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:
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.
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.
I don't know if this is a bug or expected behavior. The plot in the notebook
analyze_func_scores
showing 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 infunc_effects_config.yaml
with: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 themin_pre_selection_count
instead. I was worried there was something wrong with the thresholding, but when I looked at thefunc_scores
files themselves, it seems to properly be applying the min_pre_selection_frac cutoff. So I believe this is just a graphing issue.