热图中x轴上的对角标签方向 [英] Diagonal labels orientation on x-axis in heatmap(s)

问题描述

在R中创建热图一直是许多帖子，讨论和迭代的主题.我的主要问题是，将晶格levelplot()或基本图形image()中可用的解决方案的视觉灵活性与基本的heatmap()，phoemap的pheatmap()或gplots的heatmap.2()轻松组合在一起是很难的.这是我要更改的一个小细节-标签在x轴上的对角线方向.让我向您展示我在代码中的观点.

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)))

但是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，转移到与heatmap()相关的实际功能，聚类和所有基本视觉效果都非常简单-几乎无需进行任何调整:

Now, shifting to actual heatmap() related functions, clustering and all basic visuals are super-simple - almost no adjustment required:

heatmap(d)

所以在这里:

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) 

但是所有这些选项都没有没有旋转标签的选项. pheatmap手册建议我可以使用grid.text自定义标签方向.这是一种乐趣-尤其是在对显示的标签进行聚类和更改顺序时.除非我在这里缺少任何东西...

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，有一个旧商品image().我可以旋转标签，通常这是最可定制的解决方案，但是没有聚类选项.

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)

那我该怎么做才能获得理想的，快速的热图，并具有聚类和方向性以及不错的视觉功能，使它们骇人听闻?我最好的出价是以某种方式更改heatmap()或pheatmap()，因为这两个在调整方面似乎用途最为广泛.但是任何解决方案都欢迎.

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，您真正想要做的就是进入pheatmap:::draw_colnames并调整对grid.text()的调用中的一些设置.这是使用assignInNamespace()的一种方法. (它可能需要进行其他调整，但您会看到图片；):

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)

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