Index

_

__init__() (BaseGraphBuilder method) (ContactGraphBuilder method) (Interactions method) (KNNGraphBuilder method) (RadiusGraphBuilder method) (RipleysK method)

A

abundance() (in module athena.metrics.heterogeneity.metrics) add2uns() (in module athena.neighborhood.estimators) arcsinh() (in module athena.preprocessing.preprocess) athena module athena.dataset module athena.dataset.datasets module athena.graph_builder module athena.graph_builder.base_graph_builder module athena.graph_builder.constants module athena.graph_builder.contact_graph_builder module athena.graph_builder.graphBuilder module athena.graph_builder.knn_graph_builder module athena.graph_builder.mappings module athena.graph_builder.radius_graph_builder module athena.metrics module athena.metrics.graph module athena.metrics.graph.graph module athena.metrics.heterogeneity module athena.metrics.heterogeneity.base_metrics module athena.metrics.heterogeneity.metrics module

athena.metrics.utils module athena.neighborhood module athena.neighborhood.base_estimators module athena.neighborhood.estimators module athena.neighborhood.utils module athena.plotting module athena.plotting.utils module athena.plotting.visualization module athena.preprocessing module athena.preprocessing.preprocess module athena.utils module athena.utils.docs module athena.utils.docs.default_docs module athena.utils.general module athena.utils.tools module athena.utils.tools.graph module athena.utils.tools.image module athena.utils.tools.metric module

B

BaseGraphBuilder (class in athena.graph_builder.base_graph_builder)

build_graph() (in module athena.graph_builder.graphBuilder)

C

colormap() (in module athena.plotting.utils) compute_metrics() (in module athena.utils.tools.metric)

ContactGraphBuilder (class in athena.graph_builder.contact_graph_builder) csr_deviation() (RipleysK method)

D

ddoc() (in module athena.utils.docs.default_docs)

df2node_attr() (in module athena.utils.tools.graph) dilation() (in module athena.graph_builder.contact_graph_builder)

E

extract_centroids() (in module athena.preprocessing.preprocess) extract_mask_expr_feat() (in module athena.utils.tools.image)

extract_mask_morph_feat() (in module athena.utils.tools.image) extract_metric_results() (in module athena.utils.tools.metric)

F

fit() (Interactions method) (RipleysK method)

from_mask() (BaseGraphBuilder class method)

G

generate_h0() (Interactions method) get_cmap() (in module athena.plotting.visualization) get_edge_interactions() (in module athena.neighborhood.utils) get_group_feature() (in module athena.utils.tools.metric)

get_interaction_score() (in module athena.neighborhood.utils) get_layout() (in module athena.plotting.utils) get_node_interactions() (in module athena.neighborhood.utils) get_shape_outline() (in module athena.utils.tools.image)

H

hill_number() (in module athena.metrics.heterogeneity.metrics)

I

imc() (in module athena.dataset.datasets) imc_quickstart() (in module athena.dataset.datasets) imc_sample() (in module athena.dataset.datasets) infiltration() (in module athena.neighborhood.estimators) (in module athena.plotting.visualization) Interactions (class in athena.neighborhood.base_estimators)

interactions() (in module athena.neighborhood.estimators) (in module athena.plotting.visualization) is_categorical() (in module athena.utils.general) is_fitted() (in module athena.utils.general) is_numeric() (in module athena.utils.general) is_seq() (in module athena.utils.general)

K

KNNGraphBuilder (class in athena.graph_builder.knn_graph_builder)

M

make_cbar() (in module athena.plotting.utils) make_iterable() (in module athena.utils.general) mibi() (in module athena.dataset.datasets) modularity() (in module athena.metrics.graph.graph) module athena athena.dataset athena.dataset.datasets athena.graph_builder athena.graph_builder.base_graph_builder athena.graph_builder.constants athena.graph_builder.contact_graph_builder athena.graph_builder.graphBuilder athena.graph_builder.knn_graph_builder athena.graph_builder.mappings athena.graph_builder.radius_graph_builder athena.metrics athena.metrics.graph athena.metrics.graph.graph athena.metrics.heterogeneity athena.metrics.heterogeneity.base_metrics athena.metrics.heterogeneity.metrics athena.metrics.utils athena.neighborhood athena.neighborhood.base_estimators athena.neighborhood.estimators athena.neighborhood.utils athena.plotting athena.plotting.utils athena.plotting.visualization athena.preprocessing athena.preprocessing.preprocess athena.utils athena.utils.docs athena.utils.docs.default_docs athena.utils.general athena.utils.tools athena.utils.tools.graph athena.utils.tools.image athena.utils.tools.metric

N

napari_viewer() (in module athena.plotting.visualization)

node_attrs2df() (in module athena.utils.tools.graph)

O

order() (in module athena.utils.general)

P

permute_labels() (in module athena.neighborhood.utils) permute_labels_deprecate() (in module athena.neighborhood.utils)

predict() (Interactions method) (RipleysK method)

Q

quadratic_entropy() (in module athena.metrics.heterogeneity.metrics)

R

RadiusGraphBuilder (class in athena.graph_builder.radius_graph_builder) renyi_entropy() (in module athena.metrics.heterogeneity.metrics) richness() (in module athena.metrics.heterogeneity.metrics)

RipleysK (class in athena.neighborhood.base_estimators) ripleysK() (in module athena.neighborhood.estimators) (in module athena.plotting.visualization)

S

savefig() (in module athena.plotting.utils) shannon() (in module athena.metrics.heterogeneity.metrics)

simpson() (in module athena.metrics.heterogeneity.metrics) spatial() (in module athena.plotting.visualization)

V

VALID_MODES (Interactions attribute)

VALID_PREDICTION_TYPES (Interactions attribute)