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mosaicMPI 2.7.2 documentation - Home mosaicMPI 2.7.2 documentation - Home
  • Home
  • Tutorials
    • Getting started with MosaicMPI
    • Command-line interface and workflow
    • Customizing the config.toml file
    • Guidelines for multi-resolution factorization
  • API
    • mosaicmpi.Dataset
      • mosaicmpi.Dataset.has_cnmf_results
      • mosaicmpi.Dataset.hvf
      • mosaicmpi.Dataset.hvf_stats
      • mosaicmpi.Dataset.is_imputed
      • mosaicmpi.Dataset.is_normalized
      • mosaicmpi.Dataset.mosaicmpi_version
      • mosaicmpi.Dataset.patient_id_col
      • mosaicmpi.Dataset.add_cnmf_results
      • mosaicmpi.Dataset.append_to_history
      • mosaicmpi.Dataset.calculate_cnmf_prediction_error
      • mosaicmpi.Dataset.cross_validate_imputation
      • mosaicmpi.Dataset.from_anndata
      • mosaicmpi.Dataset.from_df
      • mosaicmpi.Dataset.from_h5ad
      • mosaicmpi.Dataset.get_approximation
      • mosaicmpi.Dataset.get_category_overrepresentation
      • mosaicmpi.Dataset.get_history
      • mosaicmpi.Dataset.get_metadata_correlation
      • mosaicmpi.Dataset.get_metadata_df
      • mosaicmpi.Dataset.get_printable_metadata_type_summary
      • mosaicmpi.Dataset.get_programs
      • mosaicmpi.Dataset.get_usages
      • mosaicmpi.Dataset.impute_knn
      • mosaicmpi.Dataset.impute_zeros
      • mosaicmpi.Dataset.initialize_cnmf
      • mosaicmpi.Dataset.map_gene_ids
      • mosaicmpi.Dataset.remove_cnmf_results
      • mosaicmpi.Dataset.remove_unfactorizable_features
      • mosaicmpi.Dataset.remove_unfactorizable_observations
      • mosaicmpi.Dataset.select_hvf
      • mosaicmpi.Dataset.select_hvf_cnmf
      • mosaicmpi.Dataset.select_hvf_stdeconvolve
      • mosaicmpi.Dataset.to_df
      • mosaicmpi.Dataset.update_obs
      • mosaicmpi.Dataset.validate_cnmf_prediction_errors
      • mosaicmpi.Dataset.validate_feature_stats
      • mosaicmpi.Dataset.write_h5ad
    • mosaicmpi.Integration
      • mosaicmpi.Integration.n_datasets
      • mosaicmpi.Integration.sample_to_patient
      • mosaicmpi.Integration.selected_k
      • mosaicmpi.Integration.compute_corr
      • mosaicmpi.Integration.compute_pairwise_thresholds
      • mosaicmpi.Integration.filter_programs_rank_reduction
      • mosaicmpi.Integration.get_category_overrepresentation
      • mosaicmpi.Integration.get_corr_matrix_lowertriangle
      • mosaicmpi.Integration.get_features_overlap_table
      • mosaicmpi.Integration.get_hvf_overlap_table
      • mosaicmpi.Integration.get_metadata_correlation
      • mosaicmpi.Integration.get_metadata_df
      • mosaicmpi.Integration.get_node_table
      • mosaicmpi.Integration.get_programs
      • mosaicmpi.Integration.get_usages
      • mosaicmpi.Integration.select_k_values
    • mosaicmpi.Network
      • mosaicmpi.Network.n_communities
      • mosaicmpi.Network.node_to_community
      • mosaicmpi.Network.ordered_community_names
      • mosaicmpi.Network.programs_in_graph
      • mosaicmpi.Network.add_community_weights_to_graph
      • mosaicmpi.Network.community_search
      • mosaicmpi.Network.compute_community_network_layout
      • mosaicmpi.Network.compute_layout
      • mosaicmpi.Network.consensus
      • mosaicmpi.Network.count_intracommunity_edges
      • mosaicmpi.Network.create_community_network
      • mosaicmpi.Network.create_program_network
      • mosaicmpi.Network.from_pkl
      • mosaicmpi.Network.get_community_category_overrepresentation
      • mosaicmpi.Network.get_community_metadata_correlation
      • mosaicmpi.Network.get_community_usage
      • mosaicmpi.Network.get_lowest_rank_programs
      • mosaicmpi.Network.get_max_corr_communities
      • mosaicmpi.Network.get_node_table
      • mosaicmpi.Network.get_representative_program_ids
      • mosaicmpi.Network.get_representative_programs
      • mosaicmpi.Network.get_sample_entropy
      • mosaicmpi.Network.get_selected_rank_program_ids
      • mosaicmpi.Network.get_vectorized_community_sort_key
      • mosaicmpi.Network.most_correlated_edge_between_datasets
      • mosaicmpi.Network.prune_communities
      • mosaicmpi.Network.read_communities_from_toml
      • mosaicmpi.Network.to_pkl
      • mosaicmpi.Network.transfer_labels
      • mosaicmpi.Network.write_communities_toml
      • mosaicmpi.Network.write_community_network_graphml
      • mosaicmpi.Network.write_program_network_graphml
    • mosaicmpi.Colors
      • mosaicmpi.Colors.ordered_community_names
      • mosaicmpi.Colors.add_missing_community_colors
      • mosaicmpi.Colors.add_missing_dataset_colors
      • mosaicmpi.Colors.add_missing_metadata_colors
      • mosaicmpi.Colors.from_config
      • mosaicmpi.Colors.from_dataset
      • mosaicmpi.Colors.from_integration
      • mosaicmpi.Colors.from_named_datasets
      • mosaicmpi.Colors.from_network
      • mosaicmpi.Colors.from_toml
      • mosaicmpi.Colors.get_metadata_colors
      • mosaicmpi.Colors.plot_community_colors_legend
      • mosaicmpi.Colors.plot_dataset_colors_legend
      • mosaicmpi.Colors.plot_metadata_colors_legend
      • mosaicmpi.Colors.reset_community_colors
      • mosaicmpi.Colors.to_toml
    • mosaicmpi.plots
      • mosaicmpi.plots.annotated_heatmap
      • mosaicmpi.plots.draw_circle_bar_plot
      • mosaicmpi.plots.draw_circle_bar_scale
      • mosaicmpi.plots.plot_community_contribution
      • mosaicmpi.plots.plot_community_network_summary
      • mosaicmpi.plots.plot_community_usage_heatmap
      • mosaicmpi.plots.plot_community_usage_per_sample
      • mosaicmpi.plots.plot_compare_integrations
      • mosaicmpi.plots.plot_feature_mean_variance
      • mosaicmpi.plots.plot_feature_missingness
      • mosaicmpi.plots.plot_feature_statistic_histogram
      • mosaicmpi.plots.plot_features_upset
      • mosaicmpi.plots.plot_geneset_heatmap
      • mosaicmpi.plots.plot_integration_hvf_upset
      • mosaicmpi.plots.plot_metadata_correlation_community_bar
      • mosaicmpi.plots.plot_metadata_correlation_community_network
      • mosaicmpi.plots.plot_metadata_correlation_program_bar
      • mosaicmpi.plots.plot_metadata_correlation_program_network
      • mosaicmpi.plots.plot_metadata_transfer
      • mosaicmpi.plots.plot_overrepresentation_community_bar
      • mosaicmpi.plots.plot_overrepresentation_community_heatmap
      • mosaicmpi.plots.plot_overrepresentation_community_network
      • mosaicmpi.plots.plot_overrepresentation_program_bar
      • mosaicmpi.plots.plot_overrepresentation_program_network
      • mosaicmpi.plots.plot_pairwise_corr
      • mosaicmpi.plots.plot_pairwise_corr_overlaid
      • mosaicmpi.plots.plot_program_correlation_matrix
      • mosaicmpi.plots.plot_program_network_communities
      • mosaicmpi.plots.plot_program_network_datasets
      • mosaicmpi.plots.plot_program_network_npatients
      • mosaicmpi.plots.plot_program_network_nsamples
      • mosaicmpi.plots.plot_rank_reduction
      • mosaicmpi.plots.plot_representative_program_nes
      • mosaicmpi.plots.plot_sample_entropy
      • mosaicmpi.plots.plot_sample_numbers
      • mosaicmpi.plots.plot_stability_error
      • mosaicmpi.plots.plot_stratified_hvf_upset
      • mosaicmpi.plots.plot_usage_heatmap
    • mosaicmpi
      • mosaicmpi.biomart
        • mosaicmpi.biomart.BiomartAttribute
        • mosaicmpi.biomart.BiomartAttributePage
        • mosaicmpi.biomart.BiomartDatabase
        • mosaicmpi.biomart.BiomartDataset
        • mosaicmpi.biomart.BiomartFilter
        • mosaicmpi.biomart.BiomartServer
      • mosaicmpi.cli
        • mosaicmpi.cli.post_cli
      • mosaicmpi.cnmf
        • mosaicmpi.cnmf.fast_ols_all_cols
        • mosaicmpi.cnmf.get_highvar_genes
        • mosaicmpi.cnmf.get_highvar_genes_sparse
        • mosaicmpi.cnmf.cNMF
      • mosaicmpi.colors
        • mosaicmpi.colors.Colors
      • mosaicmpi.config
        • mosaicmpi.config.recursive_update
        • mosaicmpi.config.Config
      • mosaicmpi.dataset
        • mosaicmpi.dataset.Dataset
      • mosaicmpi.genesets
        • mosaicmpi.genesets.order_genesets
        • mosaicmpi.genesets.program_gprofiler
        • mosaicmpi.genesets.program_ssgsea
      • mosaicmpi.integration
        • mosaicmpi.integration.Integration
      • mosaicmpi.nancorrmp
        • mosaicmpi.nancorrmp.NaNCorrMp
      • mosaicmpi.network
        • mosaicmpi.network.compare_community_jaccard_similarity
        • mosaicmpi.network.Network
      • mosaicmpi.orphan
      • mosaicmpi.plots
        • mosaicmpi.plots.annotated_heatmap
        • mosaicmpi.plots.draw_circle_bar_plot
        • mosaicmpi.plots.draw_circle_bar_scale
        • mosaicmpi.plots.plot_community_contribution
        • mosaicmpi.plots.plot_community_network_summary
        • mosaicmpi.plots.plot_community_usage_heatmap
        • mosaicmpi.plots.plot_community_usage_per_sample
        • mosaicmpi.plots.plot_compare_integrations
        • mosaicmpi.plots.plot_feature_mean_variance
        • mosaicmpi.plots.plot_feature_missingness
        • mosaicmpi.plots.plot_feature_statistic_histogram
        • mosaicmpi.plots.plot_features_upset
        • mosaicmpi.plots.plot_geneset_heatmap
        • mosaicmpi.plots.plot_integration_hvf_upset
        • mosaicmpi.plots.plot_metadata_correlation_community_bar
        • mosaicmpi.plots.plot_metadata_correlation_community_network
        • mosaicmpi.plots.plot_metadata_correlation_program_bar
        • mosaicmpi.plots.plot_metadata_correlation_program_network
        • mosaicmpi.plots.plot_metadata_transfer
        • mosaicmpi.plots.plot_overrepresentation_community_bar
        • mosaicmpi.plots.plot_overrepresentation_community_heatmap
        • mosaicmpi.plots.plot_overrepresentation_community_network
        • mosaicmpi.plots.plot_overrepresentation_program_bar
        • mosaicmpi.plots.plot_overrepresentation_program_network
        • mosaicmpi.plots.plot_pairwise_corr
        • mosaicmpi.plots.plot_pairwise_corr_overlaid
        • mosaicmpi.plots.plot_program_correlation_matrix
        • mosaicmpi.plots.plot_program_network_communities
        • mosaicmpi.plots.plot_program_network_datasets
        • mosaicmpi.plots.plot_program_network_npatients
        • mosaicmpi.plots.plot_program_network_nsamples
        • mosaicmpi.plots.plot_rank_reduction
        • mosaicmpi.plots.plot_representative_program_nes
        • mosaicmpi.plots.plot_sample_entropy
        • mosaicmpi.plots.plot_sample_numbers
        • mosaicmpi.plots.plot_stability_error
        • mosaicmpi.plots.plot_stratified_hvf_upset
        • mosaicmpi.plots.plot_usage_heatmap
      • mosaicmpi.utils
        • mosaicmpi.utils.get_adjusted_dpi
        • mosaicmpi.utils.load_df_from_npz
        • mosaicmpi.utils.newline_wrap
        • mosaicmpi.utils.node_to_program
        • mosaicmpi.utils.program_to_node
        • mosaicmpi.utils.save_df_to_npz
        • mosaicmpi.utils.save_df_to_text
        • mosaicmpi.utils.save_fig
        • mosaicmpi.utils.start_logging
  • Module Index
  • .rst

mosaicmpi

mosaicmpi#

Modules

mosaicmpi.biomart

mosaicmpi.cli

mosaicmpi.cnmf

mosaicmpi.colors

mosaicmpi.config

mosaicmpi.dataset

mosaicmpi.genesets

mosaicmpi.integration

mosaicmpi.nancorrmp

mosaicmpi.network

mosaicmpi.orphan

mosaicmpi.plots

mosaicmpi.utils

previous

mosaicmpi.plots.plot_usage_heatmap

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mosaicmpi.biomart

By Theodore Verhey

© Copyright 2023, Theodore Verhey.