R热图与发散的调色板 [英] R heatmap with diverging colour palette

问题描述

我试图在R中创建一个简单的热图，使用发散的调色板。我想使用一个渐变，以便低于阈值N的所有数字被指定为一种颜色（例如紫色），并且高于阈值的所有数字被指定为另一种颜色（例如橙色）。

下面是一个示例数据集：

  Division，COL1，COL2，COL3，COL4，COL5，COL6，COL7 
 Division 1,31.9221884012222,75.8181694429368,97.0480443444103,96.295954938978,70.5677134916896,63.0451830103993,93.0396212730557 $ b $二级组2,85.7012346852571,29.0621076244861,16.9130333233625,94.6443660184741,19.9103083927184,61.9562198873609,72.3791105207056 
司3,47.1665125340223,99.4153356179595,8.51091076619923,79.1276383213699,41.915355855599,7.45079894550145,24.6946100145578 
部4,66.0743870772421,24.6163331903517,78.694460215047， 42.04714265652,50.2694897353649,73.0409651994705,87.3745442833751 
司5,29.6664374880493,35.4036891367286,19.2967326845974,5.48460693098605,32.4517334811389,15.5926876701415,76.0523204226047 
司6,95.4969164915383,8.63230894319713,61.7535551078618,24.5590241160244,25.5453423131257,56.397921172902,44.4693325087428 $ b $二级组7,87.5015622004867,28.7770316936076,56.5095080062747,34.6680747810751,28.1923673115671,65.0204187724739,13.795713102445 
司8,70.1077231671661,72.4712177179754,38.4903231170028,36.1821102909744,97.0875509083271,17.184783378616,78.2292529474944 
部9,47.3570406902581,90.2257485780865,65.6037972308695， 77.0234781783074,25.6294377148151,84.900529962033,82.5080851092935 
司10,58.0811711959541,0.493217632174492,58.5604055318981,53.5780876874924,9.12552657537162,20.313960686326,78.1371118500829 
司11,34.6708688884974,76.711881859228,22.6064443588257,22.1724311355501,5.48891355283558,79.1159523651004,56.8405059166253 
 Division 12,33.6812808644027,44.1363711375743,70.6362190190703,3.78900407813489,16.6075889021158,9.12654218263924,39.9711143691093 
  

这里是一个简单的从上面的数据生成热图。

  data < -  read.csv（dataset.csv，sep = ，）
 row.names（data）< -  data $ Division 
 data < -  data [，2：7] 
 data_matrix   / pre> 
 
 
如何修改上述代码以产生：
 
 
 
 
 
 a所有数字的颜色渐变（橙色）ABOVE 50（数字从50开始越深）
 
 
所有数字的颜色渐变（紫色）BELOW 50 50）
 
 
很高兴（但可选）在网格单元格中写入数字
 
 
 
 
 
 
 
 
  []  
 
 
 
我刚看过这问题SO ，这似乎是非常相似的。答案使用ggplot（我没有经验），我已经无法适应ggplot解决方案我的稍微复杂的数据。
解决方案
这应该让你大部分的方式。 （请注意，如果您希望绘制的颜色与单元格的实际（而不是重新缩放的）值对应，则需要设置 scale =none。 
  ncol < -  100 
 
 ##制作n种颜色的向量
 cols <  -  RColorBrewer ::: brewer.pal（11，PuOr）＃或c（紫色，白色，橙色）
 rampcols < -  colorRampPalette（colors = cols，space = Lab）（ncol）
 rampcols [（n / 2）+ 1] < -  rgb（t（col2rgb（green）），maxColorValue = 256）
 
具有n + 1个断点的向量
 rampbreaks < -  seq（0，100，length.out = ncol + 1）
 
 ##试试
 heatmap（data_matrix， Rowv = NA，Colv = NA，scale =none，
 col = slopcols，breaks = rampbreaks）
  
 
 
 
 > 
 
 
 
  EDIT  
 
 
 
为了更精确地控制阈值的位置，我建议您创建两个独立的调色板 - 一个用于小于阈值并且一个用于高于阈值的值，然后将它们缝合在一起。尝试这样，用 Min ， Max ， Thresh 等：
  nHalf < -  50 
 
 Min < 0 
 Max < -  100 
 Thresh < -  50 
 
 ##为低于阈值的值设置颜色向量
 rc1<  -  colorRampPalette （颜色= c（白色））的颜色的向量，其中颜色的值大于阈值
 rc2  rampcols < -  c（rc1，rc2）
 ##在您的示例中，此行设置49到51之间的值的颜色。
 rampcols [c（nHalf，nHalf + 1）] < -  rgb（t（col2rgb（green）），maxColorValue = 256）
 
 rb1 < ，Thresh，length.out = nHalf + 1）
 rb2  rampbreaks < -  c（rb1，rb2 ）
 
 heatmap（data_matrix，Rowv = NA，Colv = NA，scale =none，
 col = slopcols，breaks = rampbreaks）
  
 
I am trying to create a simple heatmap in R, using a diverging colour palette. I want to use a gradient so that all numbers below a threshold N are designated a color (say purple), and all numbers above the threshold are designated another color (say orange). The further away the number is from the threshold, the darker the color should be.


Here is a sample dataset:
Division,COL1,COL2,COL3,COL4,COL5,COL6,COL7
Division 1,31.9221884012222,75.8181694429368,97.0480443444103,96.295954938978,70.5677134916186,63.0451830103993,93.0396212730557
Division 2,85.7012346852571,29.0621076244861,16.9130333233625,94.6443660184741,19.9103083927184,61.9562198873609,72.3791105207056
Division 3,47.1665125340223,99.4153356179595,8.51091076619923,79.1276383213699,41.915355855599,7.45079894550145,24.6946100145578
Division 4,66.0743870772421,24.6163331903517,78.694460215047,42.04714265652,50.2694897353649,73.0409651994705,87.3745442833751
Division 5,29.6664374880493,35.4036891367286,19.2967326845974,5.48460693098605,32.4517334811389,15.5926876701415,76.0523204226047
Division 6,95.4969164915383,8.63230894319713,61.7535551078618,24.5590241160244,25.5453423131257,56.397921172902,44.4693325087428
Division 7,87.5015622004867,28.7770316936076,56.5095080062747,34.6680747810751,28.1923673115671,65.0204187724739,13.795713102445
Division 8,70.1077231671661,72.4712177179754,38.4903231170028,36.1821102909744,97.0875509083271,17.184783378616,78.2292529474944
Division 9,47.3570406902581,90.2257485780865,65.6037972308695,77.0234781783074,25.6294377148151,84.900529962033,82.5080851092935
Division 10,58.0811711959541,0.493217632174492,58.5604055318981,53.5780876874924,9.12552657537162,20.313960686326,78.1371118500829
Division 11,34.6708688884974,76.711881859228,22.6064443588257,22.1724311355501,5.48891355283558,79.1159523651004,56.8405059166253
Division 12,33.6812808644027,44.1363711375743,70.6362190190703,3.78900407813489,16.6075889021158,9.12654218263924,39.9711143691093
Here is a simple snippet to produce a heatmap from the above data
data <- read.csv("dataset.csv", sep=",")
row.names(data) <- data$Division
data <- data[,2:7]
data_matrix <- data.matrix(data) 
heatmap(data_matrix, Rowv=NA, Colv=NA, col = heat.colors(256), scale="column", margins=c(5,10))
How can I modify the above code to produce:


a color gradient (orange) for all numbers ABOVE 50 (darker the further the number is from 50)
a color gradient (purple) for all numbers BELOW 50 (darker the further the number is from 50)
Nice to have (but optional) write the number value in the grid cell
Nice to have (but optional), use a different color for grid cell that is EXACTLY the threshold number (50 in this case)


[[Edit]]

I have just seen this question on SO, which seems to be very similar. The answer uses ggplot (which I have no experience of), and I have so far, been unable to adapt the ggplot solution to my slightly more complicated data.
解决方案
This should get you most of the way. (Note that you'll need to set scale="none" if you want the plotted colors to correspond to the actual (rather than the rescaled) values of the cells).
ncol <- 100

## Make a vector with n colors
cols <- RColorBrewer:::brewer.pal(11,"PuOr")  # OR c("purple","white","orange")  
rampcols <- colorRampPalette(colors = cols, space="Lab")(ncol)
rampcols[(n/2) + 1] <- rgb(t(col2rgb("green")), maxColorValue=256) 

## Make a vector with n+1 breaks
rampbreaks <- seq(0, 100, length.out = ncol+1)

## Try it out
heatmap(data_matrix, Rowv = NA, Colv = NA, scale="none",
        col = rampcols, breaks = rampbreaks)


EDIT

For finer control over the placement of the threshold, I'd suggest creating two separate palettes -- one for values less than the threshold and one for values above the threshold -- and then "suturing" them together. Try something like this, playing around with different values for Min, Max, Thresh, etc.:
nHalf <- 50

Min <- 0
Max <- 100
Thresh <- 50

## Make vector of colors for values below threshold
rc1 <- colorRampPalette(colors = c("purple", "white"), space="Lab")(nHalf)    
## Make vector of colors for values above threshold
rc2 <- colorRampPalette(colors = c("white", "orange"), space="Lab")(nHalf)
rampcols <- c(rc1, rc2)
## In your example, this line sets the color for values between 49 and 51. 
rampcols[c(nHalf, nHalf+1)] <- rgb(t(col2rgb("green")), maxColorValue=256) 

rb1 <- seq(Min, Thresh, length.out=nHalf+1)
rb2 <- seq(Thresh, Max, length.out=nHalf+1)[-1]
rampbreaks <- c(rb1, rb2)

heatmap(data_matrix, Rowv = NA, Colv = NA, scale="none",
        col = rampcols, breaks = rampbreaks)


                        
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