BAITS.VDJ.tl.compute_migraIdx

BAITS.VDJ.tl.compute_migraIdx#

BAITS.VDJ.tl.compute_migraIdx(df, sample_col='sample', clone_col='clone', chain_col='Cgene', cluster_col='spatial_cluster', x_col='X', y_col='Y')#

Compute migration index between spatial clusters for BCR clones.

This metric quantifies the degree of clonal overlap between two clusters in a given sample and chain, weighted by Shannon entropy of clone distribution.

Parameters:

  • df (pandas.DataFrame) – Input dataframe containing clone, chain, cluster, and coordinate info.

  • sample_col (str, default='sample') – Column name for sample identifier.

  • clone_col (str, default='clone') – Column name for clone identifier.

  • chain_col (str, default='Cgene') – Column name for BCR chain.

  • cluster_col (str, default='spatial_cluster') – Column name for spatial cluster.

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

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

Returns:

Dataframe with columns: [‘sample’, ‘chain’, ‘cluster_source’, ‘cluster_target’, ‘BCR_cross’] representing migration index between cluster pairs.

Return type:

pandas.DataFrame

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