omicverse.pl.ccc_network_plot

omicverse.pl.ccc_network_plot#

omicverse.pl.ccc_network_plot(adata, *, plot_type='circle', comparison_adata=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, value='sum', top_n=None, ligand=None, receptor=None, normalize_to_sender=True, rotate_names=True, min_interaction_threshold=0.0, node_positions=None, embedding_points=None, palette=None, ncols=None, nrows=None, figsize=(7, 7), title=None, verbose=True, show=False, save=False)[source]#

Plot cell-cell communication networks with multiple graph styles.

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="circle") – Network style to render. Supported values include aggregated circle views, pathway-filtered circle networks, interaction flow plots, bipartite ligand-receptor layouts, embedding-based networks, differential comparison networks, chord summaries, and diffusion-style visualizations.

  • comparison_adata (anndata.AnnData or None, default=None) – Second communication AnnData used by plot_type='diff_network' to compute differential edges between two conditions.

  • display_by ({"aggregation", "interaction"}, default="aggregation") – Whether to summarize networks at the signaling/pathway aggregation level or at the individual interaction level when the chosen plot_type supports both.

  • sender_use (str, sequence of str, or None, default=None) – Optional sender cell types to keep in the plot.

  • receiver_use (str, sequence of str, or None, default=None) – Optional receiver cell types to keep in the plot.

  • signaling (str, sequence of str, or None, default=None) – Signaling pathway name or names to visualize. Required by several pathway-specific network views.

  • interaction_use (str, sequence of str, or None, default=None) – Interaction names to keep when plotting interaction-level networks.

  • pair_lr_use (str, sequence of str, or None, default=None) – Ligand-receptor pair identifiers used to filter individual or interaction-focused plots.

  • 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.

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

  • top_n (int or None, default=None) – Number of top pathways, interactions, or pairs retained for plot types that rank results before drawing. Circle-style network views keep all significant edges by default; flow-style views use an internal default of 20 when top_n is omitted.

  • ligand (str or None, default=None) – Ligand name used by ligand-centric plots such as bipartite or ligand-receptor chord views.

  • receptor (str, sequence of str, or None, default=None) – Receptor name or names used by receptor-specific network views.

  • normalize_to_sender (bool, default=True) – Whether to normalize outgoing edge contributions per sender before plotting chord-style networks.

  • rotate_names (bool, default=True) – Whether to rotate node labels to follow the circle in chord-like layouts.

  • min_interaction_threshold (float, default=0.0) – Minimum edge weight shown in focused or thresholded network views.

  • node_positions (mapping, array-like, or None, default=None) – Precomputed node coordinates used by embedding_network or other layouts that require explicit positions.

  • embedding_points (array-like or None, default=None) – Optional background embedding coordinates plotted together with embedding_network edges.

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

  • ncols (int or None, default=None) – Number of subplot columns used by multi-panel network views such as individual_outgoing and individual_incoming. When omitted, a plot-specific default is used.

  • nrows (int or None, default=None) – Number of subplot rows used by multi-panel network views such as individual_outgoing and individual_incoming. When omitted, the value is inferred from ncols and the number of selected panels.

  • figsize (tuple of float, default=(7, 7)) – 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) – Reserved for method-specific progress output. Network views remain silent by default; this parameter keeps the ccc_* API uniform.

  • 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 network.

Return type:

tuple

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