Factorminer 的 Hclust 对象不会在 Pheatmap 中聚类树状图

Question

交叉发布：https://www.biostars.org/p/450365/

我正在尝试使用pheatmap::pheatmap 创建一个包含 20 行和 10 列的矩阵的热图。为了对列进行聚类，我使用了在输入矩阵上运行 FactoMineR::HCPC 后获得的 hclust 对象。但是，当我使用 hclust 对象时，

这是我的代码：

library(tidyverse)
library(pheatmap)
library(FactoMineR)

# reproducible df of 20 rows and 10 columns
set.seed(100)
tmp <- matrix(rnorm(10000), nrow = 20, ncol = 10)
tmp <- as.data.frame(tmp)
colnames(tmp) <- paste0('col_', seq(1:ncol(tmp)))
rownames(tmp) <- paste0('row_', seq(1:nrow(tmp)))

# use FactoMineR HCPC for clustering data
res.pcahcpc <- FactoMineR::PCA(X = t(tmp), graph = F)
res.pcahcpc <- FactoMineR::HCPC(res.pcahcpc, nb.clust = 4, graph = F)

# get hclust object from FactoMineR::HCPC
pcahcpc.tree <- res.pcahcpc$call$t$tree

# hclust object
> pcahcpc.tree

Call:
flashClust::hclust(d = dissi, method = method, members = weight)

Cluster method   : ward 
Distance         : euclidean 
Number of objects: 10 

# get cluster information for heatmap annotation
res.pcahcpc <- res.pcahcpc$data.clust # clusters
colnames(res.pcahcpc)[ncol(res.pcahcpc)] <- "PCA_HCPC"
res.pcahcpc <- res.pcahcpc[,'PCA_HCPC', drop = F]

# clusters
> head(res.pcahcpc)
      PCA_HCPC
col_1        1
col_2        1
col_3        4
col_4        2
col_5        3
col_6        1

# create heatmap using PCA HCPC clustering
tmp %>%
  pheatmap(cellwidth = 15, cellheight = 15,
           annotation_col = res.pcahcpc,
           cluster_cols = pcahcpc.tree)

运行上面的代码给了我下面的热图，这很奇怪，因为它根本没有通过 FactorMiner PCA HCPC 对列进行聚类。有人能解释一下为什么吗？

Answer 1

要得到正确的树状图，首先需要根据pcahcpc.tree$labels中给出的信息对tmp的列重新排序。

idx <- as.numeric(gsub("col_","", pcahcpc.tree$labels))
pheatmap(tmp[, idx], cellwidth=15, cellheight=12,
         annotation_col = res.pcahcpc,
         cluster_cols = pcahcpc.tree)

pheatmap 列的树状图现在与stats:::plot.hclust 给出的树状图相同

plot(pcahcpc.tree)