问题描述
在 R 中创建热图已成为许多帖子、讨论和迭代的主题.我的主要问题是，将 lattice levelplot() 或基本图形 image() 中可用解决方案的视觉灵活性与基本的 heatmap()，pheatmap 的 pheatmap() 或 gplots 的 heatmap.2().这是我想要更改的一个小细节 - x 轴上标签的对角线方向.让我告诉你我在代码中的观点.
Creating heatmaps in R has been a topic of many posts, discussions and iterations. My main problem is that it's tricky to combine visual flexibility of solutions available in lattice levelplot() or basic graphics image(), with effortless clustering of basic's heatmap(), pheatmap's pheatmap() or gplots' heatmap.2(). It's a tiny detail I want to change - diagonal orientation of labels on x-axis. Let me show you my point in the code.
#example data
d <- matrix(rnorm(25), 5, 5)
colnames(d) = paste("bip", 1:5, sep = "")
rownames(d) = paste("blob", 1:5, sep = "")
您可以使用 levelplot() 轻松将方向更改为对角线:
You can change orientation to diagonal easily with levelplot():
require(lattice)
levelplot(d, scale=list(x=list(rot=45)))
但应用聚类似乎很痛苦.其他视觉选项也是如此，例如在热图单元格周围添加边框.
but applying the clustering seems pain. So does other visual options like adding borders around heatmap cells.
现在，转移到实际的 heatmap() 相关函数、聚类和所有基本视觉效果都非常简单——几乎不需要调整:
Now, shifting to actual heatmap() related functions, clustering and all basic visuals are super-simple - almost no adjustment required:
heatmap(d)
这里也是这样:
require(gplots)
heatmap.2(d, key=F)
最后，我最喜欢的一个:
and finally, my favourite one:
require(pheatmap)
pheatmap(d)
但是所有这些都没有旋转标签的选项.pheatmap 手册建议我可以使用 grid.text 来自定义我的标签.这是多么令人高兴——尤其是在聚类和更改显示标签的顺序时.除非我在这里遗漏了什么......
But all of those have no option to rotate the labels. Manual for pheatmap suggests that I can use grid.text to custom-orient my labels. What a joy it is - especially when clustering and changing the ordering of displayed labels. Unless I'm missing something here...
最后，还有一个老好用的image().我可以旋转标签，一般来说这是最可定制的解决方案，但没有集群选项.
Finally, there is an old good image(). I can rotate labels, in general it' most customizable solution, but no clustering option.
image(1:nrow(d),1:ncol(d), d, axes=F, ylab="", xlab="")
text(1:ncol(d), 0, srt = 45, labels = rownames(d), xpd = TRUE)
axis(1, label=F)
axis(2, 1:nrow(d), colnames(d), las=1)
那么我应该怎么做才能获得理想的、快速的热图、集群和方向以及漂亮的视觉特征黑客?我的最佳出价是更改 heatmap() 或 pheatmap() 不知何故，因为这两个似乎是最通用的调整.但欢迎任何解决方案.
So what should I do to get my ideal, quick heatmap, with clustering and orientation and nice visual features hacking? My best bid is changing heatmap() or pheatmap() somehow because those two seem to be most versatile in adjustment. But any solutions welcome.
推荐答案
要修复 pheatmap，你真正想做的就是进入 pheatmap:::draw_colnames并在对 grid.text() 的调用中调整几个设置.这是使用 assignInNamespace() 的一种方法.(它可能需要额外的调整，但你明白了；):
To fix pheatmap, all you really want to do is to go into pheatmap:::draw_colnames and tweak a couple of settings in its call to grid.text(). Here's one way to do that, using assignInNamespace(). (It may need additional adjustments, but you get the picture ;):
library(grid) ## Need to attach (and not just load) grid package
library(pheatmap)
## Your data
d <- matrix(rnorm(25), 5, 5)
colnames(d) = paste("bip", 1:5, sep = "")
rownames(d) = paste("blob", 1:5, sep = "")
## Edit body of pheatmap:::draw_colnames, customizing it to your liking
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(...)) ## Was 'hjust=0' and 'rot=270'
}
## For pheatmap_1.0.8 and later:
draw_colnames_45 <- function (coln, gaps, ...) {
coord = pheatmap:::find_coordinates(length(coln), gaps)
x = coord$coord - 0.5 * coord$size
res = textGrob(coln, x = x, y = unit(1, "npc") - unit(3,"bigpts"), vjust = 0.5, hjust = 1, rot = 45, gp = gpar(...))
return(res)}
## 'Overwrite' default draw_colnames with your own version
assignInNamespace(x="draw_colnames", value="draw_colnames_45",
ns=asNamespace("pheatmap"))
## Try it out
pheatmap(d)
这篇关于热图中 x 轴上的对角线标签方向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，WP2