R – heatmap.2 with color key on top

heatmapr

I have the following code to show the color key above the heatmap. But the color key is not exact on top (a little shifted to the right) of the heatmap. Does anyone know how to make the color not shifted? Also, how to remove the white space on the right of the heatmap? Thanks.

library(gplots)
heatmap.2(
  matrix(rnorm(100*10), nrow=100)
  , dendrogram='none'
  , Colv = F
  , Rowv = F
  , trace='none'
  , col = colorRampPalette(c('blue', 'yellow'))(12)
  , labRow=NA
  , labCol=NA
  , density.info='none'
  , lmat=rbind(c(4, 2), c(1, 3)), lhei=c(2, 8), lwid=c(4, 1)
)

Best Answer

One can center the color key by adding "padding sections" ("5" and "6", in my particular case) to the lattice at the left (see the "#" comment over the last line of the code:

heatmap.2(x=matrix(rnorm(20*10), nrow=10), Rowv=NULL,Colv=NULL, 
          col = rev(rainbow(20*10, start = 0/6, end = 4/6)), 
          scale="none",
          margins=c(3,0), # ("margin.Y", "margin.X")
          trace='none', 
          symkey=FALSE, 
          symbreaks=FALSE, 
          dendrogram='none',
          density.info='histogram', 
          denscol="black",
          keysize=1, 
          #( "bottom.margin", "left.margin", "top.margin", "left.margin" )
          key.par=list(mar=c(3.5,0,3,0)),
          # lmat -- added 2 lattice sections (5 and 6) for padding
          lmat=rbind(c(5, 4, 2), c(6, 1, 3)), lhei=c(2.5, 5), lwid=c(1, 10, 1))

Related Solutions

Recenter heatmap.2 in R

If you read the documentation for ?heatplot.2 carefully, you'll see at the bottom of the list of arguments the following:

lmat, lhei, lwid visual layout: position matrix, column height, column width. See below for details

And the details are:

This layout can be overriden by specifiying appropriate values for lmat, lwid, and lhei. lmat controls the relative postition of each element, while lwid controls the column width, and lhei controls the row height. See the help page for layout for details on how to use these arguments.

So for example:

data(mtcars)
 x  <- as.matrix(mtcars)
 rc <- rainbow(nrow(x), start=0, end=.3)
 cc <- rainbow(ncol(x), start=0, end=.3)

 ##
 ## demonstrate the effect of row and column dendrogram options
 ##
 gplots:::heatmap.2(x,key = FALSE,dendrogram = "row",lhei = c(0.05,0.95))

enter image description here

and I imagine the setting lwid would behave similarly. Although I should add that if you include both dendrograms, then the space in the upper left is necessary to make room for the dendrograms.

R: Centering heatmap.2 key (gplots package)

The solution seem to be just adding symbreaks to your heatmap.2. Here is a fully reproducible example with your data:

library(gplots)
#read your example data
heatmapInputActual <- read.table(textConnection(
"8.408458 5.661144 0.00000000
4.620846 4.932283 -0.46570468
-4.638912 -3.471838 -0.12146109
-4.822829 -3.946024 0.06403327
3.948832 4.520447 -0.31945941
"),as.is=TRUE)
#convert sample data to matrix
heatmapInputActual <- as.matrix(heatmapInputActual)
#just add symbreaks to the end of your code
heatmap.2(heatmapInputActual, dendrogram="none", Rowv=FALSE, Colv=FALSE, 
          col = bluered(256), scale="none", key=TRUE, density.info="none", 
          trace="none", cexRow=0.125, cexCol=0.125, symm=F,symkey=T,symbreaks=T)

enter image description here

Best Answer

Related Solutions

Recenter heatmap.2 in R

R: Centering heatmap.2 key (gplots package)

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