PCAplot.r

## colors in colorpalette should be in hexadecimal format, without alpha shading i.e. #FF0000 (red)
## my favorite palette (color blind accessible)
cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7", "#000000")
## try to make the colorpalette at least as long as the number of categories
## alpha is a numerical value from 0 to 1

PCAplot <- function(eset=NULL, categories=NULL, title=NULL, colorpalette=NULL, alpha=1){
  # get metadata
  pd <- pData(eset)  
# adjust alpha to hexadecimal format
  alpha <- sprintf("%x", ceiling(alpha*255))
  # add alpha to colors
  colorpalette <- paste(colorpalette, alpha, sep="")
  # extract expression values
  eset <- exprs(eset) 
  # PCA transformations
  myPca <- prcomp(t(eset))
  tmpPCAData <- as.data.frame(myPca$x[,1:4])

  colors <- colorpalette[factor(as.character(unlist(pd[,categories])))]
  legend_values=unique(cbind(colors, as.character(pd[,categories])))
  pairs(tmpPCAData, bg=colors, col="#606060", cex=2, pch=21, main=title, oma=c(8,5,5,14))
  legend("right", cex=0.7, col="#606060", pt.bg=legend_values[,1], pt.cex=1.5, legend=legend_values[,2],  pch=21, bty="n", x.intersp=1)
  }