Index

_

_css_rgb_or_hex_to_hex() (in module spac.visualization) _neighborhood_profile_core() (in module spac.spatial_analysis) _ordered_unique_figs() (in module spac.visualization) _parallel_message_pass() (in module spac.utag_functions) _plot_spatial_distance_dispatch() (in module spac.visualization)

_prepare_spatial_distance_data() (in module spac.visualization) _select_input_features() (in module spac.transformations) _select_values_anndata() (in module spac.data_utils) _select_values_dataframe() (in module spac.data_utils) _validate_transformation_inputs() (in module spac.transformations)

A

add_pin_color_rules() (in module spac.data_utils), [1], [2] add_probabilities_to_centroid() (in module spac.utag_functions), [1], [2] add_rescaled_features() (in module spac.data_utils), [1], [2] annotation_category_relations() (in module spac.utils), [1], [2] append_annotation() (in module spac.data_utils), [1], [2]

apply_per_batch() (in module spac.transformations), [1], [2] apply_phenotypes() (in module spac.phenotyping), [1], [2] arcsinh_transformation() (in module spac.transformations), [1], [2] arcsinh_transformation_core() (in module spac.transformations), [1], [2] assign_manual_phenotypes() (in module spac.phenotyping), [1], [2]

B

batch_normalize() (in module spac.transformations), [1], [2] bin2cat() (in module spac.data_utils), [1], [2]

boxplot() (in module spac.visualization), [1], [2] boxplot_interactive() (in module spac.visualization), [1], [2]

C

calculate_centroid() (in module spac.data_utils), [1], [2] calculate_nearest_neighbor() (in module spac.spatial_analysis), [1], [2] check_annotation() (in module spac.utils), [1], [2] check_column_name() (in module spac.utils), [1], [2] check_distances() (in module spac.utils), [1], [2] check_feature() (in module spac.utils), [1], [2] check_label() (in module spac.utils), [1], [2] check_list_in_list() (in module spac.utils), [1], [2]

check_table() (in module spac.utils), [1], [2] color_mapping() (in module spac.utils), [1], [2] combine_annotations() (in module spac.data_utils), [1], [2] combine_dfs() (in module spac.data_utils), [1], [2] combine_phenotypes() (in module spac.phenotyping), [1], [2] compute_boxplot_metrics() (in module spac.utils), [1], [2] concatinate_regions() (in module spac.data_utils), [1], [2] custom_message_passing() (in module spac.utag_functions), [1], [2]

D

decode_phenotype() (in module spac.phenotyping), [1], [2]

dimensionality_reduction_plot() (in module spac.visualization), [1], [2] downsample_cells() (in module spac.data_utils), [1], [2]

G

generate_phenotypes_dict() (in module spac.phenotyping), [1], [2]

get_cluster_info() (in module spac.transformations), [1], [2] get_defined_color_map() (in module spac.utils), [1], [2]

H

heatmap() (in module spac.visualization), [1], [2]

hierarchical_heatmap() (in module spac.visualization), [1], [2] histogram() (in module spac.visualization), [1], [2]

I

ingest_cells() (in module spac.data_utils), [1], [2]

interactive_spatial_plot() (in module spac.visualization), [1], [2] is_binary_0_1() (in module spac.phenotyping), [1], [2]

K

knn_clustering() (in module spac.transformations), [1], [2]

L

load_csv_files() (in module spac.data_utils), [1], [2]

low_variance_filter() (in module spac.utag_functions), [1], [2]

M

module spac spac.data_utils, [1] spac.phenotyping, [1] spac.spatial_analysis, [1] spac.transformations, [1] spac.utag_functions, [1] spac.utils, [1] spac.visualization, [1]

N

neighborhood_profile() (in module spac.spatial_analysis), [1], [2]

normalize_features() (in module spac.transformations), [1], [2] normalize_features_core() (in module spac.transformations), [1], [2]

P

phenograph_clustering() (in module spac.transformations), [1], [2] plot_ripley_l() (in module spac.visualization), [1], [2]

present_summary_as_figure() (in module spac.visualization), [1], [2] present_summary_as_html() (in module spac.visualization), [1], [2]

R

regex_search_list() (in module spac.utils), [1], [2] relational_heatmap() (in module spac.visualization), [1], [2] rename_annotations() (in module spac.transformations), [1], [2]

rescale_features() (in module spac.data_utils), [1], [2] ripley_l() (in module spac.spatial_analysis), [1], [2] run_umap() (in module spac.transformations), [1], [2] run_utag_clustering() (in module spac.transformations), [1], [2]

S

sankey_plot() (in module spac.visualization), [1], [2] select_values() (in module spac.data_utils), [1], [2] spac module spac.data_utils module, [1] spac.phenotyping module, [1] spac.spatial_analysis module, [1] spac.transformations module, [1]

spac.utag_functions module, [1] spac.utils module, [1] spac.visualization module, [1] sparse_matrix_dstack() (in module spac.utag_functions), [1], [2] spatial_interaction() (in module spac.spatial_analysis), [1], [2] spatial_plot() (in module spac.visualization), [1], [2] spell_out_special_characters() (in module spac.utils), [1], [2] subtract_min_per_region() (in module spac.data_utils), [1], [2] subtract_min_quantile() (in module spac.data_utils), [1], [2] summarize_dataframe() (in module spac.data_utils), [1], [2]

T

text_to_others() (in module spac.utils), [1], [2] threshold_heatmap() (in module spac.visualization), [1], [2]

tsne() (in module spac.transformations), [1], [2] tsne_plot() (in module spac.visualization), [1], [2]

U

utag() (in module spac.utag_functions), [1], [2]

V

visualize_2D_scatter() (in module spac.visualization), [1], [2]

visualize_nearest_neighbor() (in module spac.visualization), [1], [2]

Z

z_score() (in module spac.utag_functions), [1], [2]

z_score_normalization() (in module spac.transformations), [1], [2]