cytonormpy.CytoNorm.run_clustering

cytonormpy.CytoNorm.run_clustering#

CytoNorm.run_clustering(n_cells=None, test_cluster_cv=True, cluster_cv_threshold=2, markers=None, **kwargs)#

Runs the clustering step. The clustering will be performed on as many cells as n_cells specifies. The remaining cells are then imputed from the initial clustering information. For FlowSOM, unclassified cells will be subjected to the same SOM and predicted.

Parameters:

  • n_cells (Optional[int]) – Number of cells used for training. If None, all cells are used for training. Defaults to None.

  • test_cluster_cv (bool) – If True, CV of clusters per batch are calculated. Raises a warning if the calculated CV is above the threshold.

  • cluster_cv_threshold – The CV cutoff that is used to determine the appropriateness of the clustering.

  • markers (Optional[list[str]]) – Optional. Selects markers that are used for clustering.

  • kwargs – keyword arguments ultimately passed to the train function of the clusterer. Refer to the respective documentation.

Return type:

None

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