stereo.algorithm.get_niche.GetNiche.main¶
- GetNiche.main(niche_distance, cluster_1, cluster_2, cluster_res_key=None, method='fixed', theta=0.1, filter_raw=True, 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.cluster_res_key (
Optional[str]) – the key which specifies the clustering result in data.tl.result.method (
str) – method for calculating niche, choose from ‘fixed’ or ‘adaptive’.theta (
float) – the parameter used to control border region selection, only available for ‘adaptive’ method.filter_raw (
bool) – this function will create a new data object by filtering cells, this parameter determine whether to filter raw data meanwhile, default to True.inplace (
bool) – whether to replace the previous express matrix or get a new StereoExpData object with the new express matrix, default by False. # noqa
return: a new StereoExpData or AnnBasedStereoExpData object representing a niche.