How to add an additional single column heatmap at the side of main heatmap in R

Question

I have the following scripts:

library("gplots")
mydata <- mtcars
mydata.nr <- nrow(mydata)
mydata.newval <-  data.frame(row.names=rownames(mydata),new.val=-log(runif(mydata.nr)))

# Functions
hclustfunc <- function(x) hclust(x, method="complete")
distfunc <- function(x) dist(x,method="euclidean")

# Set colors
hmcols <- rev(redgreen(256));

# Plot the scaled data
heatmap.2(as.matrix(mydata),dendrogram="row",scale="row",col=hmcols,trace="none", margin=c(8,9), hclust=hclustfunc,distfun=distfunc);

Which generate the following heatmap: enter image description here

Now given a new data.frame which contain new values for each cars:

mydata.nr <- nrow(mydata)
mydata.newval <-  data.frame(row.names=rownames(mydata),new.val=-log(runif(mydata.nr)))

I want to create a single column heatmap with gradient gray positioned next to row names. How can I achieve that in R heatmap.2?

I'd recommend the scavenging approach: look at the source code for `persp3D` or other packages which put up a colorscale by default in their graphics, and copy the code for your own use. — Carl Witthoft, Dec 26 '13 at 13:27
If you want some more flexibility, you might try ggplot. http://stackoverflow.com/questions/6673162/reproducing-lattice-dendrogram-graph-with-ggplot2 — kdauria, Jan 01 '14 at 17:21

score 3 · Accepted Answer · edited May 23 '17 at 10:27

Does this do what you want? You can use the RowSideColors option to add a column to the side of the heatmap.

new.vals = mydata.newval[,1]
mydata.newval$scaled = ( new.vals - min(new.vals) ) / 
                       ( max(new.vals) - min(new.vals) )
mydata.newval$gray = gray( mydata.newval$scaled )

heatmap.2( as.matrix(mydata), 
           dendrogram = "row", scale = "row",
           col = hmcols, trace = "none", 
           margin = c(8,9), 
           hclust = hclustfunc, distfun = distfunc,
           RowSideColors=mydata.newval$gray )

enter image description here

If you want the gray column in between the heatmap and the labels, there isn't a simple way to do that with heatmap.2; I don't think it was designed for such purposes. One way to hack it together would be to make the gray values go from 10 to 11 (or something out of the range of the rest of the data). Then you would change the colors mapped to the breaks (see here). However, this would make your key look pretty funky.

# heatmap.2 does the clustering BEFORE the scaling. 
# Clustering after scaling might give different results
# heatmap.2 also reorders the dendrogram according to rowMeans.
# (Code copied directly from the heatmap.2 function)
x = as.matrix(mydata)
Rowv = rowMeans(x, na.rm = TRUE)
hcr = hclustfunc(distfunc(x))
ddr = as.dendrogram(hcr)
ddr = reorder(ddr, Rowv) # the row dendrogram

# Scale the data as heatmap.2 does
rm = rowMeans(x, na.rm = TRUE)
x = sweep(x, 1, rm)
sx =  apply(x, 1, sd, na.rm = TRUE)
x = sweep(x, 1, sx, "/")

# add the new data as a column
new.vals = mydata.newval[,1]
new.vals.scaled = ( new.vals - min(new.vals) ) / 
                  ( max(new.vals) - min(new.vals) ) # scaled from 0 to 1
x = cbind( x, gray = max(x) + new.vals.scaled + 0.1 )

# make the custom breaks and colors
edge = max(abs(x-1.1))
breaks = seq(-edge,edge+1.1,length.out=1000)
gradient1 = greenred( sum( breaks[-length(breaks)] <= edge ) )
gradient2 = colorpanel( sum( breaks[-length(breaks)] > edge ), "white", "black" )
hm.colors = c(gradient1,gradient2)

hm = heatmap.2( x, col=hm.colors, breaks=breaks,
           scale="none", 
           dendrogram="row", Rowv=ddr,
           trace="none", margins=c(8,9) )

enter image description here

Although this hack works, I would look for a more robust solution using more flexible packages that play with different viewports using the grid package.

How to add an additional single column heatmap at the side of main heatmap in R

1 Answers1

Linked