Adding cell quality scoring using the Feldman et al. method to recipe

[gwaybio]

From Feldman et al. 2019:

Adding data per site to capture Figure 2D, and adding a cell quality metric to filter cells as performed in Figure 2E.

Currently, the filtering method is not exactly as Figure 2E. We filter cells that have more than 1 different perfectly matching barcode.

[gwaybio]

Another TODO

Add barcode_col argument to

pooled-cell-painting-profiling-recipe/0.preprocess-sites/1.process-spots.py

Lines 228 to 232 in 886a601

	crispr_barcode_gene_df = cell_quality.assign_cell_quality(
	count_df=crispr_barcode_gene_df,
	parent_cols=spot_parent_cols,
	score_col=spot_score_cols[0],
	).assign(

Only the Feldman method uses this argument, it defaults to None, but it needs to be specified. Figure out what to specify barcode_col as if any other method besides Feldman is used. Maybe it is harmless to add the Feldman barcode_col to every assign_cell_quality() arg