dandelion.plotting.clone_rarefaction

dandelion.plotting.clone_rarefaction(vdj_data, color, clone_key=None, palette=None, figsize=(5, 3), chain_status_include=['Single pair', 'Orphan VDJ', 'Orphan VDJ-exception', 'Extra pair', 'Extra pair-exception'], save=None)[source]

Plot rarefaction curve for cell numbers vs clone size.

Parameters:

  • vdj_data (AnnData | Dandelion) – AnnData or Dandelion object.

  • color (str) – Column name to split the calculation of clone numbers for a given number of cells for e.g. sample, patient etc.

  • clone_key (str | None, optional) – Column name specifying the clone_id column in metadata/obs.

  • palette (list[str] | None, optional) – Color mapping for unique elements in color. Will try to retrieve from AnnData .uns slot if present.

  • figsize (tuple[float, float], optional) – Size of plot.

  • chain_status_include (list[Literal[“Single pair”, “Orphan VDJ”, “Orphan VDJ-exception”, “Orphan VJ”, “Orphan VJ-exception”, “Extra pair”, “Extra pair-exception”, ]], optional) – chain statuses to include.

  • save (str | None, optional) – Save path.

Returns:

rarefaction plot.

Return type:

ggplot