Border cells in heatmap

Question

I am trying to construct a heatmap in R using a correlation matrix and ap value matrix.

I use this tutorial to build the heatmap without problems. It works perfectly. I can even introduce some values from a second matrix (the p value matrix) in the right cells.
But when I try to highlight the corresponding cells it doesn't work. I use this code to generate the borders. I use RStudio v0.97 with the packages gplots, RColorBrewer. The code is :

library(gplots)
library(RColorBrewer)

my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)

nx = 5
ny = 10

mat1 <- matrix(rnorm(nx*ny,100,50),nx,ny)
mat2 <- mat1>150 #matrix used for the example instead of the p value matrix

makeRects <- function(tfMat,border){
  cAbove = expand.grid(1:nx,1:ny)[tfMat,]
  xl=cAbove[,1]-0.49
  yb=cAbove[,2]-0.49
  xr=cAbove[,1]+0.49
  yt=cAbove[,2]+0.49
  rect(xl,yb,xr,yt,border=border,lwd=3)
}            #this is the function to make the rectangles/borders
heatmap.2(mat1,
      Rowv = FALSE,         # don't reorganize columns 
      cellnote = mat2,      # check correspondance between rectangles and mat2 values
      main = "Correlation", # heat map title
      notecol="black",      # change font color of cell labels to black
      notecex=0.5,      # change the scaling of the cell labels
      density.info="none",  # turns off density plot inside color legend
      trace="none",         # turns off trace lines inside the heat map
      margins =c(12,9),     # widens margins around plot
      col=my_palette,       # use on color palette defined earlier 
      dendrogram="row",     # don't draw a row dendrogram
      Colv="NA",            # turn off column clustering
      add.expr = {makeRects(mat2,"black")}) #add the borders

I think something is wrong either with the makeRects function, or with the re-ordering of the rows via the heatmap.2 function. The rectangles appear in the heatmap, but they are not at the right positions. I have been scratching my head all day without finding what is wrong.

Any suggestions?

Answer 1

It would be helpful if you included some example data for folks to run your code on, and you should also specify any packages that are required to run your code. For example,

library(gplots)
library(Hmisc) 

x <- matrix(rnorm(100), ncol = 5)
y <- matrix(rnorm(100), ncol = 5)
keep <- rcorr(x, y)
matrr <- keep$r
matrp <- keep$P

In your makeRects() function you refer to nx and ny , but they are never defined.

In your call to heatmap.2() you refer to matrl , but it is never defined.

If you add definitions for these three objects to your question, we may be able to troubleshoot your plotting issue.