R package circlize: circos heatmap colors not showing up

March 16, 2022

I am trying to create a circular plot using circlize package. When using hex color codes, my plot does not show up anything but when I use actual color names, it shows. Why is that?

Code:

suppressPackageStartupMessages({
  library(tidyverse) 
  library(circlize) 
})

# input data
dput(annot)

structure(list(Case_type = c("Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "Initial CNS Tumor", 
"Initial CNS Tumor", "Initial CNS Tumor", "no evidence of disease", 
"no evidence of disease", "no evidence of disease", "Progressive", 
"Progressive", "Progressive", "Progressive", "Progressive", "Progressive", 
"Progressive", "Progressive", "Progressive", "Progressive", "Recurrence", 
"Recurrence", "Recurrence", "Recurrence", "Recurrence", "Recurrence", 
"Recurrence", "Recurrence")), row.names = c("15635-32", "15635-37", 
"15635-38", "15635-42", "15635-43", "15635-53", "15635-58", "15635-60", 
"15635-63", "15635-70", "15635-75", "15635-80", "15635-87", "15635-100", 
"15635-108", "15635-132", "15635-134", "15635-135", "15635-2", 
"15635-7", "15635-11", "15635-145", "15635-150", "15635-154", 
"15635-161", "15635-169", "15635-170", "15635-187", "15635-197", 
"15635-214", "15635-228", "15635-225", "15635-234", "15635-239", 
"15635-251", "15635-246", "15635-254", "15635-182", "15635-45", 
"15635-46", "15635-68", "15635-90", "15635-101", "15635-127", 
"15635-1", "15635-148", "15635-156", "15635-29", "15635-31", 
"15635-215", "15635-81", "15635-120", "15635-129", "15635-158", 
"15635-279"), class = "data.frame")

# split into 4 categories
split <- factor(annot$Case_type)
circos.clear()

# does not work with the hex color codes
col_fun1 <- list('Initial CNS Tumor' = '#59acff',
                 'Recurrence' = '#ffac59',
                 'Progressive' = '#ffff59',
                 'no evidence of disease' = '#acff59')
circos.par(start.degree = 30, gap.degree = 1, points.overflow.warning = FALSE)
circos.heatmap(annot, 
               split = split, 
               col = col_fun1, 
               track.height = 0.4, 
               bg.border = "gray50",
               show.sector.labels = T)
circos.clear()

When I use non-hex color names, it works:

# this works
col_fun2 <- list('Initial CNS Tumor' = 'yellow',
                 'Recurrence' = 'blue',
                 'Progressive' = 'green',
                 'no evidence of disease' = 'orange')
circos.par(start.degree = 30, gap.degree = 1, points.overflow.warning = FALSE)
circos.heatmap(annot, 
               split = split, 
               col = col_fun2, 
               track.height = 0.4, 
               bg.border = "gray50",
               show.sector.labels = T)
circos.clear()

>Solution :

According to the docs, when describing the argument col

If the values are characters, the color should be a named color vector.

Whereas you are passing a list rather than a named vector. So if you unlist col_fun1 (or create it with c() instead of list()), you get

circos.par(start.degree = 30, gap.degree = 1, points.overflow.warning = FALSE)
circos.heatmap(annot, 
               split = split, 
               col = unlist(col_fun1),
               track.height = 0.4, 
               bg.border = "gray50",
               show.sector.labels = T)
circos.clear()