I have used metagenomeSeq to normalize the read counts and was able to generate a heatmap. However, I cannot find a way to also show and export the color scale of the heatmap. The codes that I used for making a heatmap is just the same as in the manual document of metagenomeSeq:
trials = pData(mydata)$Farm
heatmapColColors = brewer.pal(12, "Set3")[as.integer(factor(trials))]
heatmapCols = colorRampPalette(brewer.pal(9, "RdBu"))(50)
plotMRheatmap(obj =mydata, n = 200, cexRow = 0.4, cexCol = 0.4, trace = "none", col = heatmapCols, ColSideColors = heatmapColColors)
Thank you in advance!