Hello,

I am trying to keep my heatmap column labels within the borders of the image.

This is my code:

# Notes from http://mannheimiagoesprogramming.blogspot.com/2012/06/drawing-heatmaps-in-r-with-heatmap2.html
# this comes from a csv file made by make_heatmap.pl
library(gplots)
for (sex in c("male","female")) {
    print(sex)
    filename <- paste("arranged_read_",sex,".csv",collapse=NULL,sep="")
    print(filename)
    data <- read.csv(filename, header = T, stringsAsFactors=F)
    row.names(data) <- data$Gene.Symbol
    data <- data[,2:7]
#make heatmap normalized by row
    filename <- paste(sex,"_heatmap_normRow.png",collapse=NULL,sep="")
    png(filename=filename)
    heatmap.2(as.matrix(data), col=redgreen(75), scale="row", key=T, keysize=1.5,density.info="none", trace="none",cexCol=0.5, labRow=NA)
#make heatmap normalized by column
    filename <- paste(sex,"_heatmap_normColumn.png",collapse=NULL,sep="")
    png(filename=filename)
    heatmap.2(as.matrix(data), col=redgreen(75), scale="column", key=T, keysize=1.5,density.info="none", trace="none",cexCol=0.9, labRow=NA)
#
    data <-log2(data)
    library(preprocessCore)
    data2 = normalize.quantiles(as.matrix(data))
    rownames(data2) = rownames(data)
    colnames(data2) = colnames(data)
    filename <- paste(sex,"_boxplot.png",collapse=NULL,sep="")
    png(filename=filename)
    boxplot(data2, cex.axis=0.8, las=2, main="Distribution after normalization",ylab="Log2(Intensity)")#boxplot command writes to boxplot.png
}

However the labels run off of the page. Resizing the image just stretches the labels, and I can't shrink the label font size, as the label isn't legible.

Much appreciated,
-Dave