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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Heatmap color not showing up? #43

Closed ahdee closed 4 years ago

ahdee commented 4 years ago

Hi, I'm using version. pathfindR_1.5.0.9007

When I tried this example the heatmap plots however there is no color associated with logfold change

pathfindR::term_gene_heatmap(RA_output)

Interestingly, the upset plot shows color for the default heatmap, however, the log fold color scheme is discrete, just what is up or down and not a gradient. Any chance to get it to plot with a continuous gradient color scheme instead?

here is a picture of the upset plot.

dFKKdZJ 1

thanks!

egeulgen commented 4 years ago

in term_gene_heatmap(), if you supply the input data frame (i.e. the input for run_pathfindR()), the visualization of the heatmap with continuous color scheme is produced:

term_gene_heatmap(result_df = RA_output, 
                  genes_df = RA_input)

same with UpSet_plot():

UpSet_plot(result_df = RA_output, 
           genes_df = RA_input)