如何改变heatmap.2的颜色范围在R？ [英] How to change heatmap.2 color range in R?

问题描述

我使用gplot产生热图，显示治疗组与配对对照组的log2倍变化。使用以下代码：

  heatmap.2（as.matrix（SeqCountTable），col = redgreen（75），
 density.info =none，trace =none，dendrogram = c（row），
 symm = F，symkey = T，symbreaks = T，scale =none）
  

我输出一个具有实际倍数变化值的热图（即非Row-Z得分）之后，在每个生物学家最喜欢的红黑绿配色方案中。

log2倍变化的实际范围是-3 / +7，许多值在-2 / -1和+ 1 / + 2范围内，分别显示为深红色/绿色。这使得整个热图非常暗，很难解释。

• 是否有一种倾斜颜色渐变的方法，也就是说，从黑色到相当明亮的梯度在较小的范围内发生？


• 和/或将颜色范围更改为不对称，即数据所用的范围为-3 / + 7，而不是像当前尺度的-7 / + 7 ，黑色仍然居中在零？

解决方案我得到的颜色范围是不对称的，只需将symkey参数改为FALSE

  symm = F，symkey = F，symbreaks = T，scale =none
  

解决colorRampPalette的颜色问题，并使用breaks参数指定每种颜色的范围，例如

  colors = c（seq（-3，-2，length = 100），seq（-2,0.5，length = 100），seq（0.5,6，length = 100 ））
 
 my_palette<  -  colorRampPalette（c（red，black，green））（n = 299）
  

总共

  heatmap.2（as.matrix（SeqCountTable） ，col = my_palette，
 breaks = colors，density.info =none，trace =none，
 dendrogram = c（row），symm = F，symkey = F，symbreaks = T，scale =none）
  

I'm using gplot to produce a heatmap showing log2-fold changes of a treatment groups versus paired controls. With the following code:

 heatmap.2(as.matrix(SeqCountTable), col=redgreen(75), 
           density.info="none", trace="none", dendrogram=c("row"), 
            symm=F,symkey=T,symbreaks=T, scale="none") 

I output a heat map with real fold change values (i.e., non Row-Z score) which is what I'm after, in the Red-Black-Green color scheme that is every biologist's favorite!

The actual range of log2-fold change is -3/+7, with many values in the -2/-1 and +1/+2 range, which appear as dark red/green (respectively). This makes the whole heatmap quite dark and so difficult to interpret.

• Is there a way of skewing the color gradient to make it less linear? That is, so that the gradient from black to quite bright occurs over a smaller range?
• And / or change the color range to be asymmetric, i.e., to run from -3/+7, as the data does, rather than -7/+7 as the scale currently does, with black still centered on zero?

解决方案

I got the color range to be asymmetric simply by changing the symkey argument to FALSE

symm=F,symkey=F,symbreaks=T, scale="none"

Solved the color issue with colorRampPalette with the breaks argument to specify the range of each color, e.g.

colors = c(seq(-3,-2,length=100),seq(-2,0.5,length=100),seq(0.5,6,length=100))

my_palette <- colorRampPalette(c("red", "black", "green"))(n = 299)

Altogether

heatmap.2(as.matrix(SeqCountTable), col=my_palette, 
    breaks=colors, density.info="none", trace="none", 
        dendrogram=c("row"), symm=F,symkey=F,symbreaks=T, scale="none")

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