R/plotDensities.R

In Jfortin1/shinyMethyl: Interactive visualization for Illumina methylation arrays

## Plot of the densities
#' @importFrom stats density
#' @importFrom graphics lines
densitiesPlot <- function(matrix.x,
                          matrix.y,
                          quantiles,
                          sampleNames,
                          bw,
                          main,
                          xlab,
                          xlim,
                          ylim,
                          lty=1,
                          lwd=1,
                          mean=FALSE,
                          col,
                          from,
                          to,
                          bty="o"
){
    meanSample <- apply(matrix.x, 1, mean)
    plot(matrix.x[,1],
         matrix.x[,2],
         main=main,
         ylab="Density", 
         xlab=xlab,
         col="white",
         xlim=xlim, 
         ylim=ylim,
         bty=bty)

    ## Will plot individual densities        
    if (!mean){
        ##Wanna make sure colors are not randomly drawn
        o <- order(col, decreasing=FALSE)
        col <- col[o]
        matrix.x <- matrix.x[,o]
        matrix.y <- matrix.y[,o]
        
        for (j in seq_len(ncol(matrix.x))){
            lines(matrix.x[,j],
                  matrix.y[,j],
                  col=col[j],
                  lwd=lwd,
                  lty=lty)
        }
    } else {
        ## Make sure to remove missing values
        non.na.indices <- which(!is.na(col))
        col  <- col[non.na.indices]
        quantiles  <- quantiles[, non.na.indices]
        
        unique.col <- unique(col)
        n <- length(unique.col)
        for (i in 1:n){
            indices <- which(col==unique.col[[i]])
            current.color <- col[indices][1]
            if (length(indices==1)){
                currentMean <- quantiles[,indices]
            } else {
                currentMean <- apply(quantiles[,indices],1,mean)
            }
            lines(density(currentMean, bw=bw, from=from, to=to),
                  lwd=lwd,
                  lty=lty,
                  col=current.color)
        }
    }
}


## To add selected density
#' @importFrom graphics lines
addHoverDensity <- function(selectedSamples=c(),
                            sampleNames,
                            matrix.x,
                            matrix.y,
                            col
){
    n <- length(selectedSamples)
    if (n >= 1){
        for (kk in seq_len(n)){
            lines(matrix.x[,selectedSamples[kk]],
                  matrix.y[,selectedSamples[kk]],
                  col="black",
                  lwd=4,
                  lty=3)
        }
        lines(matrix.x[,selectedSamples[n]],
              matrix.y[,selectedSamples[n]],
              col="black",
              lwd=3,
              lty=1)
    }
}