dms-vep / dms-vep-pipeline-3

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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Issue with displaying cutoff in 'analyze_func_scores' #87

Closed bblarsen-sci closed 1 year ago

bblarsen-sci commented 1 year ago

I don't know if this is a bug or expected behavior. The plot in the notebook analyze_func_scoresshowing the distribution of pre_counts has a red line showing where the threshold cutoff is applied for each sample (image attached). These values are set in func_effects_config.yaml with:

min_pre_selection_count: 20
min_pre_selection_frac: 0.00001

Thresholding the barcode counts should take the higher of these two numbers (I believe). It appears that regardless of what min_pre_selection_frac is set to, it always displays the red threshold line at the min_pre_selection_count instead. I was worried there was something wrong with the thresholding, but when I looked at the func_scores files themselves, it seems to properly be applying the min_pre_selection_frac cutoff. So I believe this is just a graphing issue.

Screenshot 2023-11-07 at 7 52 21 AM
jbloom commented 1 year ago

The bug was actually how it was being reported upstream of analyze_func_scores, not in the plotting itself. Will be fixed once I merge #88 and make version 3.5.4.