API

Core functions

class convexgating.tools.CONVEX_GATING(adata, cluster_numbers, cluster_string, save_path='/home/docs/checkouts/readthedocs.org/user_builds/convexgating/checkouts/latest/docs', add_noise=True, update_anndata=True, focus='f1')[source]

Derives gating strategies for selected clusters.

Parameters:

  • adata (object) – AnnData object, with label information in adata.obs.

  • cluster_numbers (list) – List containing the cluster numbers or names to derive gating strategies for.

  • cluster_string (str) – Column name in adata.obs with label or cluster information corresponding to cluster_numbers.

  • save_path (str, optional) – Path to folder where gating output will be saved. Creates folder if it doesn’t exist. Default is the current working directory.

  • add_noise (bool, optional) – Indicates whether a small amount of random noise is added for internal stability. Default is True.

  • update_anndata (bool, optional) – Indicates whether gating output is saved in adata.uns in addition to the output folder. Default is True.

  • focus (str, optional) – Specifies whether CG focuses on high “f1” (default) or “recall”.

Returns:

adata – AnnData object containing gating information if update_anndata is True.

Return type:

object

Notes

Gating output is saved in the location specified by the save_path parameter.

class convexgating.tools.gating_strategy(adata, cluster_numbers, cluster_string, save_path='/home/docs/checkouts/readthedocs.org/user_builds/convexgating/checkouts/latest/docs', add_noise=True, focus='f1')[source]

Learning gating strategy for specific cell clusters.

Parameters:

  • adata (AnnData object) – complete input Data for gating.

  • cluster_numbers (list of strings or ints or doubles) –

    list of cluster numbers/identifieres in adata.obs[cluster_string] to find gating strategy for

    -> e.g [‘4’,’5’] to find gating strategies for cell population ‘4’ and ‘5’

  • cluster_string (string) – column name in adata.obs where cluster labels are found, e.g ‘louvain’

  • add_noise (True or False) – if True add small amount of nice to count data for more stable internal procedures

  • focus ("f1" or "recall") – default focus “f1”, optional “recall”