spac package
Submodules
- spac.data_utils module
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()select_values()subtract_min_per_region()subtract_min_quantile()summarize_dataframe()- Functions
- 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
- spac.phenotyping module
- spac.spatial_analysis module
- spac.transformations module
apply_per_batch()arcsinh_transformation()arcsinh_transformation_core()batch_normalize()get_cluster_info()knn_clustering()normalize_features()normalize_features_core()phenograph_clustering()rename_annotations()run_umap()run_utag_clustering()tsne()z_score_normalization()- Functions
- 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
- spac.utag_functions module
- spac.utils module
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()spell_out_special_characters()text_to_others()- Functions
- spac.visualization module
boxplot()boxplot_interactive()dimensionality_reduction_plot()heatmap()hierarchical_heatmap()histogram()interactive_spatial_plot()plot_ripley_l()present_summary_as_figure()present_summary_as_html()relational_heatmap()sankey_plot()spatial_plot()threshold_heatmap()tsne_plot()visualize_2D_scatter()visualize_nearest_neighbor()- Functions
- 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