Hi,
I'd like to see what is the log2FC in a certain DEG comparison of the genes in a KEGG pathway. I have done so in the past with the R package pathview. Unfortunately, whenever there is a "node" that contains many collapsed genes (which, in some pathways, is like 50% of the nodes) it calculates the average of all the collapsed genes in the node but labels it with just the first gene's name.
I would like to plot the log2FC of all the genes involved while still retaining the relationship between them. In order to see clearly that, e.g, in a downregulated pathway, the up-regulated genes happen to be acting as inhibitors.
I'm not looking for GSEA or enrichment analyses, those are solved. I'm just looking for visualization with the collapsed genes.
So far I have also tried ggkegg but I couldn't manage to "decollapse" the nodes.
Have any of you faced this issue before? Is there another method capable of doing this?
