R/plotPCA.R

In Jfortin1/shinyMethyl: Interactive visualization for Illumina methylation arrays

plotPCA <- function(pca,
                    pc1,
                    pc2,
                    col,
                    covariates,
                    selectedCov,
                    bty="o"
){
    xMin <- min(pca[,as.numeric(pc1)])
    xMax <- max(pca[,as.numeric(pc1)])
    xRange <- xMax - xMin
    xlim <- c(xMin-0.05*xRange, xMax+0.20*xRange)
    xlab <- paste("PC",as.numeric(pc1), " scores", sep="")
    ylab <- paste("PC",as.numeric(pc2), " scores", sep="")
    
    plot(pca[,as.numeric(pc1)],
         pca[,as.numeric(pc2)],
         col = col,
         pch = 18,
         cex = 2,
         xlab = xlab,
         ylab = ylab,
         xlim = xlim,
         main = "Principal component analysis (PCA)",
         cex.main = 1.5,
         cex.lab = 1.5,
         bty = bty)
    uColor <- unique(col)
    uCov   <- unique(covariates[,match(selectedCov, colnames(covariates))])
    
    legend("bottomright",
           legend = uCov,
           pch = 18,
           col = uColor,
           cex = 1.5,
           title = selectedCov,
           bty = "n")
    grid()
}