I wanted to get some advice on how you might make your heatmap easier to read. In my case, I generated a heatmap from GSVA data which I filtered to only include significant pathways, here.
I wanted to see how each of my samples differed in the expression of these pathways. In the heatmap, there are 130 significant pathways, so my heatmap is extremely large and would be impossible to use as a figure in a manuscript.
If you had this figure, how would you try to simplify it? Would you find some way to cluster the GO terms into related pathways and generate multi heatmaps of these different pathway types?
As you can see, there are two well-separated large clusters as a determined heatmap, but I do not see a clear reason in this separation.
Anywho, I look forward to your opinions and suggestions :)
What I ended up doing was looking at the enriched KEGG pathways instead of the individual GO terms to simplify the analysis. Then plotted with pheatmap and clustered the rows (pathways).