BAITS.VDJ.tl.calculate_qc_clones

BAITS.VDJ.tl.calculate_qc_clones#

BAITS.VDJ.tl.calculate_qc_clones(df, group_by, Cgene_col, clone_col, loc_x_col='X', loc_y_col='Y', plot=True)#

Compute per-group clone counts and per-spatial-location clone counts.

Parameters:

  • df (pandas.DataFrame) – Input dataframe containing clone, chain, and spatial information.

  • group_by (str) – Column name to group by (e.g., sample or tissue region).

  • Cgene_col (str) – Column name for chain (Cgene).

  • clone_col (str) – Column containing clone identifiers.

  • loc_x_col (str, default='X') – Column name for x-coordinate.

  • loc_y_col (str, default='Y') – Column name for y-coordinate.

  • plot (bool, default=True) – Whether to generate QC boxplots.

Returns:

Original dataframe with additional columns: - ‘clone_by_group’: number of clones per group - ‘clone_by_group_spatialLoc’: number of clones per spatial location

Return type:

pandas.DataFrame

Contents