特定值的谱图颜色 [英] Pheatmap Color for Specific Value

问题描述

我对R很陌生，最近我一直在使用pheatmap库来生成热图.我的问题是我想以特定方式为我的热图着色.我将在下面描述:

I am very new to R and recently I have been playing around with the pheatmap library to generate, well, heatmaps. My problem is that I want to color my heatmap in a specific way. I'll describe below:

1. 值< 1应该是颜色渐变(例如，深蓝色到浅蓝色)
2. 精确等于1的值应该是深灰色
3. 值> 1应该是一个颜色渐变(例如，深红色到浅红色)

我在各种调色板上都使用了breaks参数和color参数，但是我似乎无法找到一个好的解决方案.我最接近的是这样的:

I have played around with the breaks parameter and the color parameter with various palettes but I can't seem to nail a good solution. the closest I've come is something like this:

pheatmap(mtx, 
     color =  c('#4444FF','#F4FF4F','#FF4444'), 
     breaks = c(0,1,2,3), 
     legend_breaks = c(0,1,2) )

但是这不允许可视化范围，即0.1应该看起来不同于0.9的阴影，即使它们都应该是蓝色.谁能提供建议或意见?我确实查看了这张票证，并考虑将1更改为NA，但是对于它来说有点太复杂了我.更不用说我不得不关闭针对作弊图的聚类，这不是我希望做的事情.谢谢！

But this doesn't allow for visualization of the ranges, i.e. 0.1 should look a different shade than 0.9 even though they should both be blue. Can anyone provide suggestions or advice? I did look at This ticket and consider changing 1 to NA, but it's a bit too complex for me. Not to mention I'd have to turn off clustering for pheatmap which is not something I wish to do. Thanks!

推荐答案

您不能为特定颜色设置颜色，但是可以使用很小的范围，例如[0.999,1.001]

You cannot set the color for a specific color but you can go for a very small range like [0.999,1.001]

应将中断设置为您在问题中提到的指定范围，并相应地分配颜色；

Should set the breaks to for the specified ranges you mentioned in the question and the assign the colors accordingly;

library(pheatmap)
bk1 <- c(seq(-2,0.9,by=0.1),0.999)
bk1 <- c(1.001,seq(1.1,3,by=0.1))
bk <- c(bk1,bk2)  #combine the break limits for purpose of graphing

my_palette <- c(colorRampPalette(colors = c("darkblue", "lightblue"))(n = length(bk1)-1),
              "gray38", "gray38",
              c(colorRampPalette(colors = c("darkred", "tomato1"))(n = length(bk2)-1)))

pheatmap(df, color = my_palette, breaks = bk, scale = "none", 
             cluster_rows = F, cluster_cols = F, margin = c(5,5))

出于演示目的，使用 rnorm.within 函数，我进行了以下数据设置:

For purpose of showing an example using rnorm.within function I made the following data-set:

   #V1 is random between -2 and 3 
   #V2 is equal to 1
   #V3 is random between 0 and 3

   df <- cbind(rnorm.within(1000, -2, 3),rep(1,1000), rnorm.within(1000,0,3))

这将是上面创建的数据的热图；

And this will be the heatmap for the data created above;

这篇关于特定值的谱图颜色的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！