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MuVIcell

From cell-type stratified features to multicellular coordinated programs

API Reference

This document provides a comprehensive reference for the MuVIcell package API.

Data Module (muvicell.data)

Functions

  • load_muon_data(path) - Load muon data from file
  • save_muon_data(mdata, path) - Save muon data to file

Preprocessing Module (muvicell.preprocessing)

Functions

  • normalize_views(mdata, ...) - Normalize data in each view
  • filter_views(mdata, ...) - Filter cells and genes
  • find_highly_variable_genes(mdata, ...) - Find HVGs
  • subset_to_hvg(mdata, ...) - Subset to HVGs
  • preprocess_for_muvi(mdata, ...) - Complete preprocessing pipeline

Analysis Module (muvicell.analysis)

Functions

  • muvi_reconstruction_info(model, mdata, ...) - Assess reconstruction performance
  • muvi_variance_by_view_info(model, ...) - Analyze variance explained
  • muvi_featureclass_variance_info(model, mdata, ...) - Variance by feature class
  • muvi_variable_loadings_info(model, mdata, ...) - Extract variable load
  • muvi_selected_features_info(variable_loadings, ...) - Get feature loadings
  • muvi_factor_scores_info(model, mdata, ...) - Get factor scores with metadata
  • muvi_kruskal_info(scores_df, ...) - Kruskal-Wallis test for categorical variables
  • muvi_kendall_info(scores_df, ...) - Kendall's tau for ordinal variables
  • muvi_confidence_ellipses_info(scores_df, ...) - Confidence for factor pairs
  • muvi_top_features_by_view_info(variable_loadings, ...) - Top features by view
  • muvi_top_features_by_class_info(variable_loadings, ...) - Top features by class
  • muvi_build_selected_anndata(mdata, selection_df, ...) - Export to AnnData

Visualization Module (MuVIcell.visualization)

Functions

  • muvi_reconstruction_plot(stats_df, ...) - Plot reconstruction performance
  • muvi_variance_by_view_plot(df, ...) - Plot variance explained by view
  • muvi_featureclass_variance_plot(df, ...) - Plot variance by feature class
  • muvi_plot_top_loadings_heatmap(variable_loadings, ...) - Heatmap of top loadings
  • muvi_selected_features_plot(df_long, ...) - Plot selected feature loadings
  • muvi_violin_plot(scores_df, ...) - Violin plots of factor scores
  • muvi_confidence_ellipses_plot(scores_df, ellipses_df, ...) - Plot confidence

Synthetic Module (MuVIcell.synthetic)

Functions

  • generate_synthetic_data(...) - Generate synthetic multi-view data
  • add_latent_structure(mdata, ...) - Add latent factor structure
  • generate_batch_effects(mdata, ...) - Add batch effects
  • simulate_missing_data(mdata, ...) - Simulate missing data

For detailed parameter descriptions and examples, see the function docstrings and tutorial notebook.