spac
  • spac modules
    • add_pin_color_rules
    • add_rescaled_features
    • append_annotation
    • bin2cat
    • calculate_centroid
    • combine_annotations
    • combine_dfs
    • concatinate_regions
    • downsample_cells
    • ingest_cells
    • load_csv_files
    • rescale_features
    • spac.data_utils module
      • append_annotation
      • ingest_cells
      • concatinate_regions
      • rescale_features
      • add_rescaled_features
      • subtract_min_per_region
      • subtract_min_quantile
      • load_csv_files
      • select_values
      • _select_values_dataframe
      • _select_values_anndata
      • downsample_cells
      • calculate_centroid
      • bin2cat
      • combine_dfs
      • add_pin_color_rules
      • combine_annotations
      • summarize_dataframe
    • _select_values_anndata
    • _select_values_dataframe
    • select_values
    • subtract_min_per_region
    • subtract_min_quantile
    • summarize_dataframe
    • apply_phenotypes
    • assign_manual_phenotypes
    • combine_phenotypes
    • decode_phenotype
    • generate_phenotypes_dict
    • is_binary_0_1
    • spac.phenotyping module
      • is_binary_0_1
      • decode_phenotype
      • generate_phenotypes_dict
      • apply_phenotypes
      • combine_phenotypes
      • assign_manual_phenotypes
    • calculate_nearest_neighbor
    • _neighborhood_profile_core
    • neighborhood_profile
    • ripley_l
    • spac.spatial_analysis module
      • spatial_interaction
      • ripley_l
      • neighborhood_profile
      • _neighborhood_profile_core
      • calculate_nearest_neighbor
    • spatial_interaction
    • apply_per_batch
    • arcsinh_transformation_core
    • arcsinh_transformation
    • batch_normalize
    • get_cluster_info
    • knn_clustering
    • normalize_features_core
    • normalize_features
    • phenograph_clustering
    • rename_annotations
    • spac.transformations module
      • phenograph_clustering
      • knn_clustering
      • get_cluster_info
      • tsne
      • run_umap
      • _validate_transformation_inputs
      • _select_input_features
      • batch_normalize
      • rename_annotations
      • normalize_features
      • normalize_features_core
      • arcsinh_transformation
      • arcsinh_transformation_core
      • z_score_normalization
      • apply_per_batch
      • run_utag_clustering
    • run_umap
    • run_utag_clustering
    • _select_input_features
    • tsne
    • _validate_transformation_inputs
    • z_score_normalization
    • add_probabilities_to_centroid
    • custom_message_passing
    • low_variance_filter
    • _parallel_message_pass
    • spac.utag_functions module
      • z_score
      • sparse_matrix_dstack
      • _parallel_message_pass
      • custom_message_passing
      • low_variance_filter
      • add_probabilities_to_centroid
      • utag
    • sparse_matrix_dstack
    • utag
    • z_score
    • annotation_category_relations
    • check_annotation
    • check_column_name
    • check_distances
    • check_feature
    • check_label
    • check_list_in_list
    • check_table
    • color_mapping
    • compute_boxplot_metrics
    • get_defined_color_map
    • regex_search_list
    • spac.utils module
      • regex_search_list
      • check_list_in_list
      • check_table
      • check_annotation
      • check_feature
      • check_column_name
      • check_distances
      • text_to_others
      • annotation_category_relations
      • color_mapping
      • check_label
      • spell_out_special_characters
      • get_defined_color_map
      • compute_boxplot_metrics
    • spell_out_special_characters
    • text_to_others
    • boxplot_interactive
    • boxplot
    • _css_rgb_or_hex_to_hex
    • dimensionality_reduction_plot
    • heatmap
    • hierarchical_heatmap
    • histogram
    • interactive_spatial_plot
    • _ordered_unique_figs
    • plot_ripley_l
    • _plot_spatial_distance_dispatch
    • _prepare_spatial_distance_data
    • present_summary_as_figure
    • present_summary_as_html
    • relational_heatmap
    • spac.visualization module
      • visualize_2D_scatter
      • dimensionality_reduction_plot
      • tsne_plot
      • histogram
      • heatmap
      • hierarchical_heatmap
      • threshold_heatmap
      • spatial_plot
      • boxplot
      • boxplot_interactive
      • interactive_spatial_plot
      • sankey_plot
      • relational_heatmap
      • plot_ripley_l
      • _prepare_spatial_distance_data
      • _plot_spatial_distance_dispatch
      • _css_rgb_or_hex_to_hex
      • _ordered_unique_figs
      • visualize_nearest_neighbor
      • present_summary_as_html
      • present_summary_as_figure
    • sankey_plot
    • spatial_plot
    • threshold_heatmap
    • tsne_plot
    • visualize_2D_scatter
    • visualize_nearest_neighbor
spac
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