R/plotQC.R

In Jfortin1/shinyMethyl: Interactive visualization for Illumina methylation arrays

plotQC <- function(unmethQuantiles,
                   methQuantiles, 
                   sampleNames,
                   col,
                   bty="o"
){
    
    slideNames <- substr(sampleNames,1,10)
    
    med <- as.integer(nrow(methQuantiles[[3]])/2)
    x <- log2(unlist(unmethQuantiles[[3]][med,]))
    y <- log2(unlist(methQuantiles[[3]][med,]))
    
    range.x <- max(x)-min(x)
    range.y <- max(y)-min(y)
    xlim1 <- min(x)-0.2*range.x
    xlim2 <- max(x)+0.2*range.x
    ylim1 <- min(y)-0.2*range.y
    ylim2 <- max(y)+0.2*range.y
    
    plot(x,
         y,
         xlim = c(xlim1, xlim2),
         ylim = c(ylim1, ylim2),
         cex = 1,
         pch = 20,
         col = col,
         main = "QC Plot",
         bty=bty)
    grid()
}

addHoverQC <- function(y,
                       selectedSamples = c(),
                       unmethQuantiles,
                       methQuantiles
){
    med <- as.integer(nrow(methQuantiles[[3]])/2)
    mediansU <- unlist(unmethQuantiles[[3]][med,])
    mediansM <- unlist(methQuantiles[[3]][med,])
    
    ## To put a circle around the last entry: 
    n <- length(selectedSamples)
    if (n>=1){
        points(log2(mediansU[selectedSamples[n]]), 
               log2(mediansM[selectedSamples[n]]),
               col = "black",
               cex=3,
               pch=1,
               lwd=2)
    }
    ## Make the points black:
    points(log2(mediansU[selectedSamples]), 
           log2(mediansM[selectedSamples]),
           col = "black",
           cex = 1,
           pch = 17)
}