clustering changes in complex heatmap everytime

Question

[biology_inform]

Hi all, I created a heatmap with using row_km option. And I am trying to get rownames in the clusters with row_order() option but everytime I run it gives different heatmap and clustering. Is there any way to do this stable and get one heatmap with one type of clustering? set.seed(123) is set

[Nitin Narwade]

This is strange to me. Just out of curiosity, did you use set.seed(123) right before using Heatmap(..., row_km = ..., column_km = ...)?

BTW, your heatmap looks nice (aesthetically) ;)

Regards,

Nitin N.

[biology_inform]

firstly, thanks :) I used set.seed(123) just before raw data import which is in the beginning before the data ordering. Should I use just before Heatmap(....)?

Answer 1

[Ming Tommy Tang]

Hi, this exact github issue answers your question https://github.com/jokergoo/ComplexHeatmap/issues/737

[biology_inform]

thank you