ## apply scaling X1 <- scaleGen(obj) ## compute PCAs with and without scaling pcaObj <- dudi.pca(obj, scale = FALSE, scannf = FALSE) # pca with no scaling pcaX1 <- dudi.pca(X1, scale = FALSE, scannf = FALSE, nf = 100) # pca scaled using scaleGen() pcaX2 <- dudi.pca(obj, scale = TRUE, scannf = FALSE, nf = 100) # pca scaled in-PCA ## get the loadings of alleles for the two scalings U1 <- pcaObj$c1 U2 <- pcaX1$c1 U3 <- pcaX2$c1 ## find an optimal plane to compare loadings ## use a procustean rotation of loadings tables pro1 <- procuste(U1, U2, nf = 2) pro2 <- procuste(U2, U3, nf = 2) pro3 <- procuste(U1, U3, nf = 2) ## graphics par(mfrow=c(2, 3)) # eigenvalues barplot(pcaObj$eig, main = "Eigenvalues\n no scaling") barplot(pcaX1$eig, main = "Eigenvalues\n scaleGen scaling") barplot(pcaX2$eig, main = "Eigenvalues\n in-PCA scaling") # differences between loadings of alleles s.match(pro1$scorX, pro1$scorY, clab = 0, sub = "no scaling -> scaling (procustean rotation)") s.match(pro2$scorX, pro2$scorY, clab = 0, sub = "scaling scaleGen -> in-PCA scaling") s.match(pro3$scorX, pro3$scorY, clab = 0, sub = "no scaling -> in-PCA scaling") ## End(Not run)
The function selPopSize checks the sample size of each population in
a genind object and keeps only genotypes of populations
having a given minimum size.
## S4 method for signature 'genind' selPopSize(x,pop=NULL,nMin=10)## S4 method for signature 'genind' selPopSize(x,pop=NULL,nMin=10)
x |
a genind object |
pop |
a vector of characters or a factor giving the population of each genotype in 'x'. If not provided, seeked from x$pop. |
nMin |
the minimum sample size for a population to be
retained. Samples sizes strictly less than |
A genind object.
Thibaut Jombart [email protected]
## Not run: data(microbov) table(pop(microbov)) obj <- selPopSize(microbov, n=50) obj table(pop(obj)) ## End(Not run)## Not run: data(microbov) table(pop(microbov)) obj <- selPopSize(microbov, n=50) obj table(pop(obj)) ## End(Not run)
The function seploc splits an object (genind,
genpop or genlight) by marker. For
genind and genpop objects, the method
returns a list of objects whose components each correspond to a
marker. For genlight objects, the methods returns blocks
of SNPs.
## S4 method for signature 'genind' seploc(x,truenames=TRUE,res.type=c("genind","matrix")) ## S4 method for signature 'genpop' seploc(x,truenames=TRUE,res.type=c("genpop","matrix")) ## S4 method for signature 'genlight' seploc(x, n.block=NULL, block.size=NULL, random=FALSE, parallel=FALSE, n.cores=NULL)## S4 method for signature 'genind' seploc(x,truenames=TRUE,res.type=c("genind","matrix")) ## S4 method for signature 'genpop' seploc(x,truenames=TRUE,res.type=c("genpop","matrix")) ## S4 method for signature 'genlight' seploc(x, n.block=NULL, block.size=NULL, random=FALSE, parallel=FALSE, n.cores=NULL)
x |
|
truenames |
a logical indicating whether true names should be used (TRUE, default) instead of generic labels (FALSE). |
res.type |
a character indicating the type of returned results, a genind or genpop object (default) or a matrix of data corresponding to the 'tab' slot. |
n.block |
an integer indicating the number of blocks of SNPs to be returned. |
block.size |
an integer indicating the size (in number of SNPs) of the blocks to be returned. |
random |
should blocks be formed of contiguous SNPs, or should they be made or randomly chosen SNPs. |
parallel |
a logical indicating whether multiple cores -if
available- should be used for the computations (TRUE, default), or
not (FALSE); requires the package |
n.cores |
if |
The function seploc returns an list of objects of the
same class as the initial object, or a list of matrices similar to
x$tab.
Thibaut Jombart [email protected]
## Not run: ## example on genind objects data(microbov) # separate all markers obj <- seploc(microbov) names(obj) obj$INRA5 ## example on genlight objects x <- glSim(100, 1000, 0, ploidy=2) # simulate data x <- x[,order(glSum(x))] # reorder loci by frequency of 2nd allele glPlot(x, main="All data") # plot data foo <- seploc(x, n.block=3) # form 3 blocks foo glPlot(foo[[1]], main="1st block") # plot 1st block glPlot(foo[[2]], main="2nd block") # plot 2nd block glPlot(foo[[3]], main="3rd block") # plot 3rd block foo <- seploc(x, block.size=600, random=TRUE) # split data, randomize loci foo # note the different block sizes glPlot(foo[[1]]) ## End(Not run)## Not run: ## example on genind objects data(microbov) # separate all markers obj <- seploc(microbov) names(obj) obj$INRA5 ## example on genlight objects x <- glSim(100, 1000, 0, ploidy=2) # simulate data x <- x[,order(glSum(x))] # reorder loci by frequency of 2nd allele glPlot(x, main="All data") # plot data foo <- seploc(x, n.block=3) # form 3 blocks foo glPlot(foo[[1]], main="1st block") # plot 1st block glPlot(foo[[2]], main="2nd block") # plot 2nd block glPlot(foo[[3]], main="3rd block") # plot 3rd block foo <- seploc(x, block.size=600, random=TRUE) # split data, randomize loci foo # note the different block sizes glPlot(foo[[1]]) ## End(Not run)
The function seppop splits a genind or a
genlight object by population, returning a list of
objects whose components each correspond to a population.
For genind objects, the output can either be a list of
genind (default), or a list of matrices corresponding to
the @tab slot.
## S4 method for signature 'genind' seppop(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"), drop=FALSE, treatOther=TRUE, keepNA = FALSE, quiet=TRUE) ## S4 method for signature 'genlight' seppop(x,pop=NULL, treatOther=TRUE, keepNA = FALSE, quiet=TRUE, ...)## S4 method for signature 'genind' seppop(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"), drop=FALSE, treatOther=TRUE, keepNA = FALSE, quiet=TRUE) ## S4 method for signature 'genlight' seppop(x,pop=NULL, treatOther=TRUE, keepNA = FALSE, quiet=TRUE, ...)
x |
a genind object |
pop |
a factor giving the population of each genotype in 'x' OR a formula specifying which strata are to be used when converting to a genpop object. If none provided, population factors are sought in x@pop, but if given, the argument prevails on x@pop. |
truenames |
a logical indicating whether true names should be used (TRUE, default) instead of generic labels (FALSE); used if res.type is "matrix". |
res.type |
a character indicating the type of returned results, a list of genind object (default) or a matrix of data corresponding to the 'tab' slots. |
drop |
a logical stating whether alleles that are no longer present in a subset of data should be discarded (TRUE) or kept anyway (FALSE, default). |
treatOther |
a logical stating whether elements of the
|
keepNA |
If there are individuals with missing population information, should they be pooled into a separate population (TRUE), or excluded (FALSE, default). |
quiet |
a logical indicating whether warnings should be issued
when trying to subset components of the |
... |
further arguments passed to the genlight constructor. |
According to 'res.type': a list of genind object (default) or a matrix of data corresponding to the 'tab' slots.
Thibaut Jombart [email protected]
## Not run: data(microbov) strata(microbov) <- data.frame(other(microbov)) obj <- seppop(microbov) names(obj) obj$Salers ### example using strata obj2 <- seppop(microbov, ~coun/spe) names(obj2) obj2$AF_BI #### example for genlight objects #### x <- new("genlight", list(a=rep(1,1e3),b=rep(0,1e3),c=rep(1, 1e3))) x pop(x) # no population info pop(x) <- c("pop1","pop2", "pop1") # set population memberships pop(x) seppop(x) as.matrix(seppop(x)$pop1)[,1:20] as.matrix(seppop(x)$pop2)[,1:20,drop=FALSE] ## End(Not run)## Not run: data(microbov) strata(microbov) <- data.frame(other(microbov)) obj <- seppop(microbov) names(obj) obj$Salers ### example using strata obj2 <- seppop(microbov, ~coun/spe) names(obj2) obj2$AF_BI #### example for genlight objects #### x <- new("genlight", list(a=rep(1,1e3),b=rep(0,1e3),c=rep(1, 1e3))) x pop(x) # no population info pop(x) <- c("pop1","pop2", "pop1") # set population memberships pop(x) seppop(x) as.matrix(seppop(x)$pop1)[,1:20] as.matrix(seppop(x)$pop2)[,1:20,drop=FALSE] ## End(Not run)
The SeqTrack algorithm [1] aims at reconstructing genealogies of sampled haplotypes or genotypes for which a collection date is available. Contrary to phylogenetic methods which aims at reconstructing hypothetical ancestors for observed sequences, SeqTrack considers that ancestors and descendents are sampled together, and therefore infers ancestry relationships among the sampled sequences.
This approach proved more efficient than phylogenetic approaches for
reconstructing transmission trees in densely sampled disease outbreaks
[1]. This implementation defines a generic function seqTrack
with methods for specific object classes.
seqTrack(...) ## S3 method for class 'matrix' seqTrack(x, x.names, x.dates, best = c("min", "max"), prox.mat = NULL, mu = NULL, haplo.length = NULL, ...) ## S3 method for class 'seqTrack' as.igraph(x, col.pal=redpal, ...) ## S3 method for class 'seqTrack' plot(x, y=NULL, col.pal=redpal, ...) plotSeqTrack(x, xy, use.arrows=TRUE, annot=TRUE, labels=NULL, col=NULL, bg="grey", add=FALSE, quiet=FALSE, date.range=NULL, jitter.arrows=0, plot=TRUE, ...) get.likelihood(...) ## S3 method for class 'seqTrack' get.likelihood(x, mu, haplo.length, ...)seqTrack(...) ## S3 method for class 'matrix' seqTrack(x, x.names, x.dates, best = c("min", "max"), prox.mat = NULL, mu = NULL, haplo.length = NULL, ...) ## S3 method for class 'seqTrack' as.igraph(x, col.pal=redpal, ...) ## S3 method for class 'seqTrack' plot(x, y=NULL, col.pal=redpal, ...) plotSeqTrack(x, xy, use.arrows=TRUE, annot=TRUE, labels=NULL, col=NULL, bg="grey", add=FALSE, quiet=FALSE, date.range=NULL, jitter.arrows=0, plot=TRUE, ...) get.likelihood(...) ## S3 method for class 'seqTrack' get.likelihood(x, mu, haplo.length, ...)
x |
for seqTrack, a matrix giving weights to pairs of ancestries
such that x[i,j] is the weight of 'i ancestor of j'. For
plotSeqTrack and get.likelihood. seqTrack, a |
x.names |
a character vector giving the labels of the haplotypes/genotypes |
x.dates |
a vector of collection dates for the sampled
haplotypes/genotypes. Dates must have the POSIXct format. See
|
best |
a character string matching 'min' or 'max', indicating whether genealogies should minimize or maximize the sum of weights of ancestries. |
prox.mat |
an optional matrix of proximities between
haplotypes/genotypes used to resolve ties in the choice of
ancestors, by picking up the 'closest' ancestor amongst possible
ancestors, in the sense of |
mu |
(optional) a mutation rate, per site and per day. When 'x'
contains numbers of mutations, used to resolve ties using a maximum
likelihood approach (requires |
haplo.length |
(optional) the length of analysed sequences in
number of nucleotides. When 'x' contains numbers of mutations, used
to resolve ties using a maximum likelihood approach (requires
|
y |
unused argument, for compatibility with 'plot'. |
col.pal |
a color palette to be used to represent weights using
colors on the edges of the graph. See |
xy |
spatial coordinates of the sampled haplotypes/genotypes. |
use.arrows |
a logical indicating whether arrows should be used to represented ancestries (pointing from ancestor to descendent, TRUE), or whether segments shall be used (FALSE). |
annot |
a logical indicating whether arrows or segments representing ancestries should be annotated (TRUE) or not (FALSE). |
labels |
a character vector containing annotations of the ancestries. If left empty, ancestries are annotated by the descendent. |
col |
a vector of colors to be used for plotting ancestries. |
bg |
a color to be used as background. |
add |
a logical stating whether the plot should be added to current figure (TRUE), or drawn as a new plot (FALSE, default). |
quiet |
a logical stating whether messages other than errors should be displayed (FALSE, default), or hidden (TRUE). |
date.range |
a vector of length two with POSIXct format indicating the time window for which ancestries should be displayed. |
jitter.arrows |
a positive number indicating the amount of noise
to be added to coordinates of arrows; useful when several arrows
overlap. See |
plot |
a logical stating whether a plot should be drawn (TRUE, default), or not (FALSE). In all cases, the function invisibly returns plotting information. |
... |
further arguments to be passed to other methods |
=== Maximum parsimony genealogies ===
Maximum parsimony genealogies can be obtained easily using this
implementation of seqTrack. One has to provide in x a matrix of
genetic distances. The most straightforward distance is the number of
differing nucleotides. See dist.dna in the ape
package for a wide range of genetic distances between aligned
sequences. The argument best should be set to "min" (its
default value), so that the identified genealogy minimizes the total
number of mutations. If x contains number of mutations, then
mu and haplo.length should also be provided for
resolving ties in equally parsimonious ancestors using maximum
likelihood.
=== Likelihood of observed genetic differentiation ===
The probability of oberving a given number of mutations between a
sequence and its ancestor can be computed using
get.likelihood.seqTrack. Note that this is only possible
if x contained number of mutations.
=== Plotting/converting seqTrack objects to graphs ===
seqTrack objects are best plotted as graphs. From adegenet_1.3-5
onwards, seqTrack objects can be converted to igraph objects (from the
package igraph), which can in turn be plotted and manipulated
using classical graph tools. The plot method does this operation
automatically, using colors to represent edge weights, and using
time-ordering of the data from top (ancient) to bottom (recent).
=== output of seqTrack ===
seqTrack function returns data.frame with the class seqTrack,
in which each row is an inferred ancestry described by the following columns:
- id: indices identifying haplotypes/genotypes
- ances: index of the inferred ancestor
- weight: weight of the inferred ancestries
- date: date of the haplotype/genotype
- ances.date: date of the ancestor
=== output of plotSeqTrack ===
This graphical function invisibly returns the coordinates of the
arrows/segments drawn and their colors, as a data.frame.
Thibaut Jombart [email protected]
Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease outbreaks from genetic data: a graph approach. Heredity. doi: 10.1038/hdy.2010.78.
dist.dna in the ape package to compute pairwise
genetic distances in aligned sequences.
## Not run: if(require(ape && require(igraph))){ ## ANALYSIS OF SIMULATED DATA ## ## SIMULATE A GENEALOGY dat <- haploGen(seq.l=1e4, repro=function(){sample(1:4,1)}, gen.time=1, t.max=3) plot(dat, main="Simulated data") ## SEQTRACK ANALYSIS res <- seqTrack(dat, mu=0.0001, haplo.length=1e4) plot(res, main="seqTrack reconstruction") ## PROPORTION OF CORRECT RECONSTRUCTION mean(dat$ances==res$ances,na.rm=TRUE) ## ANALYSIS OF PANDEMIC A/H1N1 INFLUENZA DATA ## ## note: ## this is for reproduction purpose only ## seqTrack is best kept for the analysis ## of densely sampled outbreaks, which ## is not the case of this dataset. ## dat <- read.csv(system.file("files/pdH1N1-data.csv",package="adegenet")) ha <- read.dna(system.file("files/pdH1N1-HA.fasta",package="adegenet"), format="fa") na <- read.dna(system.file("files/pdH1N1-NA.fasta",package="adegenet"), format="fa") ## COMPUTE NUCLEOTIDIC DISTANCES nbNucl <- ncol(as.matrix(ha)) + ncol(as.matrix(na)) D <- dist.dna(ha,model="raw")*ncol(as.matrix(ha)) + dist.dna(na,model="raw")*ncol(as.matrix(na)) D <- round(as.matrix(D)) ## MATRIX OF SPATIAL CONNECTIVITY ## (to promote local transmissions) xy <- cbind(dat$lon, dat$lat) temp <- as.matrix(dist(xy)) M <- 1* (temp < 1e-10) ## SEQTRACK ANALYSIS dat$date <- as.POSIXct(dat$date) res <- seqTrack(D, rownames(dat), dat$date, prox.mat=M, mu=.00502/365, haplo.le=nbNucl) ## COMPUTE GENETIC LIKELIHOOD p <- get.likelihood(res, mu=.00502/365, haplo.length=nbNucl) # (these could be shown as colors when plotting results) # (but mutations will be used instead) ## EXAMINE RESULTS head(res) tail(res) range(res$weight, na.rm=TRUE) barplot(table(res$weight)/sum(!is.na(res$weight)), ylab="Frequency", xlab="Mutations between inferred ancestor and descendent", col="orange") ## DISPLAY SPATIO-TEMPORAL DYNAMICS if(require(maps)){ myDates <- as.integer(difftime(dat$date, as.POSIXct("2009-01-21"), unit="day")) myMonth <- as.POSIXct( c("2009-02-01", "2009-03-01","2009-04-01","2009-05-01","2009-06-01","2009-07-01")) x.month <- as.integer(difftime(myMonth, as.POSIXct("2009-01-21"), unit="day")) ## FIRST STAGE: ## SPREAD TO THE USA AND CANADA curRange <- as.POSIXct(c("2009-03-29","2009-04-25")) par(bg="deepskyblue") map("world", fill=TRUE, col="grey") opal <- palette() palette(rev(heat.colors(10))) plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2,date.range=curRange, col=res$weight+1) title(paste(curRange, collapse=" to ")) legend("bottom", lty=1, leg=0:8, title="number of mutations", col=1:9, lwd=2, horiz=TRUE) ## SECOND STAGE: ## SPREAD WITHIN AMERICA, FIRST SEEDING OUTSIDE AMERICA curRange <- as.POSIXct(c("2009-04-30","2009-05-07")) par(bg="deepskyblue") map("world", fill=TRUE, col="grey") opal <- palette() palette(rev(heat.colors(10))) plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2, date.range=curRange, col=res$weight+1) title(paste(curRange, collapse=" to ")) legend("bottom", lty=1, leg=0:8, title="number of mutations", col=1:9,lwd=2, horiz=TRUE) ## THIRD STAGE: ## PANDEMIC curRange <- as.POSIXct(c("2009-05-15","2009-05-25")) par(bg="deepskyblue") map("world", fill=TRUE, col="grey") opal <- palette() palette(rev(heat.colors(10))) plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2, date.range=curRange, col=res$weight+1) title(paste(curRange, collapse=" to ")) legend("bottom", lty=1, leg=0:8, title="number of mutations", col=1:9,lwd=2, horiz=TRUE) } } ## End(Not run)## Not run: if(require(ape && require(igraph))){ ## ANALYSIS OF SIMULATED DATA ## ## SIMULATE A GENEALOGY dat <- haploGen(seq.l=1e4, repro=function(){sample(1:4,1)}, gen.time=1, t.max=3) plot(dat, main="Simulated data") ## SEQTRACK ANALYSIS res <- seqTrack(dat, mu=0.0001, haplo.length=1e4) plot(res, main="seqTrack reconstruction") ## PROPORTION OF CORRECT RECONSTRUCTION mean(dat$ances==res$ances,na.rm=TRUE) ## ANALYSIS OF PANDEMIC A/H1N1 INFLUENZA DATA ## ## note: ## this is for reproduction purpose only ## seqTrack is best kept for the analysis ## of densely sampled outbreaks, which ## is not the case of this dataset. ## dat <- read.csv(system.file("files/pdH1N1-data.csv",package="adegenet")) ha <- read.dna(system.file("files/pdH1N1-HA.fasta",package="adegenet"), format="fa") na <- read.dna(system.file("files/pdH1N1-NA.fasta",package="adegenet"), format="fa") ## COMPUTE NUCLEOTIDIC DISTANCES nbNucl <- ncol(as.matrix(ha)) + ncol(as.matrix(na)) D <- dist.dna(ha,model="raw")*ncol(as.matrix(ha)) + dist.dna(na,model="raw")*ncol(as.matrix(na)) D <- round(as.matrix(D)) ## MATRIX OF SPATIAL CONNECTIVITY ## (to promote local transmissions) xy <- cbind(dat$lon, dat$lat) temp <- as.matrix(dist(xy)) M <- 1* (temp < 1e-10) ## SEQTRACK ANALYSIS dat$date <- as.POSIXct(dat$date) res <- seqTrack(D, rownames(dat), dat$date, prox.mat=M, mu=.00502/365, haplo.le=nbNucl) ## COMPUTE GENETIC LIKELIHOOD p <- get.likelihood(res, mu=.00502/365, haplo.length=nbNucl) # (these could be shown as colors when plotting results) # (but mutations will be used instead) ## EXAMINE RESULTS head(res) tail(res) range(res$weight, na.rm=TRUE) barplot(table(res$weight)/sum(!is.na(res$weight)), ylab="Frequency", xlab="Mutations between inferred ancestor and descendent", col="orange") ## DISPLAY SPATIO-TEMPORAL DYNAMICS if(require(maps)){ myDates <- as.integer(difftime(dat$date, as.POSIXct("2009-01-21"), unit="day")) myMonth <- as.POSIXct( c("2009-02-01", "2009-03-01","2009-04-01","2009-05-01","2009-06-01","2009-07-01")) x.month <- as.integer(difftime(myMonth, as.POSIXct("2009-01-21"), unit="day")) ## FIRST STAGE: ## SPREAD TO THE USA AND CANADA curRange <- as.POSIXct(c("2009-03-29","2009-04-25")) par(bg="deepskyblue") map("world", fill=TRUE, col="grey") opal <- palette() palette(rev(heat.colors(10))) plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2,date.range=curRange, col=res$weight+1) title(paste(curRange, collapse=" to ")) legend("bottom", lty=1, leg=0:8, title="number of mutations", col=1:9, lwd=2, horiz=TRUE) ## SECOND STAGE: ## SPREAD WITHIN AMERICA, FIRST SEEDING OUTSIDE AMERICA curRange <- as.POSIXct(c("2009-04-30","2009-05-07")) par(bg="deepskyblue") map("world", fill=TRUE, col="grey") opal <- palette() palette(rev(heat.colors(10))) plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2, date.range=curRange, col=res$weight+1) title(paste(curRange, collapse=" to ")) legend("bottom", lty=1, leg=0:8, title="number of mutations", col=1:9,lwd=2, horiz=TRUE) ## THIRD STAGE: ## PANDEMIC curRange <- as.POSIXct(c("2009-05-15","2009-05-25")) par(bg="deepskyblue") map("world", fill=TRUE, col="grey") opal <- palette() palette(rev(heat.colors(10))) plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2, date.range=curRange, col=res$weight+1) title(paste(curRange, collapse=" to ")) legend("bottom", lty=1, leg=0:8, title="number of mutations", col=1:9,lwd=2, horiz=TRUE) } } ## End(Not run)
These functions take an alignement of sequences and translate SNPs
into a genind object. Note that only polymorphic loci
are retained.
Currently, accepted sequence formats are:
- DNAbin (ape package): function DNAbin2genind
- alignment (seqinr package): function alignment2genind
DNAbin2genind(x, pop=NULL, exp.char=c("a","t","g","c"), polyThres=1/100) alignment2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char="-", polyThres=1/100)DNAbin2genind(x, pop=NULL, exp.char=c("a","t","g","c"), polyThres=1/100) alignment2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char="-", polyThres=1/100)
x |
an object containing aligned sequences. |
pop |
an optional factor giving the population to which each sequence belongs. |
exp.char |
a vector of single character providing expected values; all other characters will be turned to NA. |
na.char |
a vector of single characters providing values that should be
considered as NA. If not NULL, this is used instead of |
polyThres |
the minimum frequency of a minor allele for a locus to be considered as polymorphic (defaults to 0.01). |
an object of the class genind
Thibaut Jombart [email protected]
import2genind, read.genetix,
read.fstat, read.structure,
read.genepop, DNAbin,
as.alignment.
## Not run: data(woodmouse) x <- DNAbin2genind(woodmouse) x genind2df(x) ## End(Not run) if(require(seqinr)){ mase.res <- read.alignment(file=system.file("sequences/test.mase",package="seqinr"), format = "mase") mase.res x <- alignment2genind(mase.res) x locNames(x) # list of polymorphic sites genind2df(x) ## look at Euclidean distances D <- dist(tab(x)) D ## summarise with a PCoA pco1 <- dudi.pco(D, scannf=FALSE,nf=2) scatter(pco1, posi="bottomright") title("Principal Coordinate Analysis\n-based on proteic distances-") }## Not run: data(woodmouse) x <- DNAbin2genind(woodmouse) x genind2df(x) ## End(Not run) if(require(seqinr)){ mase.res <- read.alignment(file=system.file("sequences/test.mase",package="seqinr"), format = "mase") mase.res x <- alignment2genind(mase.res) x locNames(x) # list of polymorphic sites genind2df(x) ## look at Euclidean distances D <- dist(tab(x)) D ## summarise with a PCoA pco1 <- dudi.pco(D, scannf=FALSE,nf=2) scatter(pco1, posi="bottomright") title("Principal Coordinate Analysis\n-based on proteic distances-") }
The following methods allow the user to quickly change the population of a genind object.
setPop(x, formula = NULL) setPop(x) <- valuesetPop(x, formula = NULL) setPop(x) <- value
x |
a genind or genlight object |
formula |
a nested formula indicating the order of the population strata. |
value |
same as formula |
Zhian N. Kamvar
data(microbov) strata(microbov) <- data.frame(other(microbov)) # Currently set on just head(pop(microbov)) # setting the strata to both Pop and Subpop setPop(microbov) <- ~coun/breed head(pop(microbov)) ## Not run: # Can be used to create objects as well. microbov.old <- setPop(microbov, ~spe) head(pop(microbov.old)) ## End(Not run)data(microbov) strata(microbov) <- data.frame(other(microbov)) # Currently set on just head(pop(microbov)) # setting the strata to both Pop and Subpop setPop(microbov) <- ~coun/breed head(pop(microbov)) ## Not run: # Can be used to create objects as well. microbov.old <- setPop(microbov, ~spe) head(pop(microbov.old)) ## End(Not run)
Genetic data analysis can be a harsh, tiring, daunting task. Sometimes, a mere break will not cut it. Sometimes, you need a kitten.
showmekittens(x = NULL, list = FALSE)showmekittens(x = NULL, list = FALSE)
x |
the name or index of the video to display; if NULL, a random video is chosen |
list |
a logical indicating if the list of available videos should be displayed |
Please send us more! Either pull request or submit an issue with a URL (use
adegenetIssues()).
Thibaut Jombart [email protected]
This simple data set was obtained by sampling two populations evolving in a
island model, simulated using Easypop (2.0.1). See source for
simulation details. Sample sizes were respectively 100 and 30 genotypes. The
genotypes were given spatial coordinates so that both populations were
spatially differentiated.
sim2pop is a genind object with a matrix of xy coordinates as
supplementary component.
Thibaut Jombart [email protected]
Easypop version 2.0.1 was run with the following parameters:
-
two diploid populations, one sex, random mating
- 1000 individuals per
population
- proportion of migration: 0.002
- 20 loci
- mutation
rate: 0.0001 (KAM model)
- maximum of 50 allelic states
- 1000
generations (last one taken)
Balloux F (2001) Easypop (version 1.7): a computer program for oppulation genetics simulations Journal of Heredity, 92: 301-302
## Not run: data(sim2pop) if(require(hierfstat)){ ## try and find the Fst temp <- genind2hierfstat(sim2pop) varcomp.glob(temp[,1],temp[,-1]) # Fst = 0.038 } ## run monmonier algorithm # build connection network gab <- chooseCN(sim2pop@other$xy,ask=FALSE,type=2) # filter random noise pca1 <- dudi.pca(sim2pop@tab,scale=FALSE, scannf=FALSE, nf=1) # run the algorithm mon1 <- monmonier(sim2pop@other$xy,dist(pca1$l1[,1]),gab, scanthres=FALSE) # graphical display temp <- sim2pop@pop levels(temp) <- c(17,19) temp <- as.numeric(as.character(temp)) plot(mon1) points(sim2pop@other$xy,pch=temp,cex=2) legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19)) ## End(Not run)## Not run: data(sim2pop) if(require(hierfstat)){ ## try and find the Fst temp <- genind2hierfstat(sim2pop) varcomp.glob(temp[,1],temp[,-1]) # Fst = 0.038 } ## run monmonier algorithm # build connection network gab <- chooseCN(sim2pop@other$xy,ask=FALSE,type=2) # filter random noise pca1 <- dudi.pca(sim2pop@tab,scale=FALSE, scannf=FALSE, nf=1) # run the algorithm mon1 <- monmonier(sim2pop@other$xy,dist(pca1$l1[,1]),gab, scanthres=FALSE) # graphical display temp <- sim2pop@pop levels(temp) <- c(17,19) temp <- as.numeric(as.character(temp)) plot(mon1) points(sim2pop@other$xy,pch=temp,cex=2) legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19)) ## End(Not run)
This function implements the fast maximum-likelihood genetic clustering
approach described in Beugin et al (2018). The underlying model is very close
to the model implemented by STRUCTURE, but allows for much faster estimation
of genetic clusters thanks to the use of the Expectation-Maximization (EM)
algorithm. Optionally, the model can explicitely account for hybridization
and detect different types of hybrids (see hybrids and
hybrid.coef arguments). The method is fully documented in a dedicated
tutorial which can be accessed using adegenetTutorial("snapclust").
snapclust( x, k, pop.ini = "ward", max.iter = 100, n.start = 10, n.start.kmeans = 50, hybrids = FALSE, dim.ini = 100, hybrid.coef = NULL, parent.lab = c("A", "B"), ... )snapclust( x, k, pop.ini = "ward", max.iter = 100, n.start = 10, n.start.kmeans = 50, hybrids = FALSE, dim.ini = 100, hybrid.coef = NULL, parent.lab = c("A", "B"), ... )
x |
a genind object |
k |
the number of clusters to look for |
pop.ini |
parameter indicating how the initial group membership should
be found. If |
max.iter |
the maximum number of iteration of the EM algorithm |
n.start |
the number of times the EM algorithm is run, each time with different random starting conditions |
n.start.kmeans |
the number of times the K-means algorithm is run to define the starting point of the ML-EM algorithm, each time with different random starting conditions |
hybrids |
a logical indicating if hybrids should be modelled explicitely; this is currently implemented for 2 groups only. |
dim.ini |
the number of PCA axes to retain in the dimension reduction
step for |
hybrid.coef |
a vector of hybridization coefficients, defining the proportion of hybrid gene pool coming from the first parental population; this is symmetrized around 0.5, so that e.g. c(0.25, 0.5) will be converted to c(0.25, 0.5, 0.75) |
parent.lab |
a vector of 2 character strings used to label the two
parental populations; only used if hybrids are detected (see argument
|
... |
further arguments passed on to |
The method is described in Beugin et al (2018) A fast likelihood
solution to the genetic clustering problem. Methods in Ecology and
Evolution doi:10.1111/2041-210X.12968. A dedicated
tutorial is available by typing adegenetTutorial("snapclust").
The function snapclust returns a list with the following
components:
$group a factor indicating the maximum-likelihood assignment of
individuals to groups; if identified, hybrids are labelled after
hybridization coefficients, e.g. 0.5_A - 0.5_B for F1, 0.75_A - 0.25_B for
backcross F1 / A, etc.
$ll: the log-likelihood of the model
$proba: a matrix of group membership probabilities, with
individuals in rows and groups in columns; each value correspond to the
probability that a given individual genotype was generated under a given
group, under Hardy-Weinberg hypotheses.
$converged a logical indicating if the algorithm converged; if
FALSE, it is doubtful that the result is an actual Maximum Likelihood
estimate.
$n.iter an integer indicating the number of iterations the EM
algorithm was run for.
Thibaut Jombart [email protected] and Marie-Pauline Beugin
The function snapclust.choose.k to investigate the optimal
value number of clusters 'k'.
## Not run: data(microbov) ## try function using k-means initialization grp.ini <- find.clusters(microbov, n.clust=15, n.pca=150) ## run EM algo res <- snapclust(microbov, 15, pop.ini = grp.ini$grp) names(res) res$converged res$n.iter ## plot result compoplot(res) ## flag potential hybrids to.flag <- apply(res$proba,1,max)<.9 compoplot(res, subset=to.flag, show.lab=TRUE, posi="bottomleft", bg="white") ## Simulate hybrids F1 zebu <- microbov[pop="Zebu"] salers <- microbov[pop="Salers"] hyb <- hybridize(zebu, salers, n=30) x <- repool(zebu, salers, hyb) ## method without hybrids res.no.hyb <- snapclust(x, k=2, hybrids=FALSE) compoplot(res.no.hyb, col.pal=spectral, n.col=2) ## method with hybrids res.hyb <- snapclust(x, k=2, hybrids=TRUE) compoplot(res.hyb, col.pal = hybridpal(col.pal = spectral), n.col = 2) ## Simulate hybrids backcross (F1 / parental) f1.zebu <- hybridize(hyb, zebu, 20, pop = "f1.zebu") f1.salers <- hybridize(hyb, salers, 25, pop = "f1.salers") y <- repool(x, f1.zebu, f1.salers) ## method without hybrids res2.no.hyb <- snapclust(y, k = 2, hybrids = FALSE) compoplot(res2.no.hyb, col.pal = hybridpal(), n.col = 2) ## method with hybrids F1 only res2.hyb <- snapclust(y, k = 2, hybrids = TRUE) compoplot(res2.hyb, col.pal = hybridpal(), n.col = 2) ## method with back-cross res2.back <- snapclust(y, k = 2, hybrids = TRUE, hybrid.coef = c(.25,.5)) compoplot(res2.back, col.pal = hybridpal(), n.col = 2) ## End(Not run)## Not run: data(microbov) ## try function using k-means initialization grp.ini <- find.clusters(microbov, n.clust=15, n.pca=150) ## run EM algo res <- snapclust(microbov, 15, pop.ini = grp.ini$grp) names(res) res$converged res$n.iter ## plot result compoplot(res) ## flag potential hybrids to.flag <- apply(res$proba,1,max)<.9 compoplot(res, subset=to.flag, show.lab=TRUE, posi="bottomleft", bg="white") ## Simulate hybrids F1 zebu <- microbov[pop="Zebu"] salers <- microbov[pop="Salers"] hyb <- hybridize(zebu, salers, n=30) x <- repool(zebu, salers, hyb) ## method without hybrids res.no.hyb <- snapclust(x, k=2, hybrids=FALSE) compoplot(res.no.hyb, col.pal=spectral, n.col=2) ## method with hybrids res.hyb <- snapclust(x, k=2, hybrids=TRUE) compoplot(res.hyb, col.pal = hybridpal(col.pal = spectral), n.col = 2) ## Simulate hybrids backcross (F1 / parental) f1.zebu <- hybridize(hyb, zebu, 20, pop = "f1.zebu") f1.salers <- hybridize(hyb, salers, 25, pop = "f1.salers") y <- repool(x, f1.zebu, f1.salers) ## method without hybrids res2.no.hyb <- snapclust(y, k = 2, hybrids = FALSE) compoplot(res2.no.hyb, col.pal = hybridpal(), n.col = 2) ## method with hybrids F1 only res2.hyb <- snapclust(y, k = 2, hybrids = TRUE) compoplot(res2.hyb, col.pal = hybridpal(), n.col = 2) ## method with back-cross res2.back <- snapclust(y, k = 2, hybrids = TRUE, hybrid.coef = c(.25,.5)) compoplot(res2.back, col.pal = hybridpal(), n.col = 2) ## End(Not run)
This function implements methods for investigating the optimal number of
genetic clusters ('k') using the fast maximum-likelihood genetic clustering
approach described in Beugin et al (2018). The method runs
snapclust for varying values of 'k', and computes the requested
summary statistics for each clustering solution to assess goodness of
fit. The method is fully documented in a dedicated tutorial which can be
accessed using adegenetTutorial("snapclust").
snapclust.choose.k(max, ..., IC = AIC, IC.only = TRUE)snapclust.choose.k(max, ..., IC = AIC, IC.only = TRUE)
max |
An integer indicating the maximum number of clusters to seek;
|
... |
Arguments passed to |
IC |
A function computing the information criterion for
|
IC.only |
A logical (TRUE by default) indicating if IC values only
should be returned; if |
The method is described in Beugin et al (2018) A fast likelihood
solution to the genetic clustering problem. Methods in Ecology and
Evolution doi:10.1111/2041-210X.12968. A dedicated
tutorial is available by typing adegenetTutorial("snapclust").
Thibaut Jombart [email protected]
snapclust to generate individual clustering solutions,
and BIC.snapclust for computing BIC for snapclust
objects.
The class SNPbin is a formal (S4) class for storing a genotype
of binary SNPs in a compact way, using a bit-level coding scheme.
This storage is most efficient with haploid data, where the memory
taken to represent data can reduced more than 50 times. However,
SNPbin can be used for any level of ploidy, and still remain an
efficient storage mode.
A SNPbin object can be constructed from
a vector of integers giving the number of the second allele for each
locus.
SNPbin stores a single genotype. To store multiple genotypes,
use the genlight class.
SNPbin objects can be created by calls to new("SNPbin",
...), where '...' can be the following arguments:
snpa vector of integers or numeric giving numbers of copies of the second alleles for each locus. If only one unnamed argument is provided to 'new', it is considered as this one.
ploidyan integer indicating the ploidy of the genotype; if not provided, will be guessed from the data (as the maximum from the 'snp' input vector).
labelan optional character string serving as a label for the genotype.
The following slots are the content of instances of the class
SNPbin; note that in most cases, it is better to retrieve
information via accessors (see below), rather than by accessing the
slots manually.
snp:a list of vectors with the class raw.
n.loc:an integer indicating the number of SNPs of the genotype.
NA.posi:a vector of integer giving the position of missing data.
label:an optional character string serving as a label for the genotype..
ploidy:an integer indicating the ploidy of the genotype.
Here is a list of methods available for SNPbin objects. Most of
these methods are accessors, that is, functions which are used to
retrieve the content of the object. Specific manpages can exist for
accessors with more than one argument. These are indicated by a '*'
symbol next to the method's name. This list also contains methods
for conversion from SNPbin to other classes.
signature(x = "SNPbin"): usual method to subset
objects in R. The argument indicates how SNPs are to be
subsetted. It can be a vector of signed integers or of logicals.
signature(x = "SNPbin"): printing of the
object.
signature(x = "SNPbin"): similar to the @ operator;
used to access the content of slots of the object.
signature(x = "SNPbin"): similar to the @ operator;
used to replace the content of slots of the object.
signature(x = "SNPbin"): returns the number of
SNPs in the object.
signature(x = "SNPbin"): returns the names of
the slots of the object.
signature(x = "SNPbin"): returns the ploidy of
the genotype.
signature(x = "SNPbin"): converts a
SNPbin object to a vector of integers. The S4 method 'as' can
be used as well (e.g. as(x, "integer")).
signature(x = "SNPbin"): merges genotyping of
the same individual at different SNPs (all stored as
SNPbin objects) into a single SNPbin.
signature(x = "SNPbin"): same as cbind.SNPbin.
Thibaut Jombart ([email protected])
Related class:
- genlight, for storing multiple binary SNP
genotypes.
- genind, for storing other types of genetic markers.
## Not run: #### HAPLOID EXAMPLE #### ## create a genotype of 100,000 SNPs dat <- sample(c(0,1,NA), 1e5, prob=c(.495, .495, .01), replace=TRUE) dat[1:10] x <- new("SNPbin", dat) x x[1:10] # subsetting as.integer(x[1:10]) ## try a few accessors ploidy(x) nLoc(x) head(x$snp[[1]]) # internal bit-level coding ## check that conversion is OK identical(as(x, "integer"),as.integer(dat)) # SHOULD BE TRUE ## compare the size of the objects print(object.size(dat), unit="auto") print(object.size(x), unit="auto") object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION #### TETRAPLOID EXAMPLE #### ## create a genotype of 100,000 SNPs dat <- sample(c(0:4,NA), 1e5, prob=c(rep(.995/5,5), 0.005), replace=TRUE) x <- new("SNPbin", dat) identical(as(x, "integer"),as.integer(dat)) # MUST BE TRUE ## compare the size of the objects print(object.size(dat), unit="auto") print(object.size(x), unit="auto") object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION #### c, cbind #### a <- new("SNPbin", c(1,1,1,1,1)) b <- new("SNPbin", c(0,0,0,0,0)) a b ab <- c(a,b) ab identical(c(a,b),cbind(a,b)) as.integer(ab) ## End(Not run)## Not run: #### HAPLOID EXAMPLE #### ## create a genotype of 100,000 SNPs dat <- sample(c(0,1,NA), 1e5, prob=c(.495, .495, .01), replace=TRUE) dat[1:10] x <- new("SNPbin", dat) x x[1:10] # subsetting as.integer(x[1:10]) ## try a few accessors ploidy(x) nLoc(x) head(x$snp[[1]]) # internal bit-level coding ## check that conversion is OK identical(as(x, "integer"),as.integer(dat)) # SHOULD BE TRUE ## compare the size of the objects print(object.size(dat), unit="auto") print(object.size(x), unit="auto") object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION #### TETRAPLOID EXAMPLE #### ## create a genotype of 100,000 SNPs dat <- sample(c(0:4,NA), 1e5, prob=c(rep(.995/5,5), 0.005), replace=TRUE) x <- new("SNPbin", dat) identical(as(x, "integer"),as.integer(dat)) # MUST BE TRUE ## compare the size of the objects print(object.size(dat), unit="auto") print(object.size(x), unit="auto") object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION #### c, cbind #### a <- new("SNPbin", c(1,1,1,1,1)) b <- new("SNPbin", c(0,0,0,0,0)) a b ab <- c(a,b) ab identical(c(a,b),cbind(a,b)) as.integer(ab) ## End(Not run)
These functions are used to describe the distribution of polymorphic sites (SNPs) in an alignment.
The function snpposi.plot plots the positions and density of
SNPs in the alignment.
The function snpposi.test tests whether SNPs are randomly
distributed in the genome, the alternative hypothesis being that they
are clustered. This test is based on the distances of each SNP to the
closest SNP. This provides one measure of clustering for each SNP.
Different statistics can be used to summarise these values (argument
stat), but by default the statistics used is the median.
snpposi.plot and snpposi.test are generic functions with
methods for vectors of integers or numeric (indicating SNP position),
and for DNAbin objects.
snpposi.plot(...) ## S3 method for class 'integer' snpposi.plot(x, genome.size, smooth=0.1, col="royalblue", alpha=.2, codon=TRUE, start.at=1, ...) ## S3 method for class 'numeric' snpposi.plot(x, ...) ## S3 method for class 'DNAbin' snpposi.plot(x, ...) snpposi.test(...) ## S3 method for class 'integer' snpposi.test(x, genome.size, n.sim=999, stat=median, ...) ## S3 method for class 'numeric' snpposi.test(x, ...) ## S3 method for class 'DNAbin' snpposi.test(x, ...)snpposi.plot(...) ## S3 method for class 'integer' snpposi.plot(x, genome.size, smooth=0.1, col="royalblue", alpha=.2, codon=TRUE, start.at=1, ...) ## S3 method for class 'numeric' snpposi.plot(x, ...) ## S3 method for class 'DNAbin' snpposi.plot(x, ...) snpposi.test(...) ## S3 method for class 'integer' snpposi.test(x, genome.size, n.sim=999, stat=median, ...) ## S3 method for class 'numeric' snpposi.test(x, ...) ## S3 method for class 'DNAbin' snpposi.test(x, ...)
x |
a vector of integers or numerics containing SNP positions, or
a set of aligned sequences in a |
genome.size |
an integer indicating the length of genomes. |
smooth |
a smoothing parameter for the density estimation; smaller values will give more local peaks; values have to be positive but can be less than 1. |
col |
the color to be used for the plot; ignored if codon positions are represented. |
alpha |
the alpha level to be used for transparency (density curve). |
codon |
a logical indicating if codon position should be indicated (TRUE, default) or not. |
start.at |
an integer indicating at which base of a codon the alignment starts (defaults to 1); values other than 1, 2 and 3 will be ignored. |
n.sim |
an integer indicating the number of randomizations to be used in the Monte Carlo test. |
stat |
a function used to summarize the measure of physical proximity between SNPs; by default, the median is used. |
... |
further arguments to be passed to the |
A Monte Carlo test of the class randtest.
Thibaut Jombart [email protected].
The fasta2DNAbin to read fasta alignments with minimum
RAM use.
if(require(ape)){ data(woodmouse) snpposi.plot(woodmouse, codon=FALSE) snpposi.plot(woodmouse) ## Not run: snpposi.test(c(1,3,4,5), 100) snpposi.test(woodmouse) ## End(Not run) }if(require(ape)){ data(woodmouse) snpposi.plot(woodmouse, codon=FALSE) snpposi.plot(woodmouse) ## Not run: snpposi.test(c(1,3,4,5), 100) snpposi.test(woodmouse) ## End(Not run) }
The function snpzip identifies the set of alleles which contribute most
significantly to phenotypic structure.
This procedure uses Discriminant Analysis of Principal Components (DAPC) to quantify the contribution of individual alleles to between-population structure. Then, defining contribution to DAPC as the measure of distance between alleles, hierarchical clustering is used to identify two groups of alleles: structural SNPs and non-structural SNPs.
snpzip(snps, y, plot = TRUE, xval.plot = FALSE, loading.plot = FALSE, method = c("complete", "single", "average", "centroid", "mcquitty", "median", "ward"), ...)snpzip(snps, y, plot = TRUE, xval.plot = FALSE, loading.plot = FALSE, method = c("complete", "single", "average", "centroid", "mcquitty", "median", "ward"), ...)
snps |
a snps |
y |
either a |
plot |
a |
xval.plot |
a |
loading.plot |
a |
method |
the clustering method to be used. This should be
(an unambiguous abbreviation of) one of |
... |
further arguments. |
snpzip provides an objective procedure to delineate between structural
and non-structural SNPs identified by Discriminant Analysis of Principal Components
(DAPC, Jombart et al. 2010).
snpzip precedes the multivariate analysis with a cross-validation step
to ensure that the subsequent DAPC is performed optimally.
The contributions of alleles to the DAPC are then submitted to hclust,
where they define a distance matrix upon which hierarchical clustering is carried out.
To complete the procedure, snpzip uses cutree to automatically
subdivide the set of SNPs fed into the analysis into two groups:
those which contribute significantly to the phenotypic structure of interest,
and those which do not.
A list with four items if y is a factor, or two items if
y is a dapc object:
The first cites the number of principal components (PCs) of PCA retained in the DAPC.
The second item is an embedded list which
first indicates the number of structural and non-structural SNPs identified by
snpzip, second provides a list of the structuring alleles, third
gives the names of the selected alleles, and fourth details the
contributions of these structuring alleles to the DAPC.
The optional third item provides measures of discrimination success both overall and by group.
The optional fourth item contains the dapc object generated if y was a factor.
If plot=TRUE, a scatter plot will provide a visualization of the DAPC results.
If xval.plot=TRUE, the results of the cross-validation step will be displayed
as an array of the format generated by xvalDapc, and a scatter plot of
the results of cross-validation will be provided.
If loading.plot=TRUE, a loading plot will be generated to show the
contributions of alleles to the DAPC, and the SNP selection threshold will be indicated.
If the number of Discriminant Axes (n.da) in the DAPC is greater than 1,
loading.plot=TRUE will generate one loading plot for each discriminant axis.
Caitlin Collins [email protected]
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
## Not run: simpop <- glSim(100, 10000, n.snp.struc = 10, grp.size = c(0.3,0.7), LD = FALSE, alpha = 0.4, k = 4) snps <- as.matrix(simpop) phen <- simpop@pop outcome <- snpzip(snps, phen, method = "centroid") outcome ## End(Not run) ## Not run: simpop <- glSim(100, 10000, n.snp.struc = 10, grp.size = c(0.3,0.7), LD = FALSE, alpha = 0.4, k = 4) snps <- as.matrix(simpop) phen <- simpop@pop dapc1 <- dapc(snps, phen, n.da = 1, n.pca = 30) features <- snpzip(dapc1, loading.plot = TRUE, method = "average") features ## End(Not run)## Not run: simpop <- glSim(100, 10000, n.snp.struc = 10, grp.size = c(0.3,0.7), LD = FALSE, alpha = 0.4, k = 4) snps <- as.matrix(simpop) phen <- simpop@pop outcome <- snpzip(snps, phen, method = "centroid") outcome ## End(Not run) ## Not run: simpop <- glSim(100, 10000, n.snp.struc = 10, grp.size = c(0.3,0.7), LD = FALSE, alpha = 0.4, k = 4) snps <- as.matrix(simpop) phen <- simpop@pop dapc1 <- dapc(snps, phen, n.da = 1, n.pca = 30) features <- snpzip(dapc1, loading.plot = TRUE, method = "average") features ## End(Not run)
These functions implement the spatial principal component analysis
(sPCA). The function spca is a generic with methods for:
matrix: only numeric values are accepted
data.frame: same as for matrices
genind: any genind object is accepted
genpop: any genpop object is accepted
The core computation use multispati from the ade4 package.
Besides the set of spca functions, other functions include:
print.spca: prints the spca content
summary.spca: gives variance and autocorrelation
statistics
plot.spca: usefull graphics (connection network, 3 different
representations of map of scores, eigenvalues barplot and
decomposition)
screeplot.spca: decomposes spca eigenvalues into variance and
autocorrelation
colorplot.spca: represents principal components of sPCA in
space using the RGB system.
A tutorial on sPCA can be opened using:adegenetTutorial(which="spca").
spca(...) ## Default S3 method: spca(x, ...) ## S3 method for class 'matrix' spca(x, xy = NULL, cn = NULL, matWeight = NULL, center = TRUE, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'data.frame' spca(x, xy = NULL, cn = NULL, matWeight = NULL, center = TRUE, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'genind' spca(obj, xy = NULL, cn = NULL, matWeight = NULL, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'genpop' spca(obj, xy = NULL, cn = NULL, matWeight = NULL, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'spca' print(x, ...) ## S3 method for class 'spca' summary(object, ..., printres=TRUE) ## S3 method for class 'spca' plot(x, axis = 1, useLag=FALSE, ...) ## S3 method for class 'spca' screeplot(x, ..., main=NULL) ## S3 method for class 'spca' colorplot(x, axes=1:ncol(x$li), useLag=FALSE, ...)spca(...) ## Default S3 method: spca(x, ...) ## S3 method for class 'matrix' spca(x, xy = NULL, cn = NULL, matWeight = NULL, center = TRUE, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'data.frame' spca(x, xy = NULL, cn = NULL, matWeight = NULL, center = TRUE, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'genind' spca(obj, xy = NULL, cn = NULL, matWeight = NULL, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'genpop' spca(obj, xy = NULL, cn = NULL, matWeight = NULL, scale = FALSE, scannf = TRUE, nfposi = 1, nfnega = 1, type = NULL, ask = TRUE, plot.nb = TRUE, edit.nb = FALSE, truenames = TRUE, d1 = NULL, d2 = NULL, k = NULL, a = NULL, dmin = NULL, ...) ## S3 method for class 'spca' print(x, ...) ## S3 method for class 'spca' summary(object, ..., printres=TRUE) ## S3 method for class 'spca' plot(x, axis = 1, useLag=FALSE, ...) ## S3 method for class 'spca' screeplot(x, ..., main=NULL) ## S3 method for class 'spca' colorplot(x, axes=1:ncol(x$li), useLag=FALSE, ...)
x |
a |
obj |
a |
xy |
a matrix or data.frame with two columns for x and y
coordinates. Seeked from obj$other$xy if it exists when xy is not
provided. Can be NULL if a |
cn |
a connection network of the class 'nb' (package spdep). Can be NULL if xy is provided. Can be easily obtained using the function chooseCN (see details). |
matWeight |
a square matrix of spatial weights, indicating the
spatial proximities between entities. If provided, this argument
prevails over |
center |
a logical indicating whether data should be centred to a mean of zero; used implicitely for genind or genpop objects. |
scale |
a logical indicating whether data should be scaled to unit variance (TRUE) or not (FALSE, default). |
scannf |
a logical stating whether eigenvalues should be chosen interactively (TRUE, default) or not (FALSE). |
nfposi |
an integer giving the number of positive eigenvalues retained ('global structures'). |
nfnega |
an integer giving the number of negative eigenvalues retained ('local structures'). |
type |
an integer giving the type of graph (see details in
|
ask |
a logical stating whether graph should be chosen interactively (TRUE,default) or not (FALSE). |
plot.nb |
a logical stating whether the resulting graph should be plotted (TRUE, default) or not (FALSE). |
edit.nb |
a logical stating whether the resulting graph should be edited manually for corrections (TRUE) or not (FALSE, default). |
truenames |
a logical stating whether true names should be used for 'obj' (TRUE, default) instead of generic labels (FALSE) |
d1 |
the minimum distance between any two neighbours. Used if
|
d2 |
the maximum distance between any two neighbours. Used if
|
k |
the number of neighbours per point. Used if |
a |
the exponent of the inverse distance matrix. Used if
|
dmin |
the minimum distance between any two distinct points. Used
to avoid infinite spatial proximities (defined as the inversed
spatial distances). Used if |
object |
a |
printres |
a logical stating whether results should be printed on the screen (TRUE, default) or not (FALSE). |
axis |
an integer between 1 and (nfposi+nfnega) indicating which axis should be plotted. |
main |
a title for the screeplot; if NULL, a default one is used. |
... |
further arguments passed to other methods. |
axes |
the index of the columns of X to be represented. Up to three axes can be chosen. |
useLag |
a logical stating whether the lagged components
( |
The spatial principal component analysis (sPCA) is designed to
investigate spatial patterns in the genetic variability. Given
multilocus genotypes (individual level) or allelic frequency
(population level) and spatial coordinates, it finds individuals (or
population) scores maximizing the product of variance and spatial
autocorrelation (Moran's I). Large positive and negative eigenvalues
correspond to global and local structures.
Spatial weights can be obtained in several ways, depending how the
arguments xy, cn, and matWeight are set.
When several acceptable ways are used at the same time, priority is as
follows:matWeight > cn > xy
The class spca are given to lists with the following
components:
eig |
a numeric vector of eigenvalues. |
nfposi |
an integer giving the number of global structures retained. |
nfnega |
an integer giving the number of local structures retained. |
c1 |
a data.frame of alleles loadings for each axis. |
li |
a data.frame of row (individuals or populations) coordinates onto the sPCA axes. |
ls |
a data.frame of lag vectors of the row coordinates; useful to clarify maps of global scores . |
as |
a data.frame giving the coordinates of the PCA axes onto the sPCA axes. |
call |
the matched call. |
xy |
a matrix of spatial coordinates. |
lw |
a list of spatial weights of class |
Other functions have different outputs:
- summary.spca returns a list with 3 components: Istat
giving the null, minimum and maximum Moran's I values; pca
gives variance and I statistics for the principal component analysis;
spca gives variance and I statistics for the sPCA.
- plot.spca returns the matched call.
- screeplot.spca returns the matched call.
Thibaut Jombart [email protected]
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity, 101, 92–103.
Wartenberg, D. E. (1985) Multivariate spatial correlation: a method for exploratory geographical analysis. Geographical Analysis, 17, 263–283.
Moran, P.A.P. (1948) The interpretation of statistical maps. Journal of the Royal Statistical Society, B 10, 243–251.
Moran, P.A.P. (1950) Notes on continuous stochastic phenomena. Biometrika, 37, 17–23.
de Jong, P. and Sprenger, C. and van Veen, F. (1984) On extreme values of Moran's I and Geary's c. Geographical Analysis, 16, 17–24.
spcaIllus and rupica for datasets illustrating the sPCA global.rtest and local.rtest chooseCN, multispati,
multispati.randtestconvUL, from the package 'PBSmapping' to convert longitude/latitude to
UTM coordinates.
## data(spcaIllus) illustrates the sPCA ## see ?spcaIllus ## ## Not run: example(spcaIllus) example(rupica) ## End(Not run)## data(spcaIllus) illustrates the sPCA ## see ?spcaIllus ## ## Not run: example(spcaIllus) example(rupica) ## End(Not run)
The function spca_randtest implements Monte-Carlo tests for the
presence of significant spatial structures in a sPCA object. Two tests are
run, for global (positive autocorrelation) and local (negative
autocorrelation) structures, respectively. The test statistics used are the
sum of the absolute values of the corresponding eigenvalues.
spca_randtest(x, nperm = 499)spca_randtest(x, nperm = 499)
x |
A |
nperm |
The number of permutations to be used for the test. |
A list with two objects of the class 'randtest' (see
as.randtest), the first one for 'global' structures
(positivie autocorrelation) and the second for 'local' structures (negative
autocorrelation).
Original code by Valeria Montano adapted by Thibaut Jombart.
## Not run: ## Load data data(sim2pop) ## Make spca spca1 <- spca(sim2pop, type = 1, scannf = FALSE, plot.nb = FALSE) spca1 plot(spca1) ## run tests (use more permutations in practice, e.g. 999) tests <- spca_randtest(spca1, nperm = 49) ## check results tests plot(tests[[1]]) # global structures ## End(Not run)## Not run: ## Load data data(sim2pop) ## Make spca spca1 <- spca(sim2pop, type = 1, scannf = FALSE, plot.nb = FALSE) spca1 plot(spca1) ## run tests (use more permutations in practice, e.g. 999) tests <- spca_randtest(spca1, nperm = 49) ## check results tests plot(tests[[1]]) # global structures ## End(Not run)
Datasets illustrating the spatial Principal Component Analysis (Jombart et
al. 2009). These data were simulated using various models using Easypop
(2.0.1). Spatial coordinates were defined so that different spatial
patterns existed in the data. The spca-illus is a list containing the
following genind or genpop objects:
- dat2A:
2 patches
- dat2B: cline between two pop
- dat2C: repulsion among
individuals from the same gene pool
- dat3: cline and repulsion
-
dat4: patches and local alternance
spcaIllus is list of 5 components being either genind or
genpop objects.
See "source" for a reference providing simulation details.
Thibaut Jombart [email protected]
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity, 101, 92–103.
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity, 101, 92–103.
Balloux F (2001) Easypop (version 1.7): a computer program for oppulation genetics simulations Journal of Heredity, 92: 301-302
required_packages <- require(adespatial) && require(spdep) if (required_packages) { data(spcaIllus) attach(spcaIllus) opar <- par(no.readonly=TRUE) ## comparison PCA vs sPCA # PCA pca2A <- dudi.pca(dat2A$tab,center=TRUE,scale=FALSE,scannf=FALSE) pca2B <- dudi.pca(dat2B$tab,center=TRUE,scale=FALSE,scannf=FALSE) pca2C <- dudi.pca(dat2C$tab,center=TRUE,scale=FALSE,scannf=FALSE) pca3 <- dudi.pca(dat3$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2) pca4 <- dudi.pca(dat4$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2) # sPCA spca2A <-spca(dat2A,xy=dat2A$other$xy,ask=FALSE,type=1, plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0) spca2B <- spca(dat2B,xy=dat2B$other$xy,ask=FALSE,type=1, plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0) spca2C <- spca(dat2C,xy=dat2C$other$xy,ask=FALSE, type=1,plot=FALSE,scannf=FALSE,nfposi=0,nfnega=1) spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE, type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1) spca4 <- spca(dat4,xy=dat4$other$xy,ask=FALSE, type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1) # an auxiliary function for graphics plotaux <- function(x,analysis,axis=1,lab=NULL,...){ neig <- NULL if(inherits(analysis,"spca")) neig <- nb2neig(analysis$lw$neighbours) xrange <- range(x$other$xy[,1]) xlim <- xrange + c(-diff(xrange)*.1 , diff(xrange)*.45) yrange <- range(x$other$xy[,2]) ylim <- yrange + c(-diff(yrange)*.45 , diff(yrange)*.1) s.value(x$other$xy,analysis$li[,axis],include.ori=FALSE,addaxes=FALSE, cgrid=0,grid=FALSE,neig=neig,cleg=0,xlim=xlim,ylim=ylim,...) par(mar=rep(.1,4)) if(is.null(lab)) lab = gsub("[P]","",x$pop) text(x$other$xy, lab=lab, col="blue", cex=1.2, font=2) add.scatter({barplot(analysis$eig,col="grey");box(); title("Eigenvalues",line=-1)},posi="bottomright",ratio=.3) } # plots plotaux(dat2A,pca2A,sub="dat2A - PCA",pos="bottomleft",csub=2) plotaux(dat2A,spca2A,sub="dat2A - sPCA glob1",pos="bottomleft",csub=2) plotaux(dat2B,pca2B,sub="dat2B - PCA",pos="bottomleft",csub=2) plotaux(dat2B,spca2B,sub="dat2B - sPCA glob1",pos="bottomleft",csub=2) plotaux(dat2C,pca2C,sub="dat2C - PCA",pos="bottomleft",csub=2) plotaux(dat2C,spca2C,sub="dat2C - sPCA loc1",pos="bottomleft",csub=2,axis=2) par(mfrow=c(2,2)) plotaux(dat3,pca3,sub="dat3 - PCA axis1",pos="bottomleft",csub=2) plotaux(dat3,spca3,sub="dat3 - sPCA glob1",pos="bottomleft",csub=2) plotaux(dat3,pca3,sub="dat3 - PCA axis2",pos="bottomleft",csub=2,axis=2) plotaux(dat3,spca3,sub="dat3 - sPCA loc1",pos="bottomleft",csub=2,axis=2) plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis1", pos="bottomleft",csub=2) plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA glob1", pos="bottomleft",csub=2) plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis2", pos="bottomleft",csub=2,axis=2) plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA loc1", pos="bottomleft",csub=2,axis=2) # color plot par(opar) colorplot(spca3, cex=4, main="colorplot sPCA dat3") text(spca3$xy[,1], spca3$xy[,2], dat3$pop) colorplot(spca4, cex=4, main="colorplot sPCA dat4") text(spca4$xy[,1], spca4$xy[,2], dat4$other$sup.pop) # detach data detach(spcaIllus) }required_packages <- require(adespatial) && require(spdep) if (required_packages) { data(spcaIllus) attach(spcaIllus) opar <- par(no.readonly=TRUE) ## comparison PCA vs sPCA # PCA pca2A <- dudi.pca(dat2A$tab,center=TRUE,scale=FALSE,scannf=FALSE) pca2B <- dudi.pca(dat2B$tab,center=TRUE,scale=FALSE,scannf=FALSE) pca2C <- dudi.pca(dat2C$tab,center=TRUE,scale=FALSE,scannf=FALSE) pca3 <- dudi.pca(dat3$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2) pca4 <- dudi.pca(dat4$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2) # sPCA spca2A <-spca(dat2A,xy=dat2A$other$xy,ask=FALSE,type=1, plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0) spca2B <- spca(dat2B,xy=dat2B$other$xy,ask=FALSE,type=1, plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0) spca2C <- spca(dat2C,xy=dat2C$other$xy,ask=FALSE, type=1,plot=FALSE,scannf=FALSE,nfposi=0,nfnega=1) spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE, type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1) spca4 <- spca(dat4,xy=dat4$other$xy,ask=FALSE, type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1) # an auxiliary function for graphics plotaux <- function(x,analysis,axis=1,lab=NULL,...){ neig <- NULL if(inherits(analysis,"spca")) neig <- nb2neig(analysis$lw$neighbours) xrange <- range(x$other$xy[,1]) xlim <- xrange + c(-diff(xrange)*.1 , diff(xrange)*.45) yrange <- range(x$other$xy[,2]) ylim <- yrange + c(-diff(yrange)*.45 , diff(yrange)*.1) s.value(x$other$xy,analysis$li[,axis],include.ori=FALSE,addaxes=FALSE, cgrid=0,grid=FALSE,neig=neig,cleg=0,xlim=xlim,ylim=ylim,...) par(mar=rep(.1,4)) if(is.null(lab)) lab = gsub("[P]","",x$pop) text(x$other$xy, lab=lab, col="blue", cex=1.2, font=2) add.scatter({barplot(analysis$eig,col="grey");box(); title("Eigenvalues",line=-1)},posi="bottomright",ratio=.3) } # plots plotaux(dat2A,pca2A,sub="dat2A - PCA",pos="bottomleft",csub=2) plotaux(dat2A,spca2A,sub="dat2A - sPCA glob1",pos="bottomleft",csub=2) plotaux(dat2B,pca2B,sub="dat2B - PCA",pos="bottomleft",csub=2) plotaux(dat2B,spca2B,sub="dat2B - sPCA glob1",pos="bottomleft",csub=2) plotaux(dat2C,pca2C,sub="dat2C - PCA",pos="bottomleft",csub=2) plotaux(dat2C,spca2C,sub="dat2C - sPCA loc1",pos="bottomleft",csub=2,axis=2) par(mfrow=c(2,2)) plotaux(dat3,pca3,sub="dat3 - PCA axis1",pos="bottomleft",csub=2) plotaux(dat3,spca3,sub="dat3 - sPCA glob1",pos="bottomleft",csub=2) plotaux(dat3,pca3,sub="dat3 - PCA axis2",pos="bottomleft",csub=2,axis=2) plotaux(dat3,spca3,sub="dat3 - sPCA loc1",pos="bottomleft",csub=2,axis=2) plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis1", pos="bottomleft",csub=2) plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA glob1", pos="bottomleft",csub=2) plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis2", pos="bottomleft",csub=2,axis=2) plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA loc1", pos="bottomleft",csub=2,axis=2) # color plot par(opar) colorplot(spca3, cex=4, main="colorplot sPCA dat3") text(spca3$xy[,1], spca3$xy[,2], dat3$pop) colorplot(spca4, cex=4, main="colorplot sPCA dat4") text(spca4$xy[,1], spca4$xy[,2], dat4$other$sup.pop) # detach data detach(spcaIllus) }
The following methods allow the user to quickly change the strata of a genind or genlight object.
strata(x, formula = NULL, combine = TRUE, value) strata(x) <- value nameStrata(x, value) nameStrata(x) <- value splitStrata(x, value, sep = "_") splitStrata(x, sep = "_") <- value addStrata(x, value, name = "NEW") addStrata(x, name = "NEW") <- valuestrata(x, formula = NULL, combine = TRUE, value) strata(x) <- value nameStrata(x, value) nameStrata(x) <- value splitStrata(x, value, sep = "_") splitStrata(x, sep = "_") <- value addStrata(x, value, name = "NEW") addStrata(x, name = "NEW") <- value
x |
a genind or genlight object |
formula |
a nested formula indicating the order of the population strata. |
combine |
if |
value |
a data frame OR vector OR formula (see details). |
sep |
a |
name |
an optional name argument for use with addStrata if supplying a vector. Defaults to "NEW". |
strata() - Use this function to view or define population stratification of a genind or genlight object.
nameStrata() - View or rename the different levels of strata.
splitStrata() - Split strata that are combined with a common separator. This function should only be used once during a workflow.
Rationale: It is often difficult to import files with several levels of strata as most data formats do not allow unlimited population levels. This is circumvented by collapsing all population strata into a single population factor with a common separator for each observation.
addStrata() - Add levels to your population
strata. This is ideal for adding groups defined by
find.clusters. You can input a data frame or a vector, but if
you put in a vector, you have the option to name it.
These functions allow the user to seamlessly carry all possible population stratification with their genind or genlight object. Note that there are two ways of performing all methods:
modifying: strata(myData) <- myStrata
preserving:
myNewData <- strata(myData, value = myStrata)
They essentially do
the same thing except that the modifying assignment method (the one with
the "<-") will modify the object in place whereas the non-assignment
method will preserve the original object (unless you overwrite it). Due to
convention, everything right of the assignment is termed value. To
avoid confusion, here is a guide to the argument value for
each function:
strata() value = a
data.frame that defines the strata for each individual in the
rows.
nameStrata() value = a vector or
a formula that will define the names.
splitStrata() value = a formula argument with
the same number of levels as the strata you wish to split.
addStrata() value = a vector or
data.frame with the same length as the number of individuals
in your data.
The preferred use of these functions is with a formula
object. Specifically, a hierarchical formula argument is used to assign the
levels of the strata. An example of a hierarchical formula would
be:
~Country/City/Neighborhood
|
This convention was
chosen as it becomes easier to type and makes intuitive sense when defining
a hierarchy. Note: it is important to use hiearchical
formulas when specifying hierarchies as other types of formulas (eg.
~Country*City*Neighborhood) will give incorrect results.
Zhian N. Kamvar
# let's look at the microbov data set: data(microbov) microbov # We see that we have three vectors of different names in the 'other' slot. # ?microbov # These are Country, Breed, and Species names(other(microbov)) # Let's set the strata strata(microbov) <- data.frame(other(microbov)) microbov # And change the names so we know what they are nameStrata(microbov) <- ~Country/Breed/Species ## Not run: # let's see what the strata looks like by Species and Breed: head(strata(microbov, ~Breed/Species)) # If we didn't want the last column combined with the first, we can set # combine = FALSE head(strata(microbov, ~Breed/Species, combine = FALSE)) #### USING splitStrata #### # For the sake of example, we'll imagine that we have imported our data set # with all of the stratifications combined. setPop(microbov) <- ~Country/Breed/Species strata(microbov) <- NULL # This is what our data would look like after import. microbov # To set our strata here, we need to use the functions strata and splitStrata strata(microbov) <- data.frame(x = pop(microbov)) microbov # shows us that we have "one" level of stratification head(strata(microbov)) # all strata are separated by "_" splitStrata(microbov) <- ~Country/Breed/Species microbov # Now we have all of our strata named and split head(strata(microbov)) # all strata are appropriately named and split. ## End(Not run)# let's look at the microbov data set: data(microbov) microbov # We see that we have three vectors of different names in the 'other' slot. # ?microbov # These are Country, Breed, and Species names(other(microbov)) # Let's set the strata strata(microbov) <- data.frame(other(microbov)) microbov # And change the names so we know what they are nameStrata(microbov) <- ~Country/Breed/Species ## Not run: # let's see what the strata looks like by Species and Breed: head(strata(microbov, ~Breed/Species)) # If we didn't want the last column combined with the first, we can set # combine = FALSE head(strata(microbov, ~Breed/Species, combine = FALSE)) #### USING splitStrata #### # For the sake of example, we'll imagine that we have imported our data set # with all of the stratifications combined. setPop(microbov) <- ~Country/Breed/Species strata(microbov) <- NULL # This is what our data would look like after import. microbov # To set our strata here, we need to use the functions strata and splitStrata strata(microbov) <- data.frame(x = pop(microbov)) microbov # shows us that we have "one" level of stratification head(strata(microbov)) # all strata are separated by "_" splitStrata(microbov) <- ~Country/Breed/Species microbov # Now we have all of our strata named and split head(strata(microbov)) # all strata are appropriately named and split. ## End(Not run)
This data set gives the genotypes of 781 swallowtail butterflies (Papilio machaon species group) for 10 microsatellites markers. The individuals are divided into 40 populations.
swallowtails is a genind object containing 781 individuals,
10 microsatellite markers, and 40 populations.
Julian Dupuis (University of Hawaii, USA)
Dupuis, J.R. & Sperling, F.A.H. Hybrid dynamics in a species group of swallowtail butterflies. Journal of Evolutionary Biology, 10, 1932–1951.
## Not run: data(swallowtails) swallowtails # conducting a DAPC (n.pca determined using xvalDapc, see ??xvalDapc) dapc1 <- dapc(swallowtails, n.pca=40, n.da=200) # read in swallowtails_loc.csv, which contains "key", "lat", and "lon" # columns with column headers (this example contains additional columns # containing species identifications, locality descriptions, and COI # haplotype clades) input_locs <- system.file("files/swallowtails_loc.csv", package = "adegenet") loc <- read.csv(input_locs, header = TRUE) # generate mvmapper input file, automatically write the output to a csv, and # name the output csv "mvMapper_Data.csv" out <- export_to_mvmapper(dapc1, loc, write_file = TRUE, out_file = "mvMapper_Data.csv") ## End(Not run)## Not run: data(swallowtails) swallowtails # conducting a DAPC (n.pca determined using xvalDapc, see ??xvalDapc) dapc1 <- dapc(swallowtails, n.pca=40, n.da=200) # read in swallowtails_loc.csv, which contains "key", "lat", and "lon" # columns with column headers (this example contains additional columns # containing species identifications, locality descriptions, and COI # haplotype clades) input_locs <- system.file("files/swallowtails_loc.csv", package = "adegenet") loc <- read.csv(input_locs, header = TRUE) # generate mvmapper input file, automatically write the output to a csv, and # name the output csv "mvMapper_Data.csv" out <- export_to_mvmapper(dapc1, loc, write_file = TRUE, out_file = "mvMapper_Data.csv") ## End(Not run)
This accessor is used to retrieve a matrix of allele data.
By default, a matrix of integers representing allele counts is returned.
If freq is TRUE, then data are standardised as frequencies, so that for any individual and any locus the data sum to 1.
The argument NA.method allows to replace missing data (NAs).
This accessor replaces the previous function truenames as well as the function makefreq.
tab(x, ...) ## S4 method for signature 'genind' tab(x, freq = FALSE, NA.method = c("asis", "mean", "zero"), ...) ## S4 method for signature 'genpop' tab(x, freq = FALSE, NA.method = c("asis", "mean", "zero"), ...)tab(x, ...) ## S4 method for signature 'genind' tab(x, freq = FALSE, NA.method = c("asis", "mean", "zero"), ...) ## S4 method for signature 'genpop' tab(x, freq = FALSE, NA.method = c("asis", "mean", "zero"), ...)
x |
|
... |
further arguments passed to other methods. |
freq |
a logical indicating if data should be transformed into relative frequencies (TRUE); defaults to FALSE. |
NA.method |
a method to replace NA; asis: leave NAs as is; mean: replace by the mean allele frequencies; zero: replace by zero |
a matrix of integers or numeric
data(microbov) head(tab(microbov)) head(tab(microbov,freq=TRUE))data(microbov) head(tab(microbov)) head(tab(microbov,freq=TRUE))
The function truenames returns some elements of an object
(genind or genpop) using true names
(as opposed to generic labels) for individuals, markers, alleles, and
population.
Important: as of adegenet_2.0-0, these functions are deprecated as
true labels are used whenever possible. Please use the function
tab instead.
## S4 method for signature 'genind' truenames(x) ## S4 method for signature 'genpop' truenames(x)## S4 method for signature 'genind' truenames(x) ## S4 method for signature 'genpop' truenames(x)
x |
If x$pop is empty (NULL), a matrix similar to the x$tab slot but with true labels.
If x$pop exists, a list with this matrix ($tab) and a population
vector with true names ($pop).
Thibaut Jombart [email protected]
These virtual classes are only for internal use in adegenet
A virtual Class: No objects may be created from it.
Thibaut Jombart [email protected]