netmap.downstream.gene_clustering.get_hierarchical_clustering

netmap.downstream.gene_clustering.get_hierarchical_clustering(adata, genes=None)

Performs hierarchical clustering of the data matrix (layer:X) using the correlation of the genes.

Parameters

adataAnnData

A anndata object to containing the gene expression data in layer X.

genes: list (default: None)

A list of genes to be used for the clustering (default all genes)

dfpd.DataFrame

A dataframe with the correlation and the cophenetic distance

dist_linkage:

The linkage object from scipy.stats hierarchy