Index

_

__dict__ (spamosaic.utils.Config attribute), [1]

A

ADT_preprocess() (in module spamosaic.preprocessing), [1]

apply_smoothing() (spamosaic.framework.SpaMosaic method)

B

build_intra_graph() (in module spamosaic.build_graph), [1]

build_mnn_graph() (in module spamosaic.build_graph), [1]

C

cache_spatial_graph() (spamosaic.framework.SpaMosaic method) Cal_Spatial_Net() (in module spamosaic.build_graph), [1] check_batch_empty() (in module spamosaic.utils), [1] check_integrity() (spamosaic.framework.SpaMosaic method)

CL_loss (class in spamosaic.loss), [1] clr_normalize() (in module spamosaic.preprocessing), [1] clustering() (in module spamosaic.utils), [1] Config (class in spamosaic.utils), [1] convs (spamosaic.architectures.hgt.HGT attribute), [1]

D

decoder (spamosaic.architectures.hgt.HGT attribute), [1]

determine_kSize() (in module spamosaic.build_graph), [1] dict_map() (in module spamosaic.utils), [1]

E

Epigenome_preprocess() (in module spamosaic.preprocessing), [1]

F

fit() (spamosaic.preprocessing.lsiTransformer method) (spamosaic.preprocessing.tfidfTransformer method) fit_transform() (spamosaic.preprocessing.lsiTransformer method) (spamosaic.preprocessing.tfidfTransformer method) flip_axis() (in module spamosaic.utils), [1] forward() (spamosaic.architectures.gat.GAT method) (spamosaic.architectures.gat.GATConv method) (spamosaic.architectures.hg_lgcn.HG_LGCN method) (spamosaic.architectures.hg_lgcn.HG_LGCN_Conv method) (spamosaic.architectures.hg_lgcn.HG_LGCN_vanilla method) (spamosaic.architectures.hgt.HGT method) (spamosaic.architectures.wlgcn.HEAD method) (spamosaic.architectures.wlgcn.WLGCN_vanilla method) (spamosaic.loss.CL_loss method)

G

g2ts() (spamosaic.framework.SpaMosaic method) GAT (class in spamosaic.architectures.gat), [1] GATConv (class in spamosaic.architectures.gat), [1]

get_barc2batch() (in module spamosaic.utils), [1] get_umap() (in module spamosaic.utils), [1] graph_decode() (in module spamosaic.train_utils), [1] graph_recon_crit() (in module spamosaic.train_utils), [1]

H

harmony() (in module spamosaic.preprocessing), [1] HEAD (class in spamosaic.architectures.wlgcn), [1] HG_LGCN (class in spamosaic.architectures.hg_lgcn), [1]

HG_LGCN_Conv (class in spamosaic.architectures.hg_lgcn), [1] HG_LGCN_vanilla (class in spamosaic.architectures.hg_lgcn), [1] HGT (class in spamosaic.architectures.hgt), [1]

I

impute() (spamosaic.framework.SpaMosaic method)

infer_emb() (spamosaic.framework.SpaMosaic method)

L

lin (spamosaic.architectures.hgt.HGT attribute), [1] lin_dict (spamosaic.architectures.hgt.HGT attribute), [1]

load_config() (in module spamosaic.utils), [1] lsiTransformer (class in spamosaic.preprocessing), [1]

M

make_Ahat_sparse() (in module spamosaic.build_graph), [1] mclust_R() (in module spamosaic.utils), [1] message() (spamosaic.architectures.gat.GATConv method) (spamosaic.architectures.hg_lgcn.HG_LGCN_Conv method) mnn() (in module spamosaic.MNN), [1] module spamosaic spamosaic.architectures spamosaic.architectures.gat spamosaic.architectures.hg_lgcn spamosaic.architectures.hgt spamosaic.architectures.wlgcn spamosaic.build_graph spamosaic.framework spamosaic.loss spamosaic.MNN spamosaic.preprocessing spamosaic.train_utils spamosaic.utils

N

nn() (in module spamosaic.MNN), [1] nn_annoy() (in module spamosaic.MNN), [1]

nn_approx() (in module spamosaic.MNN), [1] (in module spamosaic.utils), [1] node_type (spamosaic.architectures.hgt.HGT attribute), [1]

P

plot_basis() (in module spamosaic.utils), [1] prepare_inputs() (spamosaic.framework.SpaMosaic method)

prepare_inter_graphs() (spamosaic.framework.SpaMosaic method) prepare_intra_graphs() (spamosaic.framework.SpaMosaic method) prepare_net() (spamosaic.framework.SpaMosaic method)

R

remove_outlier() (in module spamosaic.build_graph), [1]

reorder() (in module spamosaic.utils), [1] RNA_preprocess() (in module spamosaic.preprocessing), [1]

S

set_diag() (in module spamosaic.loss), [1] set_seeds() (in module spamosaic.train_utils), [1] spamosaic module SpaMosaic (class in spamosaic.framework), [1] spamosaic.architectures module spamosaic.architectures.gat module spamosaic.architectures.hg_lgcn module spamosaic.architectures.hgt module spamosaic.architectures.wlgcn module

spamosaic.build_graph module spamosaic.framework module spamosaic.loss module spamosaic.MNN module spamosaic.preprocessing module spamosaic.train_utils module spamosaic.utils module sparse_log1p_scale() (in module spamosaic.preprocessing), [1] split_adata_ob() (in module spamosaic.utils), [1]

T

tfidfTransformer (class in spamosaic.preprocessing), [1] train() (spamosaic.framework.SpaMosaic method)

train_model() (in module spamosaic.train_utils), [1] transform() (spamosaic.preprocessing.lsiTransformer method) (spamosaic.preprocessing.tfidfTransformer method)

W

WLGCN_vanilla (class in spamosaic.architectures.wlgcn), [1]