spcaIllus: Simulated data illustrating the sPCA

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Simulated data illustrating the sPCA

Description

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

Format

spcaIllus is list of 5 components being either genind or genpop objects.

Details

See "source" for a reference providing simulation details.

Author(s)

Thibaut Jombart [e-mail]

Source

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.

References

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

See Also

spca

Examples

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)
}

adegenet documentation built on Feb. 16, 2023, 6 p.m.