R draw heatmap with clusters, but hide dendrogram

Question

By default, R's heatmap will cluster rows and columns:

mtscaled = as.matrix(scale(mtcars))
heatmap(mtscaled, scale='none')

I can disable the clustering:

heatmap(mtscaled, Colv=NA, Rowv=NA, scale='none')

And then the dendrogram goes away:

But now the data is not clustered anymore.

I don't want the dendrograms to be shown, but I still want the rows and/or columns to be clustered. How can I do this?

Example of what I want:

Solution 1

library(gplots)
heatmap.2(mtscaled,dendrogram='none', Rowv=TRUE, Colv=TRUE,trace='none')

Rowv -is TRUE, which implies dendrogram is computed and reordered based on row means.

Colv - columns should be treated identically to the rows.

Solution 2

You can do this with pheatmap:

mtscaled <- as.matrix(scale(mtcars))
pheatmap::pheatmap(mtscaled, treeheight_row = 0, treeheight_col = 0)

See pheatmap output here:

Solution 3

For ComplexHeatmap, there are function parameters to remove the dendrograms:

library(ComplexHeatmap)
Heatmap(as.matrix(iris[,1:4]), name = "mat", show_column_dend = FALSE, show_row_dend = FALSE)

Solution 4

You can rely on base R structures and consider following approach based on building the hclust trees by yourself.

mtscaled = as.matrix(scale(mtcars))
row_order = hclust(dist(mtscaled))$order
column_order = hclust(dist(t(mtscaled)))$order
heatmap(mtscaled[row_order,column_order], Colv=NA, Rowv=NA, scale="none")

No need to install additional junk.

Solution 5

I had similar issue with pheatmap, which has better visualisation and heatmap or heatmap.2. Though heatmap.2 is a choice for your solution, Here is the solution with pheatmap, by extracting the order of clustered data.

library(pheatmap)
mtscaled = as.matrix(scale(mtcars))
H = pheatmap(mtscaled)

Here is the output of pheatmap

pheatmap(mtscaled[H$tree_row$order,H$tree_col$order],cluster_rows = F,cluster_cols = F)

Here is the output of pheatmap after extracting the order of clusters

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