4.0 years ago by
Seattle, WA USA
Sorry, are you asking how to make a heatmap, or how to make a better heatmap?
If you're just asking how to make a heatmap, then
matrix2png is a good recommendation. However, it will crash on large datasets, unless you explicitly specify the numbers of rows and columns as
numc options, which enable it to set up the required memory ahead of time.
If you're asking how to make a better heatmap, then reducing the heatmap to general features is recommended. You could use R with the
gplots library, which has a
heatmap.2 routine that makes it easy to render clusters via row- and column-based dendrograms alongside the heatmap, e.g.,:
> m_table <- read.table("foo.txt", as.is=T, header=T, stringsAsFactors=T)
> m_matrix <- data.matrix(m_table)
> pdf("foo.pdf", height=30, width=5)
> hwsr <- heatmap.2(m_matrix, hclustfun=function(x) hclust(x, method="ward"), scale="row", cexCol=0.5, cexRow=0.075)