omicverse.pl.ccc_stat_plot

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omicverse.pl.ccc_stat_plot#

omicverse.pl.ccc_stat_plot(adata, *, plot_type='bar', comparison_adata=None, source_adata=None, source_groupby=None, display_by='aggregation', sender_use=None, receiver_use=None, signaling=None, interaction_use=None, pair_lr_use=None, result_uns_key='liana_res', score_key='specificity_rank', pvalue_key='specificity_rank', inverse_score=True, inverse_pvalue=False, classification=None, classification_reference='cellchat', classification_fallback='family', pvalue_threshold=0.05, group_by='interaction', compare_by='overall', measure='weight', pattern='all', idents_use=None, facet_by=None, value='sum', top_n=20, min_receiver_flow=0.0, pathway_method='mean', min_lr_pairs=1, min_expression=0.1, strength_threshold=0.5, min_significant_pairs=1, palette=None, measures=None, cmap='RdYlBu_r', figsize=(8, 5), title=None, verbose=True, show=False, save=False)[source]#

Plot communication summaries, distributions, and pathway statistics.

Parameters:

  • adata (anndata.AnnData) – Communication AnnData produced by the OmicVerse CCC workflow, or a regular AnnData containing a LIANA result table in adata.uns[result_uns_key]. LIANA inputs are adapted internally to the communication format expected by ccc_*.

  • plot_type (str, default="bar") – Summary view to render. Supported values include bar plots, sankey diagrams, score distributions, signaling role analyses, pathway summaries, ligand-receptor contribution plots, differential comparisons, and pathway gene-expression summaries.

  • comparison_adata (anndata.AnnData or None, default=None) – Second communication AnnData used by comparison-style summary plots.

  • source_adata (anndata.AnnData or None, default=None) – Expression AnnData used by plot_type='gene' to summarize pathway gene expression across groups.

  • source_groupby (str or None, default=None) – Observation column in source_adata.obs used to group cells before plotting gene-expression summaries.

  • display_by ({"aggregation", "interaction"}, default="aggregation") – Whether to summarize results at the signaling/pathway level or at the interaction level.

  • sender_use (str, sequence of str, or None, default=None) – Optional sender cell types retained in sender-aware summary plots.

  • receiver_use (str, sequence of str, or None, default=None) – Optional receiver cell types retained in receiver-aware summary plots.

  • signaling (str, sequence of str, or None, default=None) – Signaling pathway name or names to visualize.

  • interaction_use (str, sequence of str, or None, default=None) – Interaction names used to restrict interaction-level statistics.

  • pair_lr_use (str, sequence of str, or None, default=None) – Ligand-receptor pair identifiers used by pair-specific statistics.

  • result_uns_key (str, default="liana_res") – adata.uns key searched when adata is not already a communication AnnData.

  • score_key (str, default="specificity_rank") – Columns used when auto-converting LIANA results.

  • pvalue_key (str, default="specificity_rank") – Columns used when auto-converting LIANA results.

  • inverse_score (bool, default=(True, False)) – Whether the LIANA score or p-value columns should be inverted during automatic conversion.

  • inverse_pvalue (bool, default=(True, False)) – Whether the LIANA score or p-value columns should be inverted during automatic conversion.

  • classification (str, mapping, or None, default=None) – Optional LIANA classification override used only during automatic conversion.

  • classification_reference (str, pandas.DataFrame, or None, default="cellchat") – Reference used to backfill pathway labels during automatic LIANA conversion.

  • classification_fallback (str or None, default="family") – Fallback pathway label strategy used during automatic LIANA conversion.

  • pvalue_threshold (float, default=0.05) – Maximum p-value retained as a significant communication event.

  • group_by ({"interaction", "classification", "pair", "sender", "receiver"}, default="interaction") – Category used to group communication events in bar, box, violin, or contribution summaries.

  • compare_by ({"overall", "celltype"}, default="overall") – Comparison mode used by summary plots that contrast communication patterns across cell types or globally.

  • measure ({"weight", "count"}, default="weight") – Communication quantity summarized by applicable statistical plots.

  • pattern ({"outgoing", "incoming", "all"}, default="all") – Signaling role direction used by role-based summaries.

  • idents_use (str, sequence of str, or None, default=None) – Optional subset of identities retained in role-change or comparison plots.

  • facet_by ({"sender", "receiver"} or None, default=None) – Split compatible plots by sender or receiver.

  • value ({"sum", "mean", "max", "count"}, default="sum") – Aggregation statistic used to summarize communication strengths before plotting.

  • top_n (int, default=20) – Number of top pathways, interactions, or pairs retained in ranked summaries.

  • min_receiver_flow (float, default=0.0) – Minimum total flow required for a receiver node to be retained in Sankey plots. This is mainly useful for plot_type='sankey', display_by='interaction' when many tiny receiver nodes make the right side unreadable.

  • pathway_method (str, default="mean") – Method used to summarize multiple ligand-receptor pairs into pathway level scores.

  • min_lr_pairs (int, default=1) – Minimum number of ligand-receptor pairs required for a pathway to be retained in pathway summaries.

  • min_expression (float, default=0.1) – Minimum grouped expression threshold used by pathway-level summaries.

  • strength_threshold (float, default=0.5) – Minimum pathway strength retained in pathway summary statistics.

  • min_significant_pairs (int, default=1) – Minimum number of significant ligand-receptor pairs required for a pathway to be highlighted.

  • palette (mapping, sequence, or None, default=None) – Color palette used for cell types, pathways, or groups.

  • measures (sequence of str or None, default=None) – Role-network measures to display, such as outgoing or incoming centrality summaries.

  • cmap (str, default="RdYlBu_r") – Colormap used by heatmap-like statistical summaries.

  • figsize (tuple of float, default=(8, 5)) – Figure size in inches.

  • title (str or None, default=None) – Custom title for the generated figure. When omitted, a plot-specific default title is used.

  • verbose (bool, default=True) – Whether pathway-summary style plots should print progress messages and summary tables. This currently affects plot_type='pathway_summary'.

  • show (bool, default=False) – Whether to immediately display the figure.

  • save (str or bool, default=False) – File path for saving the figure, or False to skip saving.

Returns:

A (fig, ax) tuple containing the Matplotlib figure and the main axes used for the rendered statistical summary.

Return type:

tuple

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