Question: How to cluster the annotation in the heat map?
gravatar for ravi
8 months ago by
ravi20 wrote:

mat = matrix(rnorm(100), 10)
foo = sample(letters[1:2], 10, replace = TRUE)
colnames(mat) = sapply(letters[1:10], function(x) paste(rep(x, 10), collapse = ""))
cn = colnames(mat)
ha2 = HeatmapAnnotation(foo = foo,
                cn = anno_text(cn, rot = 90, offset = unit(1, "npc") - unit(2, "mm"), just = "right"),
                annotation_height = unit.c(unit(5, "mm"), max_text_width(cn)))
Heatmap(mat, show_column_names = FALSE, bottom_annotation = ha2)

This gave me a heat map like following:

Here you see in the bottom annotation both a and b are not clustered. I would like to know how can I do each group (color) get clustered. I mean all samples which come under "b" at one side and samples under "a" on one side.

Can anyone please tell me how to do this? Thanks !!

heatmap rna-seq clustering R • 327 views
ADD COMMENTlink modified 8 months ago by Kevin Blighe21k • written 8 months ago by ravi20
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

ComplexHeatmap doesn't support splitting that way - it only supports splitting by rows. If you want to split by columns, you could just generate two separate heatmaps and plot them side by side with the draw function draw(hmap1 + hmap2).

In your case, you could also just plot the transpose of your data-matrix and then split by rows, as follows (NB - the key parameter to use is split):



mat=matrix(rnorm(100), 10)

foo=sample(letters[1:2], 10, replace=TRUE)

colnames(mat)=sapply(letters[1:10], function(x) paste(rep(x, 10), collapse=""))

cn = colnames(mat)

ha2 = rowAnnotation(foo=foo,
                #cn=anno_text(cn, rot=0, just="right", which="row"),
                annotation_height=unit.c(unit(5, "mm"), max_text_width(cn)))

draw(Heatmap(t(mat), split=foo, show_row_names=TRUE) + ha2, heatmap_legend_side="left", annotation_legend_side="left")


ADD COMMENTlink modified 8 months ago • written 8 months ago by Kevin Blighe21k
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