omicverse-single-cell-cellphonedb-communication

OmicVerse Single-Cell CellPhoneDB Communication

Goal

Run the reusable CellPhoneDB communication spine on single-cell AnnData: verify the expression matrix and cell-type annotations, run ov.single.run_cellphonedb_v5(...), convert the results into the visualization-ready interaction AnnData, then optionally continue into aggregated network plots, pathway summaries, ligand-receptor contribution views, bubble plots, chord diagrams, and signaling-role analysis through ov.pl.CellChatViz(...). Keep the skill centered on one processed CellPhoneDB result object rather than on the tutorial dataset.

Quick Workflow

1. Inspect the input AnnData, especially the cell-type column, gene-symbol convention, and whether the matrix looks compatible with CellPhoneDB.
2. Ensure the CellPhoneDB database archive is available or let the wrapper download it automatically.
3. Run ov.single.run_cellphonedb_v5(...) with explicit filtering, permutation, and output settings.
4. Treat the returned cpdb_results dict and adata_cpdb object as the shared handoff point for all downstream visualization branches.
5. Initialize viz = ov.pl.CellChatViz(adata_cpdb, palette=...).
6. Choose the downstream branch the user actually asked for: aggregated network, pathway-level aggregation, ligand-receptor extraction, bubble/chord views, or signaling-role analysis.
7. Validate the expected layers, sender/receiver annotations, and pathway metadata before trusting any plot.

Interface Summary

• ov.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='|', **kwargs) runs CellPhoneDB statistical analysis and returns both the raw result dict and a visualization-ready interaction AnnData.
• The wrapper filters cell types by min_cell_fraction, then runs scanpy filtering with min_genes and min_cells before invoking CellPhoneDB.
• ov.pl.CellChatViz(adata_cpdb, palette=None) initializes the CellChat-style visualization object for the processed communication result.
• compute_aggregated_network(pvalue_threshold=0.05, use_means=True) returns interaction-count and interaction-weight matrices for sender-receiver cell types.
• compute_pathway_communication(method='mean', min_lr_pairs=1, min_expression=0.1) is a real branch point with aggregation options mean, sum, max, and median.
• get_significant_pathways_v2(pathway_communication=None, strength_threshold=0.1, pvalue_threshold=0.05, min_significant_pairs=1) summarizes and ranks pathway-level communication.
• netVisual_aggregate(signaling, layout='circle', ...) branches on layout='circle' or layout='hierarchy'.
• netVisual_chord_cell(signaling=None, group_celltype=None, sources=None, targets=None, ..., normalize_to_sender=True) branches across pathway selection, sender/receiver filtering, optional grouping, and arc normalization.
• extractEnrichedLR(signaling, pvalue_threshold=0.05, mean_threshold=0.1, min_cell_pairs=1, geneLR_return=False) returns pathway-contributing ligand-receptor pairs.
• netVisual_bubble_marsilea(..., signaling=None, sources_use=None, targets_use=None, group_pathways=True, transpose=False, scale=None, ...) branches on pathway grouping, sender/receiver filters, transposition, and scaling mode.
• netAnalysis_computeCentrality(signaling=None, pvalue_threshold=0.05, use_weight=True) computes sender/receiver/mediator-style centrality summaries.
• netAnalysis_signalingRole_heatmap(pattern='outgoing', signaling=None, row_scale=True, ..., min_threshold=0.1) branches on pattern='outgoing' or pattern='incoming'.

Boundary

• Keep this as one skill because the notebook contains one tight communication-analysis job with multiple downstream views on the same adata_cpdb result.
• Do not split aggregated-network, pathway, bubble, chord, and signaling-role analysis into separate skills by default, because they all require the same processed CellPhoneDB interaction object and are weak on their own without it.
• Split only when the user already has a valid CellPhoneDB visualization AnnData and explicitly wants a visualization-only helper without rerunning analysis.
• Do not absorb unrelated preprocessing, annotation, or trajectory workflows here.

Branch Selection

• Use min_cell_fraction to exclude rare cell types before CellPhoneDB runs; increase it when noisy small groups are diluting the interaction graph.
• Use iterations high enough for a valid CellPhoneDB statistical run. Very small values can fail in the underlying CellPhoneDB implementation; a bounded smoke path should still keep permutations in a valid range.
• Use cleanup_temp=True for the normal path; switch it off only when you need to inspect temporary input files.
• Use debug=True only when you intentionally want CellPhoneDB intermediate tables.
• Use method='mean' in compute_pathway_communication for the notebook-style pathway summary; switch to sum, max, or median only when you intentionally want a different pathway aggregation rule.
• Use layout='circle' in netVisual_aggregate for the notebook-style summary view; use layout='hierarchy' only when sender/receiver partitioning is the main question.
• Use signaling=None to summarize all pathways, or a string/list of pathways when you want pathway-specific views.
• Use sources and targets in chord views, or sources_use and targets_use in bubble views, when the user wants a sender- or receiver-focused slice.
• Use group_celltype in chord views only when several cell types should collapse into a higher-level group.
• Use scale='row', scale='column', scale='row_minmax', or scale='column_minmax' in the bubble view only when the user explicitly wants normalized visual comparison instead of raw communication strength.
• Use pattern='outgoing' to study sender roles and pattern='incoming' to study receiver roles in signaling-role heatmaps.

Input Contract

• Start from an annotated AnnData with a valid cell-type column.
• Prefer human gene symbols for CellPhoneDB analysis, because CellPhoneDB is built around human ligand-receptor resources.
• Ensure the expression matrix is compatible with CellPhoneDB; the tutorial path uses log-normalized values and explicitly avoids scaled data.
• Expect the visualization-ready output object to store means and pvalues as layers and sender and receiver as observation metadata.
• Expect pathway-aware downstream methods to rely on interaction classification metadata in the variable table.

Minimal Execution Patterns

import omicverse as ov

cpdb_results, adata_cpdb = ov.single.run_cellphonedb_v5(
    adata,
    cpdb_file_path=cpdb_db,
    celltype_key="cell_type",
    iterations=1000,
    pvalue=0.05,
)

viz = ov.pl.CellChatViz(adata_cpdb, palette=palette)
count_matrix, weight_matrix = viz.compute_aggregated_network(
    pvalue_threshold=0.05,
    use_means=True,
)

pathway_comm = viz.compute_pathway_communication(
    method="mean",
    min_lr_pairs=2,
    min_expression=0.1,
)
sig_pathways, pathway_summary = viz.get_significant_pathways_v2(
    pathway_comm,
    strength_threshold=0.1,
    pvalue_threshold=0.05,
    min_significant_pairs=1,
)
fig, ax = viz.netVisual_aggregate(
    signaling=sig_pathways[:1],
    layout="circle",
)

enriched_lr = viz.extractEnrichedLR(
    signaling=["Signaling by Fibroblast growth factor"],
    pvalue_threshold=0.05,
    mean_threshold=0.1,
)
h = viz.netVisual_bubble_marsilea(
    sources_use=None,
    targets_use=None,
    signaling=["Signaling by Fibroblast growth factor"],
    scale=None,
)
centrality_scores = viz.netAnalysis_computeCentrality(
    signaling=None,
    pvalue_threshold=0.05,
    use_weight=True,
)

Validation

• Check that the cell-type column exists before calling ov.single.run_cellphonedb_v5(...).
• Check that the returned cpdb_results includes at least means and pvalues.
• Check that adata_cpdb.layers contains means and pvalues.
• Check that adata_cpdb.obs contains sender and receiver.
• Check that pathway-aware analyses have interaction classification metadata in adata_cpdb.var.
• If compute_pathway_communication(...) returns no pathways, inspect whether filtering thresholds removed too many interactions.
• If the user requests pathway-specific plots, confirm that the requested pathway names actually exist before plotting.
• If you only validated a bounded local smoke path, say so explicitly and do not claim a full publication-scale reproduction.

Resource Map

• Read the branch-selection reference when choosing CellPhoneDB filtering, pathway aggregation, bubble scaling, or signaling-role branches.
• Read the source-grounding reference before extending the skill with more interface-specific claims.
• Read the notebook-map reference when deciding whether a future communication notebook belongs here or should become a downstream-only visualization skill.
• Read the compatibility reference when CellPhoneDB permutation settings, pathway significance thresholds, or optional plotting dependencies matter.