R 用热图绘制 kmeans 聚类

发布于 2024-10-19 00:34:51 字数 343 浏览 3 评论 0原文

我想用 kmeans 对矩阵进行聚类，并能够将其绘制为热图。听起来挺琐碎的，这样的情节我见过很多。我尝试用谷歌搜索周围，但找不到解决方法。

我希望能够在此图上绘制类似面板 A 或 B 的内容。假设我有一个 250 行 5 列的矩阵。我不想聚集列，只想聚集行。

m = matrix(rnorm(25), 250, 5)

km = kmeans(m, 10)

那么如何将这 10 个集群绘制为热图？非常欢迎您的评论和帮助。

谢谢。

在此处输入图像描述

原文

I would like to cluster a matrix with kmeans, and be able to plot it as heatmap. It sounds quite trivial, and I have seen many plots like this. I have tried to google atround, but can't find a way round it.

I'd like to be able to plot something like panel A or B on this figure.
Let say I have a matrix with 250 rows and 5 columns. I don't want to cluster the columns, just the rows.

m = matrix(rnorm(25), 250, 5)

km = kmeans(m, 10)

Then how do I plot those 10 clusters as a heatmap ? You comments and helps is more than welcome.

Thanks.

enter image description here

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国产ˉ祖宗 2024-10-26 00:34:51

类似以下内容应该有效：

set.seed(100)
m = matrix(rnorm(10), 100, 5)
km = kmeans(m, 10)
m2 <- cbind(m,km$cluster)
o <- order(m2[, 6])
m2 <- m2[o, ]
library(pheatmap) # I like esoteric packages!
library(RColorBrewer)
pheatmap(m2[,1:5], cluster_rows=F,cluster_cols=F, col=brewer.pal(10,"Set3"),border_color=NA)

使用 pheatmap pacakge 创建的heatmap

Something like the following should work:

set.seed(100)
m = matrix(rnorm(10), 100, 5)
km = kmeans(m, 10)
m2 <- cbind(m,km$cluster)
o <- order(m2[, 6])
m2 <- m2[o, ]
library(pheatmap) # I like esoteric packages!
library(RColorBrewer)
pheatmap(m2[,1:5], cluster_rows=F,cluster_cols=F, col=brewer.pal(10,"Set3"),border_color=NA)

heatmap created using the pheatmap pacakge

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