Index

_

__init__() (Garfield.data.GraphAnnTorchDataset method) (Garfield.model.Garfield.Garfield method) (Garfield.modules.GNNModelVAE method) (Garfield.nn.DSBatchNorm method) (Garfield.nn.GATDecoder method) (Garfield.nn.GATEncoder method) (Garfield.nn.GCNDecoder method) (Garfield.nn.GCNEncoder method) (Garfield.trainer.EarlyStopping method) (Garfield.trainer.GarfieldTrainer method)

_apply_normalization() (Garfield.nn.GCNEncoder method) _forward_through_layers() (Garfield.nn.GATEncoder method) (Garfield.nn.GCNEncoder method)

A

aggregate_top_markers() (in module Garfield.analysis)

C

calc_marker_stats() (in module Garfield.analysis) calc_neighbor_prop() (in module Garfield.analysis) compute_contrastive_clusterloss() (in module Garfield.modules) compute_contrastive_instanceloss() (in module Garfield.modules)

compute_edge_recon_loss() (in module Garfield.modules) compute_kl_reg_loss() (in module Garfield.modules) compute_omics_recon_mmd_loss() (in module Garfield.modules) compute_omics_recon_mse_loss() (in module Garfield.modules)

D

DataProcess() (in module Garfield.preprocessing)

DSBatchNorm (class in Garfield.nn)

E

EarlyStopping (class in Garfield.trainer)

edge_level_split() (in module Garfield.data) eval_metrics() (in module Garfield.trainer)

F

filter_marker_stats() (in module Garfield.analysis)

forward() (Garfield.nn.GATEncoder method) (Garfield.nn.GCNEncoder method)

G

Garfield module Garfield (class in Garfield.model.Garfield) Garfield.analysis module Garfield.data module Garfield.model module Garfield.modules module, [1] Garfield.nn module Garfield.plot module Garfield.preprocessing module

Garfield.trainer module, [1] GarfieldTrainer (class in Garfield.trainer) GATDecoder (class in Garfield.nn) GATEncoder (class in Garfield.nn) GCNDecoder (class in Garfield.nn) GCNEncoder (class in Garfield.nn) gene_scores() (in module Garfield.preprocessing) get_enrichr_geneset() (in module Garfield.analysis) get_fast_niche_enrichr() (in module Garfield.analysis) get_nearest_neighbors() (in module Garfield.preprocessing) get_niche_enrichr() (in module Garfield.analysis) get_niche_gsea() (in module Garfield.analysis) GNNModelVAE (class in Garfield.modules) GraphAnnTorchDataset (class in Garfield.data)

I

initialize_dataloaders() (in module Garfield.data)

M

module Garfield Garfield.analysis Garfield.data Garfield.model Garfield.modules, [1] Garfield.nn Garfield.plot Garfield.preprocessing Garfield.trainer, [1]

N

niches_enrichment_barplot() (in module Garfield.plot)

niches_enrichment_dotplot() (in module Garfield.plot) node_level_split_mask() (in module Garfield.data)

P

plot_eval_metrics() (in module Garfield.trainer) plot_markers() (in module Garfield.plot) plot_multi_patterns_spatial() (in module Garfield.plot) prepare_data() (in module Garfield.data)

preprocessing() (in module Garfield.preprocessing) preprocessing_adt() (in module Garfield.preprocessing) preprocessing_atac() (in module Garfield.preprocessing) preprocessing_rna() (in module Garfield.preprocessing) print_progress() (in module Garfield.trainer)

S

set_figure_params() (Garfield.settings method)

set_gf_params() (Garfield.settings method) set_workdir() (Garfield.settings method)

W

weighted_knn_trainer() (in module Garfield.model.utils)

weighted_knn_transfer() (in module Garfield.model.utils)