R heatmap.2 manual grouping of rows and columns [d

Question

This question already has an answer here:

• How to create pre-annotated rowside column in heatmap.2 2 answers

I have the following MWE in which I make a heatmap without performing any clustering and showing any dendrogram. I want to group my rows (genes) together in categories, in a better looking way than how it is now.

This is the MWE:

#MWE
library(gplots)
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")
rownames(mymat) <- paste(rownames(mymat), c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)), sep=" --- ")
mymat #50x12 MATRIX. 50 GENES IN 5 CATEGORIES, ACROSS 4 TREATMENTS WITH 3 REPLICATES EACH
png(filename="TEST.png", height=800, width=600)
print(
heatmap.2(mymat, col=greenred(75),
      trace="none",
      keysize=1,
      margins=c(8,14),
      scale="row",
      dendrogram="none",
      Colv = FALSE,
      Rowv = FALSE,
      cexRow=0.5 + 1/log10(dim(mymat)[1]),
      cexCol=1.25,
      main="Genes grouped by categories")
)
dev.off()

Which produces this:

I would like to group the CATEGORIES in the rows together (and, if possible, the treatments in the columns as well), so it looks something like the following:

Or, maybe even better, with the CATEGORIES on the left, the same way as when clustering is performed and dendrograms are shown; however is easier and clearer...

Is there any way? Thanks!!

EDIT!!

I was made aware of the RowSideColors in the comments and I made the MWE below. However, I don't seem to be able to print the legend in the output png, plus the colors in the legend are not correct, and I cannot get the position right either. So please help me with the legend in the MWE below.

On another hand, I use the palette "Set3", consisting of 12 colors, but what if I need more than 12 colors (if I have more than 12 categories)??

NEW MWE

library(gplots)
library(RColorBrewer)
col1 <- brewer.pal(12, "Set3")
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")
mymat
mydf <- data.frame(gene=paste("gene", 1:dim(mymat)[1], sep="_"), category=c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)))
mydf
png(filename="TEST.png", height=800, width=600)
print(
    heatmap.2(mymat, col=greenred(75),
              trace="none",
              keysize=1,
              margins=c(8,6),
              scale="row",
              dendrogram="none",
              Colv = FALSE,
              Rowv = FALSE,
              cexRow=0.5 + 1/log10(dim(mymat)[1]),
              cexCol=1.25,
              main="Genes grouped by categories",
              RowSideColors=col1[as.numeric(mydf$category)]
              )
    #THE LEGEND DOESN'T WORK INSIDE print(), AND THE POSITION AND COLORS ARE WRONG
    #legend("topright",
    #       legend = unique(mydf$category),
    #       col = col1[as.numeric(mydf$category)],
    #       lty= 1,
    #       lwd = 5,
    #       cex=.7
    #       )
)
dev.off()

Which produces:

Please help me with the legend, and with the hypothetical case I need more than 12 colors. Thanks!

Answer 1

I would use pheatmap package. Your example would look something like that:

library(pheatmap)
library(RColorBrewer)

# Generte data (modified the mydf slightly)
col1 <- brewer.pal(12, "Set3")
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")

mydf <- data.frame(row.names = paste("gene", 1:dim(mymat)[1], sep="_"), category = c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)))

# add row annotations
pheatmap(mymat, cluster_cols = F, cluster_rows = F, annotation_row = mydf)

# Add gaps
pheatmap(mymat, cluster_cols = F, cluster_rows = F, annotation_row = mydf, gaps_row = c(10, 20, 30, 40))

# Save to file with dimensions that keep both row and column names readable
pheatmap(mymat, cluster_cols = F, cluster_rows = F, annotation_row = mydf, gaps_row = c(10, 20, 30, 40), cellheight = 10, cellwidth = 20, file = "TEST.png")