omicverse.single.run_cellphonedb_v5

omicverse.single.run_cellphonedb_v5#

omicverse.single.run_cellphonedb_v5(adata, cpdb_file_path, celltype_key='celltype', min_cell_fraction=0.005, min_genes=200, min_cells=3, iterations=1000, threshold=0.1, pvalue=0.05, threads=10, output_dir=None, temp_dir=None, cleanup_temp=True, debug=False, separator='|', results_key='cpdb_results', comm_key='cpdb_comm', method='statistical', degs_file_path=None, score_interactions=True, **kwargs)[source]#

Run CellPhoneDB statistical or DEGs-based analysis.

Parameters:

  • adata (AnnData) – Annotated data matrix

  • cpdb_file_path (str) – Path to CellPhoneDB database zip file (REQUIRED) If file doesn’t exist, will attempt automatic download

  • celltype_key (str) – Column name in adata.obs containing cell type annotations

  • min_cell_fraction (float) – Minimum fraction of total cells required for a cell type to be included

  • min_genes (int) – Minimum number of genes required per cell

  • min_cells (int) – Minimum number of cells required per gene

  • iterations (int) – Number of shufflings performed in the analysis

  • threshold (float) – Min % of cells expressing a gene for this to be employed in the analysis

  • pvalue (float) – P-value threshold to employ for significance

  • threads (int) – Number of threads to use in the analysis

  • output_dir (str or None) – Directory to save results. If None, creates temporary directory

  • temp_dir (str or None) – Directory for temporary files. If None, uses system temp

  • cleanup_temp (bool) – Whether to clean up temporary files after analysis

  • debug (bool) – Saves all intermediate tables employed during the analysis

  • separator (str) – String to employ to separate cells in the results dataframes

  • method ({2, 3, 'statistical', 'degs'}) – CellPhoneDB method to run. Method 2 / 'statistical' is the historical permutation-based default. Method 3 / 'degs' runs the DEGs-based analysis.

  • degs_file_path (str or None) – CellPhoneDB DEG input file. Required when method='degs'.

  • score_interactions (bool) – Whether CellPhoneDB should calculate interaction scores.

  • **kwargs (dict) – Additional parameters forwarded to the selected CellPhoneDB method.

Returns:

Raw CellPhoneDB result dict and visualization-ready communication AnnData. The same objects are also written to adata.uns[results_key] and adata.uns[comm_key] so downstream ov.pl.ccc_* plots can work directly on the original adata.

Return type:

Tuple[dict,anndata.AnnData]

Examples

# Basic usage - will download database automatically if needed cpdb_results, adata_cpdb = run_cellphonedb_v5(

adata, cpdb_file_path=’./cellphonedb.zip’, celltype_key=’celltype_minor’

)

# Advanced usage cpdb_results, adata_cpdb = run_cellphonedb_v5(

adata, cpdb_file_path=’/path/to/cellphonedb.zip’, celltype_key=’celltype_minor’, min_cell_fraction=0.01, iterations=2000, threads=20

)

Parameters:

  • results_key (str (default: 'cpdb_results'))

  • comm_key (str (default: 'cpdb_comm'))

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