plink + R PCA绘图自动设定颜色
1、plink脚本
plink --file outcome --pca 3 header tabs --sheep --out pcatest > /dev/null; rm *.log *.nosex
2、R绘图
dir() dat <- read.table("pcatest.eigenvec",header = T ) dim(dat) head(dat,3) idx <- sample(nrow(dat), nrow(dat)) dat <- dat[idx, ] temp <- as.data.frame(table(dat$FID)) dim(temp) colpoor <- c("red", "blue", "green") dat[,6] = NA for (i in 1:nrow(temp)) { dat[,6][dat$FID == temp[i, 1]] = colpoor[i] } plot(dat$PC1,dat$PC2, pch = 19, col = dat$V6)