STAVAG.gene_modules

STAVAG.gene_modules(adata, gene_list)[source]

Cluster genes into modules using correlation among selected genes.

Parameters:

  • adata (AnnData) – AnnData that contains the expression matrix adata.X and gene names in adata.var.index.

  • gene_list (Sequence[str]) – Genes to include when building modules. Each gene should exist in adata.var.index.

Returns:

Z: Linkage matrix from hierarchical clustering.

corr: Gene to gene correlation matrix as a pandas DataFrame.Index and columns are gene names in gene_list.

df: Expression matrix of the selected genes as a pandas DataFrame. Rows are cells and columns are genes.

Return type:

Tuple[np.ndarray, pd.DataFrame, pd.DataFrame]