Define specific value colouring with pheatmap in R

Question

Let's say:

m1<-matrix(rnorm(1000),ncol=100)

and defining colours:

cols = colorRampPalette(c("white", "red"))(30)

I am producing a heatmap without clustering with pheatmap function:

pheatmap(dist(t(m1)), cluster_rows = F, cluster_cols = F, show_rownames = TRUE, 
color = cols, main = 'Heatmap')

the question is, how can I define colours in order to get the same heatmap but only with pixels of specific value coloured (for example less than 0.1).

I tried to set

cols = ifelse(dist(t(m1))<0.1,'red','black')

but didn't work.

Answer 1

For a simple binary color scheme, you can use the breaks argument:

library(pheatmap)

set.seed(1)
m1<-matrix(c(rnorm(1000)), ncol=100)

pheatmap(dist(t(m1)),
         cluster_rows = F,
         cluster_cols = F,
         show_rownames = TRUE, 
         color = c("red", "black"),
         breaks = c(0, 3, 9),  # distances 0 to 3 are red, 3 to 9 black
         main = 'Heatmap')

It looks like this:

If you prefer color gradients, it can be done as follows:

m <- matrix(c(rnorm(1000)), ncol=100)
distmat <- dist(t(m))

# Returns a vector of 'num.colors.in.palette'+1 colors. The first 'cutoff.fraction'
# fraction of the palette interpolates between colors[1] and colors[2], the remainder
# between colors[3] and colors[4]. 'num.colors.in.palette' must be sufficiently large
# to get smooth color gradients.
makeColorRampPalette <- function(colors, cutoff.fraction, num.colors.in.palette)
{
  stopifnot(length(colors) == 4)
  ramp1 <- colorRampPalette(colors[1:2])(num.colors.in.palette * cutoff.fraction)
  ramp2 <- colorRampPalette(colors[3:4])(num.colors.in.palette * (1 - cutoff.fraction))
  return(c(ramp1, ramp2))
}

cutoff.distance <- 3  
cols <- makeColorRampPalette(c("white", "red",    # distances 0 to 3 colored from white to red
                               "green", "black"), # distances 3 to max(distmat) colored from green to black
                             cutoff.distance / max(distmat),
                             100)

pheatmap(distmat,
         cluster_rows = F,
         cluster_cols = F,
         show_rownames = TRUE, 
         color = cols,
         main = 'Heatmap')

Which then looks like this: