R 包 circlize：circos 热图颜色未显示

Question

我正在尝试使用 circlize 包创建一个圆形图。当使用十六进制颜色代码时，我的图不会显示任何内容，但当我使用实际颜色名称时，它会显示。这是为什么？

代码：

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()

当我使用非十六进制颜色名称时，它起作用了：

# 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()

Answer 1

根据文档，在描述参数时 col

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

而您传递的是 list 而不是命名向量。所以如果你 unlist col_fun1 （或者用 c() 而不是 list() 创建它），你会得到

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()

我的困惑是为什么第一个版本有效，而不是为什么第二个版本无效。

R 包 circlize：circos 热图颜色未显示

R package circlize: circos heatmap colors not showing up

r

heatmap

circlize

circos