R/plotControlProbes.R

In Jfortin1/shinyMethyl: Interactive visualization for Illumina methylation arrays

### To plot the internal controls
#' @importFrom graphics abline grid
plotInternalControls <- function(y,
                                 col,
                                 main,
                                 sampleNames,
                                 bty="o"
){
    n <- length(y)
    slideNames <- substr(sampleNames, 1, 10)
    plot(seq_len(n),
         y,
         pch=20,
         cex=0.7,
         main=main,
         xlab="Sample",
         ylab="Control intensity",
         ylim=c(0, 1.3*max(y)),
         col=col,
         bty=bty)
    grid()
    abline(h=0, lty=3)
}

### To add the selected array to the internal controls plot
#' @importFrom graphics points
addHoverPoints <- function(y,
                           sampleNames,
                           selectedSamples=c()
){
    ## To put a circle around the last entry: 
    n <- length(selectedSamples)
    if (n>=1){
        points(selectedSamples[n],
               y[selectedSamples[n]],
               pch = 1,
               cex = 3,
               lwd = 3)
        points(selectedSamples[seq_len(n)],
               y[selectedSamples[seq_len(n)]],
               pch = 17,
               cex = 1,
               lwd = 3)
    }
}

returnControlStat <- function(controlType,
                              greenControls,
                              redControls,
                              controlNames
){
    index <- match(controlType, controlNames)
    greenControls.current <- greenControls[[index]]
    redControls.current   <- redControls[[index]]
    
    if (controlType=="BISULFITE CONVERSION I"){
        controlStat <- (apply(greenControls.current[1:3,], 2, mean) +
                        apply(redControls.current[7:9,], 2, mean))/2 
    } else {
        if (controlType=="BISULFITE CONVERSION II"){
            controlStat <- apply(redControls.current, 2, mean)
        } else {
            if (controlType=="EXTENSION"){
                controlStat <- (apply(greenControls.current[3:4,], 2, mean) +
                                apply(redControls.current[1:2,], 2, mean))/2 
            } else {
                if (controlType=="NEGATIVE"){
                    controlStat <- (apply(greenControls.current, 2, mean) +
                                    apply(redControls.current, 2, mean))/2 
                } else {
                    if (controlType=="HYBRIDIZATION"){
                        controlStat <- apply(greenControls.current, 2, mean)
                    } else {controlStat <- apply(greenControls.current, 2, mean)
                        }
                }
            }
        }
    }
    return(controlStat)
}