How to put a legend next to a heatmap. 2 color key

Question

I have the following data frame:

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")

And with the following code:

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

pdf("output.pdf",width=10,height=20)
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
    )
dev.off()

I can get the following picture.

My question is how to put the legend next to the color key as shown above. Please note that PDF paper size can be varied according to user specifications.

I think in the bottom line I do not know how to get the exact coordinate for the legend. Please advice.

Answer 1

You can find the coordinates of points on the graph using the function locator(). In your case, you can try something like this:

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)))
coords <- locator(1) # now click on the graph where you want the legend

pdf("output.pdf",width=10,height=20)
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(coords,      
    legend = unique(dat$GO),
    col = unique(as.numeric(dat$GO)), 
    lty= 1,             
    lwd = 5,           
    cex=.7
    )
dev.off()

Coordinates range from 0 to 1.

0 1, par(xpd=TRUE). xpd=TRUE :

pdf("output.pdf",width=10,height=20)
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(y=1.1, x=.25, xpd=TRUE,     
    legend = unique(dat$GO),
    col = unique(as.numeric(dat$GO)), 
    lty= 1,             
    lwd = 5,           
    cex=.7
    )
dev.off()