Easy guide to drawing heat maps to PDF with R (with color key)

As far as I know, the native heatmap() function in R will not draw heat maps with color keys.
To this end, install library gplots and use the function heatmap.2(). You can install gplots
through Synaptic in Ubuntu.

1. Install gplots and RColorBrewer for more color options

$ R
> install.packages("gplots")
> install.packages("RColorBrewer")

2. Copy the script below and save it as “heatmap.r”

library(RColorBrewer)
library(gplots)
x=read.table("matrix.dat", header=TRUE)
mat=data.matrix(x)

pdf("heatmap.pdf", height=10, width=10)
heatmap.2(mat,
Rowv=TRUE,
Colv=TRUE,
#    dendrogram= c("none"),
distfun = dist,
hclustfun = hclust,
xlab = "X data", ylab = "Y data",
key=TRUE,
keysize=1,
trace="none",
density.info=c("none"),
margins=c(10, 8),
col=brewer.pal(10,"PiYG")
#    col=redgreen(75),
)
dev.off()

The commented line dendrogram=c(“none”) will suppress clustering of data in both axes. Another option for coloring the heatmap is given by col=redgreen(75), commonly used in log data in microarray chips.

3. Generate a data matrix as

        a       b       c       d       e
k       0       0       1       1       5
l       1       2       1       6       7
m       1       1       2       9       1
n       0       0       1       3       2
o       9       8       0       6       5

and save it as “matrix.dat”

4. Run as

$ R –vanilla < heatmap.r

5. See the heat map in heatmap.pdf

Summary

Packages used

• gplots
• RColorBrewer

• bioinformatics
• R statistical package