Changing the colour palette based on quantile values in pheatmap

Question

enter image description hereI am very new to R and I am trying to make a pheatmap out of my data. I just copied some existing code included in a tutorial and it seems it pretty nicely fitted to my data after some tweaking. I also included some quantile code, that should change the color breaks based on the data I have, because most of the values are between 0-100 but just couple of them is in thousands. I would like to make it so the small values are more variable in colours and keep the light yellow only to the most extreme values. From the legend it seems it is the other way around right now... Can somebody help me to tweak the breaks? Thanks! Here is my code and the output heatmap (changed because it contained sensitive data..).

x <- read.table("proteins_cpm_commas.tsv", header=TRUE, row.names = 1)
x <- as.matrix(x)
x
pheatmap(x,
         drop_levels       = TRUE,
         cluster_rows=F, 
         cluster_cols=F,
         treeheight_col = 0,
         treeheight_row = 0,
         fontsize          = 8,
         color             = inferno(length(mat_breaks) - 1),
         breaks            = mat_breaks,
         main              = "Title ")

mat_breaks <- seq(min(x), max(x), length.out = 20)
mat_breaks
quantile_breaks <- function(xs, n = 20) {
  breaks <- quantile(xs, probs = seq(0, 1, length.out = n))
  breaks[!duplicated(breaks)]
}
mat_breaks <- quantile_breaks(x, n = 20)
mat_breaks

Maybe have a look at the `ComplexHeatmap` package, esp. https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html. From version 2.7.1, Legend() function has a new argument break_dist that controls the distance between two neighbouring break values in the legend. — user12728748, Mar 31 '22 at 12:12

score 0 · Answer 1 · answered Mar 31 '22 at 12:53

While this post is not using the pheatmap package, since the solutions I came up with are all rather hacks, I would recommend a solution using the ComplexHeatmap package. Example using mock data:

suppressPackageStartupMessages(
    lapply(c("ComplexHeatmap",  "circlize", "viridisLite"),
        require, character.only=TRUE))
set.seed(23)
x <- matrix(rexp(2000, rate=.001), ncol=20)
quantile_breaks <- function(xs, n = 10) {
  breaks <- quantile(xs, probs = seq(0, 1, length.out = n))
  breaks[!duplicated(breaks)]
}
mat_breaks <- quantile_breaks(x, n = 11)
col_fun_prop <- colorRamp2(quantile_breaks(x, n = 11), viridisLite::inferno(11))

Heatmap(x,col =  col_fun_prop,
    heatmap_legend_param=list(
        labels=round(mat_breaks), at=mat_breaks, col_fun = col_fun_prop, 
        title = "Prop", break_dist = 1))

^{Created on 2022-03-31 by the reprex package (v2.0.1)}

Changing the colour palette based on quantile values in pheatmap

1 Answers1