inst/eval/GSE11976/myImagePlot.R

In mpierrejean/jointSeg: Joint Segmentation of Multivariate (Copy Number) Signals

                                        # ----- Define a function for plotting a matrix ----- #
myImagePlot <- function(x, min, max, ab=NULL,mar=c(4, 5, 2.5, 2), ...){
    
    yLabels <- rownames(x)
    xLabels <- colnames(x)
    title <-c()
    ## check for additional function arguments
    if( length(list(...)) ){
        Lst <- list(...)
        if( !is.null(Lst$zlim) ){
            min <- Lst$zlim[1]
            max <- Lst$zlim[2]
        }
        if( !is.null(Lst$yLabels) ){
            yLabels <- c(Lst$yLabels)
        }
        if( !is.null(Lst$xLabels) ){
            xLabels <- c(Lst$xLabels)
        }
        if( !is.null(Lst$title) ){
            title <- Lst$title
        }
    }
    ## check for null values
    if( is.null(xLabels) ){
        xLabels <- c(1:ncol(x))
    }
    if( is.null(yLabels) ){
        yLabels <- c(1:nrow(x))
    }
    
    layout(matrix(data=c(1, 2), nrow=1, ncol=2), widths=c(5, 1.2), heights=c(1, 1))

    ## white and blue range 
    ColorRamp <- colorRampPalette(c("white", "darkblue"))(199)
    ColorLevels <- seq(min, max, length=length(ColorRamp))
    
    ## Reverse Y axis
    reverse <- nrow(x) : 1
    yLabels <- yLabels[reverse]
    x <- x[reverse, ]

    ## Data Map
    par(mar=mar)
    image(1:length(xLabels), 1:length(yLabels), t(x), col=ColorRamp, xlab="", 
          ylab="", axes=FALSE, zlim=c(min, max))
    if( !is.null(title) ){
        title(main=title)
    }
    if(!is.null(ab)){abline(h=ab, col="black")}
    axis(BELOW <-1, at=1:length(xLabels), labels=xLabels, cex.axis=1.3, col.ticks=NULL, line=1, tick=FALSE)
    axis(LEFT <-2, at=1:length(yLabels), labels=yLabels, las=HORIZONTAL<-1, 
         cex.axis=1.5)

    ## Color Scale
    par(mar=c(3, 2.5, 2.5, 2))
    image(1,  ColorLevels, 
          matrix(data=ColorLevels, ncol=length(ColorLevels), nrow=1), 
          col=ColorRamp, 
          xlab="", ylab="",
          xaxt="n")
    
    layout(1)
}
## ----- END plot function ----- #