PSSP PCA

#PCA of allele frequencies based on treatment

setwd("/uufs/chpc.utah.edu/common/home/u1065430/AlleleFreq/")

#read in allele frequencies

control<-t(read.table("p_o_PSSP_Control.txt",header=F,sep=","))

drought<-t(read.table("p_o_PSSP_Drought.txt",header=F,sep=","))

irrigation<-t(read.table("p_o_PSSP_Irrigation.txt",header=F,sep=","))

LE<-t(read.table("p_o_PSSP_LE.txt",header=F,sep=","))

HE<-t(read.table("p_o_PSSP_HE.txt",header=F,sep=","))

treatment<-rbind(control[1,],drought[1,],irrigation[1,],LE[1,],HE[1,])

PCA<-prcomp(treatment,center=T,scale=F)

plot(PCA)

summary(PCA)

txt<-c("Control","Drought","Irrigation","LE","HE")

pdf("PSSP_AlleleFreqPCA.pdf")

plot(PCA$x[,1],PCA$x[,2],pch=19,xlab="PC1 (42.97%)",ylab="PC2 (24.33%)",xlim=c(-6,5),ylim=c(-4,5))

text(PCA$x[,1],PCA$x[,2],labels=txt,pos=3)