关于pheatmap绘制热图横轴标签倾斜以及几个热图代码

Oct 28, 2018 2 分钟阅读时长 R

这几天忙着做实验的同时还再帮某兄弟解决作图，这兄弟想做个热图，我就用pheatmap给他做，结果做完了发现，诶？尼玛，这横轴标签怎么是垂直的，于是又找解决方法，终于找到了一个。上代码。

#创建数据
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")
head(test)

##          Test1      Test2    Test3      Test4    Test5      Test6    Test7
## Gene1 3.478948 -1.3189620 2.022492 -1.8908125 3.063350  0.6009318 4.317662
## Gene2 4.354549  0.5188468 4.367425 -0.5386495 1.355116  1.5142165 4.480402
## Gene3 4.192323 -1.0382861 3.509188  0.8541905 3.635153  0.4159976 3.793672
## Gene4 3.353073  0.2624581 3.759387  0.5848898 3.004100 -0.4968918 1.091723
## Gene5 3.129363 -0.9422255 4.558563  0.7275991 2.571372 -1.4574945 3.016973
## Gene6 3.206768 -1.6356026 2.877822 -0.6683236 3.490102 -1.7531713 2.106235
##             Test8    Test9     Test10
## Gene1  1.83005199 2.235624 -1.3683971
## Gene2  0.38677603 3.843029 -1.0146326
## Gene3 -1.66711704 1.493430 -0.4044687
## Gene4  0.02498933 1.995961  1.8579663
## Gene5 -0.60796743 1.950566  0.6641153
## Gene6  1.21738912 2.711145 -2.3203194

library(pheatmap)
library(vegan)

## 载入需要的程辑包：permute

## 载入需要的程辑包：lattice

## This is vegan 2.5-2

library(permute)
library(lattice)
pheatmap(test)

#看到没有，图下面的Test1-10字样都是垂直的
#要想修改，就要改pheatmap包里面的东西
#修改pheatmap:::draw_colnames什么的
#先载入grid包
library(grid)
draw_colnames_45 <- function (coln, ...) {
  m = length(coln)
  x = (1:m)/m - 1/2/m
  grid.text(coln, x = x, y = unit(0.96, "npc"), vjust = .5, 
            hjust = 1, rot = 45, gp = gpar(...)) ## 注意缺省值为 'hjust=0' 和'rot=270'
}
#然后将default draw_colnames覆盖
assignInNamespace(x="draw_colnames", value="draw_colnames_45",
                  ns=asNamespace("pheatmap"))
#再作图，这回就妥了
pheatmap(test)

#可以美化下……额，这个美化不好~将就看吧
pheatmap(test, color = colorRampPalette(c("pink", "white", "red"))(100),
         scale = "none", legend = TRUE, border_color = "black",
         treeheight_row = 80, treeheight_col = 80
         )

#另外，输出图片可以用tiff(),png()等命令，这样可以调整分辨率
#不过建议用tiff()命令
#注意命令顺序，如下
tiff("test1.tiff", units="in", width=9, height=6,
     res=300) ##res设置的是分辨率)
pheatmap(test, color = colorRampPalette(c("pink", "white", "red"))(100),
         scale = "none", legend = TRUE, border_color = "black",
         treeheight_row = 80, treeheight_col = 80
         )
dev.off()

## tiff 
##    3

备注一下，方法来源于网页https://stackoverflow.com/questions/15505607/diagonal-labels-orientation-on-x-axis-in-heatmaps 另外可以看下其他的绘制热图的代码。

#载入所需包
library(ggplot2)
library(gplots)

## 
## 载入程辑包：'gplots'

## The following object is masked from 'package:stats':
## 
##     lowess

#最简单的热图
heatmap(test, scale = "none")

#而下面这个出现color key，并且横坐标字体变小，其他与上面一致
heatmap.2(test, scale = "none", trace = "none", key = TRUE, symkey = FALSE,
          density.info = "none", 
          margins = c(4, 8),
          cexRow = 1, cexCol = 1)

这几个程序啥的，我还是喜欢pheatmap，尽管微调美化上有点难度~~~

关于pheatmap绘制热图横轴标签倾斜以及几个热图代码

Dr.二哈

在读苦逼科研狗

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