dandelion.tools.productive_ratio

dandelion.tools.productive_ratio(adata, vdj, groupby, groups=None, locus='TRB')[source]

Compute the cell-level productive/non-productive contig ratio.

Only the contig with the highest umi count in a cell will be used for this tabulation.

Returns inplace AnnData with .uns[‘productive_ratio’].

Parameters:

  • adata (AnnData) – AnnData object holding the cell level metadata (.obs).

  • vdj (Dandelion) – Dandelion object holding the repertoire data (.data).

  • groupby (str) – Name of column in AnnData.obs to return the row tabulations.

  • groups (list[str] | None, optional) – Optional list of categories to return.

  • locus (Literal[“TRB”, “TRA”, “TRD”, “TRG”, “IGH”, “IGK”, “IGL”], optional) – One of the accepted locuses to perform the tabulation