Cross posted: https://stackoverflow.com/questions/62972420/hclust-object-from-factorminer-does-not-cluster-dendrogram-in-pheatmap

I am trying to create a heatmap of a matrix with 20 rows and 10 columns using `pheatmap::pheatmap`

. To cluster the columns, I am using an `hclust`

object obtained after running `FactoMineR::HCPC`

on the input matrix. However, when I use the hclust object, the

Below is my reproducible code:

```
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)
```

Running the above code gives me the heatmap below and as you can see, it is not clustering the columns by FactoMineR PCA HCPC at all (the top annotation colors should've been grouped). How do I use hclust object from FactoMineR::HCPC to force clustering in pheatmap?

The pcahcpc.tree seems to be a valid hclust object: