R Heatmap: Hide cellnote for cell value = 0

Question

I have a working heatmap, built with gplots , as shown here:

heatmap.2(as.matrix(matrix1),cellnote=as.matrix(matrix1),
    notecol="black",margins =c(9,6),trace="none",density.info="none",
    col=my_palette,Rowv=NA,Colv=NA,dendrogram="none",scale="row")

The underlying data in matrix1 looks as follows:

A       AA        AAA        BBB         CASH

CASH    0         0          0           0
JSUB    0.22171   0          0           2.20712
SECR    2.92828   1.97112    3.53786     0.91444
SENR    18.86672 11.53339   15.06844    21.57709
SSEN    5.707     1.96225    0.57815     2.93462
SSUB    0.36507   0.07968    0           0.44985
SUB     1.0539    0          0           2.37103
T1      0         0          0           0.56024
T2      1.87901   0          0           3.00718
UT2     0         0          0           0.15787

My matrix1 , which was created as a pivot table with the cast function using the reshape package, contains many zeroes. Whenever the value in my matrix is zero, I would not want to display a 'cellnote', as this merely confuses the heatmap.

I have however, so far, not figured out how to do this and am grateful for any advice.

Thank you!

Answer 1

For me it works just to make a new matrix replacing zeros with NAs and pass this as the argument to cellnote .

matrix2 <- as.matrix(matrix1)
matrix2[matrix2 == 0] <- NA

Re-running the code using matrix2

heatmap.2(as.matrix(matrix1),cellnote=matrix2,
      notecol="black",margins =c(9,6),trace="none",density.info="none",
      col=my_palette,Rowv=NA,Colv=NA,dendrogram="none",scale="row")

Gives

(By the way you didn't give my_palette , so I hashed it out for this example.)