在R中设置自定义色标

Question

我正在尝试在R中设置自定义比例.我的数据范围从-5.4到+3.6,我想将数据居中于0(白色).我希望对数据进行缩放,使得我在0以上和以下具有相同数量的渐变(我现在正在拍摄7个).我遇到的问题是我无法正确缩放,我不确定我的问题在哪里.

我的代码(源数据在底部的Pastebin链接中):

   png('127-2_4_compare_other.png',width = 1200, height = 800, units = "px")
   colfunc <- colorRampPalette(c("blue", "white", "red"))
   f <- function(m) t(m)[,nrow(m):1]
   colorBarz=matrix(seq(-5.5,4,len=15),nrow=1)
   colorBarx=1
   source("127-2_4.CompareMatrix.txt")
   colorBary=seq(-5.4,3.6,len=15)
   cus_breaks=c(-5.400, -4.725, -4.050, -3.375, -2.700, -2.025, -1.350, -0.675,  0.45, 0.90, 1.35, 1.80, 2.25, 2.70, 3.15, 3.60)
   layout(matrix(c(1,2), 1, 2, byrow = TRUE), widths=c(9,1))
   image(f(Compare2and4),axes=FALSE,ylab="Amino acids",xlab="Position",main="Sample 2 vs. 4",col=colfunc(15),breaks=cus_breaks)
   axis(1, seq(from = 0, to = 1, by = 0.03703), labels=c(1:11,1:17))
   axis(2, seq(from = 0, to = 1, by = 0.0526),labels=rev(c("A","R","N","D","C","E","Q","G","H","I","L","K","M","F","P","S","T","W","Y","V")),las=2)
   image(colorBarx,colorBary,colorBarz,col=colfunc(15),axes=FALSE,xlab="",ylab="log(Sample4 / Sample2)",breaks=cus_breaks)
   axis(2,las=2)
   dev.off()

我正在寻找0到3.6之间的7个均匀分割的箱子和0到-5.4以下的7个均匀分开的箱子,我想要在白色箱子的中间点击0.此外,如果任何人都可以查看热图代码本身,以确保没有明显的错误,我会非常感激.源数据的Pastebin

Answer 1

您提出的色标的一个问题是色标上每个点之间的感知距离不相等。相同颜色距离是指与负端相比，正端的数据值范围更大。我建议不要重新发明轮子，并利用ggplot.

默认情况下，发散色标将以白色作为值 0 处的中点。

例如：

Compare2and4_t <- t(Compare2and4)[,nrow(Compare2and4):1]
am_ac <- c("A","R","N","D","C","E","Q","G","H","I","L","K","M","F","P","S","T","W","Y","V")
pdat <- data.frame(x = 1:nrow(Compare2and4_t), 
                   y = factor(rep(am_ac, each = nrow(Compare2and4_t)), levels = rev(am_ac)),
                   val = c(Compare2and4_t))

library(ggplot2)
library(scales)

ggplot(pdat, aes(x, y, fill = val)) + 
  geom_tile() +
  scale_fill_gradient2(low = 'darkblue', high = 'darkred', 
                       limits = c(-5.4, 3.6), oob = squish) +
  coord_equal(expand = FALSE) +
  scale_x_continuous(breaks = unique(pdat$x)) +
  theme_classic() +
  labs(x = 'Position', y = 'Amino acids')