| indpca {hierfstat} | R Documentation |
PCA on a matrix of individuals genotypes frequencies
Description
Carry out a PCA on the centered, unscaled matrix of individual's allele frequencies.
Usage
indpca(dat,ind.labels=NULL,scale=FALSE)
## S3 method for class 'indpca'
print(x,...)
## S3 method for class 'indpca'
plot(x,eigen=FALSE,ax1=1,ax2=2,...)
Arguments
dat |
A data frame with population of origin as first column, and genotypes in following columns. |
ind.labels |
a vector of labels for the different individuals |
scale |
whether to standardize each column to variance 1 or to leave it as is (default) |
x |
an indpca object |
eigen |
whether to plot in an additional windows screeplot of the inertias for the different axes |
ax1 |
which PCA coordinates to plot on the x axis |
ax2 |
which PCA coordinates to plot on the y axis |
... |
further arguments to pass to print or plot |
Value
An object of class indpca with components
call |
The function call |
ipca |
an object of class pca and dudi (see dudi.pca) in package ade4 |
mati |
the original non centered matrice of individuals X alleles frequencies |
Author(s)
Jerome Goudet jerome.goudet@unil.ch
Examples
##not run
data(gtrunchier)
x<-indpca(gtrunchier[,-2],ind.labels=gtrunchier[,2])
plot(x,col=gtrunchier[,1],cex=0.7)