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Run PCA on genotyping large dataset on matrix of 0/1

library("FactoMineR")
library("factoextra")
expressiondata = read.csv("final_nui_genotyped_filtered.csv",sep = ",")
expression = as.data.frame(expressiondata[, -c(1)])
expression = t(expression)
colnames(expression) = expressiondata$nui
check1<-read.table("sample_breed_only",header=T)
final <-cbind(expression,check1)
check_pca<-PCA(final[,-2317], graph = FALSE)
fviz_pca_ind(check_pca,geom.ind = "point",col.ind = final$breed,palette = c("#00AFBB", "#E7B800", "#FC4E07","#6a5acd","#3cb371"),addEllipses = TRUE,legend.title = "Groups")

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