spac modules
============

.. toctree::
   :maxdepth: 1

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