stereo.core.StPipeline.phenograph#

StPipeline.phenograph(phenograph_k=30, pca_res_key='pca', n_jobs=10, res_key='phenograph', seed=0)[source]#

Cluster cells into subgroups by Phenograph.

Parameters:

  • phenograph_k (int) – the k value of Phenograph.

  • pca_res_key (str) – the key of PCA analysis to get corresponding result from self.result.

  • n_jobs (int) – the number of parallel jobs to run for neighbors search. If set to -1, all CPUs will be used. Too high value may cause segment fault.

  • res_key (str) – the key for storing result of Phenograph clustering.

  • seed (int) – leiden initialization of the optimization.

Returns:

Clustering result of Phenograph is stored in self.result where the key is 'phenograph'.