stereo.algorithm.get_niche.GetNiche.main#

GetNiche.main(niche_distance, cluster_1, cluster_2, cluster_res_key=None, inplace=False)[source]#

To ensure the accuracy and specificity of this juxtacrine signaling model, we extract cells bordering their niches and statistically calculate their CCC activity scores of L-R pairs under the assumption that intercellular L-R communications routinely exist among closely neighboring cells

Parameters:

  • niche_distance (float) – the maximum distance between cells in order to form a niche.

  • cluster_1 (str) – one cell cluster in the interaction.

  • cluster_2 (str) – the other cell cluster in the interaction.

  • coord_key – the key which specifies the coordiate of cells.

  • cluster_res_key (Optional[str]) – the key which specifies the clustering result in data.tl.result.

  • inplace (bool) – whether to inplace the previous express matrix or get a new StereoExpData object with the new express matrix, default by False. # noqa