Deeptools - removing small clusters

Question

[jamzaleg84]

Hello,

I'm using the plotProfile tool from deeptools in order to visualize if there are any clusters that are more enriched for one genotype over another (posting picture below). It seems like the first cluster has the highest intensity, but a corresponding heatmap I made using the plotHeatmap tool showed that the other clusters have more clear differences but that is masked by the large intensity of cluster 1.

Furthermore, when I went to check cluster 1 it appears like there are only two regions (thus explaining the WARNING: Group 'cluster_1' is too small for plotting, you might want to remove it.)

I know I could just remove the two regions from the consensus bed file I used and rerun compute matrix, but I was wondering if there is a way i could ask plotProfile to ignore a certain cluster?

Answer 1

[Trivas]

In my experience, DeepTools isn't very amenable to coding quick changes to its files. You might be able to manually edit the .mat file from computeMatrix but it'll be a lot easier if you manually remove the regions from your bed file and rerun. Luckily it's pretty quick!

[jamzaleg84]

Sorry, as a followup, I'd like to ask is there anyway to make the intensity level y-axis to be relative to each specific cluster. I've noticed that even if I remove the large cluster, the later clusters (like cluster 7 and beyond are too small to see, because the scale is much lower than the intensity of the earlier clusters). If not does anyone have a suggestion on what to do? Thank you!

[Friederike]

You can manually set different ymax/ymin values, see https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html