Index

_

_f_g_function() (in module spac._ripley) _l_function() (in module spac._ripley) _l_multiple_function() (in module spac._ripley) _neighborhood_profile_core() (in module spac.spatial_analysis) _parallel_message_pass() (in module spac.utag_functions) _plot_spatial_distance_dispatch() (in module spac.visualization)

_ppp() (in module spac._ripley) _prepare_spatial_distance_data() (in module spac.visualization) _reshape_res() (in module spac._ripley) _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] add_probabilities_to_centroid() (in module spac.utag_functions), [1] add_rescaled_features() (in module spac.data_utils), [1] annotation_category_relations() (in module spac.utils), [1] append_annotation() (in module spac.data_utils), [1]

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

B

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

bin2cat() (in module spac.data_utils), [1] boxplot() (in module spac.visualization), [1]

C

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

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

D

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

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

G

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

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

H

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

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

I

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

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

L

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

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

M

module spac spac.data_utils spac.phenotyping spac.spatial_analysis spac.transformations spac.utag_functions spac.utils spac.visualization

N

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

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

P

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

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

R

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

ripley() (in module spac._ripley) ripley_l() (in module spac.spatial_analysis), [1] run_umap() (in module spac.transformations), [1] run_utag_clustering() (in module spac.transformations), [1]

S

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

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

T

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

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

U

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

V

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

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

Z

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

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