Rotate a part of the dendrogram

[NicolasHipp]

Hello,
I'm a newbie in R utilisation and I try to use ComplexHeatmap to visualize my data. I work on single cell qPCR analysis and i would like to rotate a part of the dendrogram.
I try to change the order with a vector in the "column_dend_reorder" command, but I don't understand how it works.

Does anybody performed this before?
Thks,
Nicolas :)

[jokergoo]

Hi,

Maybe you can check the dendextend package:

https://cran.r-project.org/web/packages/dendextend/vignettes/introduction.html#changing-a-dendrograms-structure

There is a rotate() function which can adjust the order of branches in a dendrogram.

In your case, you should generate a dendrogram for columns first:

column_dend = as.dendrogram(hclust(t(mat)))
column_dend = rotate(column_dend, ...)  # define how you rotate the branches

In the vignette I mentioned above, the author use "pipe-style syntax", so:

dend15 %>% 
   set("labels_colors") %>% 
   rotate(5:1)

is identical to

rotate(set(dend15, "labels_colors"), 5:1)

and sent it to Heatmap():

Heatmap(mat, cluster_columns = column_dend, ...)

[NicolasHipp]

Hi,

I tried this solution and it works perfectly ::)

Thks for the help ! :)

Nicolas