Uneven representation of conditions in Peaks to Gene Heatmap

[cassidmm]

Hi! I have been using ArchR to analyze a large joint snRNA and snATAC-seq data set that has two experimental conditions, "A" and "B". When I plot the peak to gene heatmap (plotPeak2GeneHeatmap) and group by condition, Group "A" is significantly overrepresented in the groupings (i.e., the groupBy bar above the heatmap shows more of Group "A" than Group "B"). I have verified that in the ArchR object, there is a roughly equal number of cells in Group "A" and "B", and that they do not significantly differ in quality.

I was wondering if others have observed something similar or perhaps that this might mean there are significant differences in peak2gene linkages between Group "A" and "B" - if so, is there another way you've gone about demonstrating this? Since the peak2genelinkage data is not calculated per cell, I was wondering if there is a way I could break it out per group? Or if there is something else I should adjust when plotting the heatmap?

Thanks in advance!