plotPlinkPca <- function(file, file2, x = 1, y = 2){
library(ggplot2)
library(grid)
library(gridExtra)
if(missing(file2)) {
mydata <- data.frame(read.table(file))
rownames(mydata) <- mydata[,2]
mydata <- mydata[,3:ncol(mydata)]
p <- ggplot(mydata,aes(x=mydata[,x],y=mydata[,y]))
p <- p + geom_point() + ggtitle("PCA") + xlab(paste("PC",x, sep ="")) + ylab(paste("PC",y, sep = ""))
return(p)
} else {
mydata <- data.frame(read.table(file))
group <- read.table(file2, stringsAsFactors = FALSE)
colnames(group) <- c("group")
rownames(mydata) <- mydata[,2]
mydata <- mydata[,3:ncol(mydata)]
mydata <- cbind(mydata,group)
p <- ggplot(mydata,aes(x=mydata[,x],y=mydata[,y],color=group))
p <- p + geom_point() + scale_color_brewer(palette="Set1") + ggtitle("PCA") + xlab(paste("PC",x, sep ="")) + ylab(paste("PC",y, sep = ""))
return(p)
}
}
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