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

Question

I have the following data:

dat <- structure(list(GO = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 3L, 3L, 3L, 4L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("apoptotic process", 
"metabolic process", "negative regulation of apoptotic process", 
"positive regulation of apoptotic process", "signal transduction"
), class = "factor"), ProbeGene = structure(c(14L, 15L, 2L, 12L, 
7L, 11L, 16L, 8L, 19L, 13L, 3L, 1L, 18L, 4L, 10L, 5L, 9L, 17L, 
20L, 6L), .Label = c("1416787_at Acvr1", "1418835_at Phlda1", 
"1419282_at Ccl12", "1423240_at Src", "1424896_at Gpr85", "1434186_at Lpar4", 
"1434670_at Kif5a", "1440374_at Pde1c", "1440681_at Chrna7", 
"1440803_x_at Tacr3", "1442017_at LOC101056574", "1448815_at Ogg1", 
"1448821_at Tyr", "1451338_at Nisch", "1454721_at Arel1", "1456300_at Ilvbl", 
"1456989_at Oxgr1", "1457580_at Chd8", "1457827_at Arsj", "1460657_at Wnt10a"
), class = "factor"), foo = c(1.412475312, 1.413647397, 1.41297239, 
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781, 
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781, 
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781, 
-0.707106781, -0.707106781), bar = c(-0.645532476, -0.741475951, 
-0.655185417, -0.707106781, -0.707106781, -0.707106781, -0.707106781, 
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781, 
-0.707106781, -0.707106781, -0.707106781, -0.707106781, -0.707106781, 
-0.707106781, -0.707106781, -0.707106781), aux = c(-0.766942837, 
-0.672171445, -0.757786973, 1.414213562, 1.414213562, 1.414213562, 
1.414213562, 1.414213562, 1.414213562, 1.414213562, 1.414213562, 
1.414213562, 1.414213562, 1.414213562, 1.414213562, 1.414213562, 
1.414213562, 1.414213562, 1.414213562, 1.414213562)), .Names = c("GO", 
"ProbeGene", "foo", "bar", "aux"), row.names = c(50L, 35L, 45L, 
74L, 61L, 101L, 96L, 68L, 69L, 75L, 113L, 127L, 109L, 135L, 150L, 
152L, 183L, 190L, 197L, 191L), class = "data.frame")

It looks like this (they are sorted by GO column):

> dat
                                          GO               ProbeGene        foo        bar        aux
50                         apoptotic process        1451338_at Nisch  1.4124753 -0.6455325 -0.7669428
35                         apoptotic process        1454721_at Arel1  1.4136474 -0.7414760 -0.6721714
45                         apoptotic process       1418835_at Phlda1  1.4129724 -0.6551854 -0.7577870
74                         metabolic process         1448815_at Ogg1 -0.7071068 -0.7071068  1.4142136
61                         metabolic process        1434670_at Kif5a -0.7071068 -0.7071068  1.4142136
101                        metabolic process 1442017_at LOC101056574 -0.7071068 -0.7071068  1.4142136
96                         metabolic process        1456300_at Ilvbl -0.7071068 -0.7071068  1.4142136
68                         metabolic process        1440374_at Pde1c -0.7071068 -0.7071068  1.4142136
69                         metabolic process         1457827_at Arsj -0.7071068 -0.7071068  1.4142136
75                         metabolic process          1448821_at Tyr -0.7071068 -0.7071068  1.4142136
113 negative regulation of apoptotic process        1419282_at Ccl12 -0.7071068 -0.7071068  1.4142136
127 negative regulation of apoptotic process        1416787_at Acvr1 -0.7071068 -0.7071068  1.4142136
109 negative regulation of apoptotic process         1457580_at Chd8 -0.7071068 -0.7071068  1.4142136
135 positive regulation of apoptotic process          1423240_at Src -0.7071068 -0.7071068  1.4142136
150                      signal transduction      1440803_x_at Tacr3 -0.7071068 -0.7071068  1.4142136
152                      signal transduction        1424896_at Gpr85 -0.7071068 -0.7071068  1.4142136
183                      signal transduction       1440681_at Chrna7 -0.7071068 -0.7071068  1.4142136
190                      signal transduction        1456989_at Oxgr1 -0.7071068 -0.7071068  1.4142136
197                      signal transduction       1460657_at Wnt10a -0.7071068 -0.7071068  1.4142136
191                      signal transduction        1434186_at Lpar4 -0.7071068 -0.7071068  1.4142136
> 

What I want to do is to create a heatmap with row side color that denote the GO columns. In the end it will look like this (I manually add the blue column):

I'm stuck with the following code:

library(gplots)
dat.tmp <- dat
dat.tmp$GO <- NULL
rownames(dat.tmp) <- dat.tmp$ProbeGene
dat.tmp$ProbeGene <- NULL
heatmap.2(as.matrix(dat.tmp),margin=c(5,15),dendrogram="none",trace="none",scale="row")

Answer 1

This would be one approach, though it's not exactly like what you have:

# Note the Rowv=TRUE argument to prevent reordering of rows
heatmap.2(as.matrix(dat.tmp),margin=c(5,15),dendrogram="none",trace="none",scale="row",
          Rowv=FALSE, RowSideColors=as.character(as.numeric(dat$GO)))

legend("topright",      
    legend = unique(dat$GO),
    col = unique(as.numeric(dat$GO)), 
    lty= 1,             
    lwd = 5,           
    cex=.7
    )

Answer 2

You need to use the RowSideColours argument. However, that doesn't add text on its own. Unfortunately, that's not trivial to do automatically. I've "eye-balled" it here.

library(gplots)
dat.tmp <- dat
dat.tmp$GO <- NULL
rownames(dat.tmp) <- dat.tmp$ProbeGene
dat.tmp$ProbeGene <- NULL

# Create a colour vector
colours <- colorRampPalette(c("steelblue", "lightblue"))(5)[dat$GO]

# Use RowSideColors
heatmap.2(as.matrix(dat.tmp), margin=c(5,15),
          dendrogram="none",trace="none",scale="row",
          RowSideColors = colours, Rowv = FALSE)

# Add text
get.uni <- !duplicated(dat$GO)
text(x = rep(0.1, 5), y = c(0.8,  0.55,  0.3,  0.18, 0), 
     labels = dat$GO[get.uni],
     las = 2, col = "black", cex = 0.5, xpd = TRUE)

Which gives you something that looks like this:

So you need to use a legend as @Frank suggests or you need to fiddle with it yourself depending on what device size you have/want.

Edit

You can get a (I think) prettier result by playing around with the layout via lmat.

lmat <- rbind(c(5,3,4), c(1,1,2))
lhei <- c(0.25, 0.75)
lwid <- c(1, 1, 4)

heatmap.2(as.matrix(dat.tmp), margin=c(5,15),
          dendrogram="none",trace="none",scale="row",
          RowSideColors = colours, Rowv = FALSE,
          lmat = lmat, lhei = lhei, lwid = lwid)

get.uni <- !duplicated(dat$GO)
text(x = rep(0.1, 5), y = c(0.8,  0.55,  0.3,  0.2, 0), 
     labels = dat$GO[get.uni],
     las = 2, col = "black", cex = 0.7, xpd = TRUE)

Which again needs some tweaking --- especially the colour key.