Index

A

add_hvf_to_jointadata() (in module spatialmeta.pp) add_obs_to_adata() (in module spatialmeta.pp) AlignmentModule (class in spatialmeta.model)

AnnDataJointSMST (class in spatialmeta) AnnDataSM (class in spatialmeta) AnnDataST (class in spatialmeta)

C

calculate_dot_df() (in module spatialmeta.pp) calculate_metabolite_enrichment() (in module spatialmeta.pp) calculate_qc_metrics_sm() (in module spatialmeta.pp) calculate_scale_factor() (in module spatialmeta.pp) ConditionalVAESM() (in module spatialmeta.model)

ConditionalVAESTSM() (in module spatialmeta.model) corrcoef_stsm_inall() (in module spatialmeta.pp) corrcoef_stsm_ingroup() (in module spatialmeta.pp) create_fig() (in module spatialmeta.pl) create_subplots() (in module spatialmeta.pl)

F

filter_cells_sm() (in module spatialmeta.pp) filter_metabolites_sm() (in module spatialmeta.pp) fit() (in module spatialmeta.model.ConditionalVAESM) (in module spatialmeta.model.ConditionalVAESTSM)

fit_alignment() (in module spatialmeta.model.AlignmentModule) fit_vae() (in module spatialmeta.model.AlignmentModule)

G

get_latent_embedding() (in module spatialmeta.model.ConditionalVAESM) (in module spatialmeta.model.ConditionalVAESTSM) get_modality_contribution() (in module spatialmeta.model.ConditionalVAESTSM)

get_mz_reference() (in module spatialmeta.pp) get_normalized_expression() (in module spatialmeta.model.ConditionalVAESM) (in module spatialmeta.model.ConditionalVAESTSM)

J

joint_adata_sm_st() (in module spatialmeta.pp)

L

list_datasets() (in module spatialmeta.data) load_adata() (in module spatialmeta.data)

load_imzML_and_ibd() (in module spatialmeta.data) load_Vicari_2024_msi() (in module spatialmeta.data)

M

make_colormap() (in module spatialmeta.pl) merge_and_assign_var_data() (in module spatialmeta.pp)

merge_sm_pos_neg() (in module spatialmeta.pp) metabolite_annotation() (in module spatialmeta.pp)

N

new_spot_sample() (in module spatialmeta.pp)

normalize_total_joint_adata_sm_st() (in module spatialmeta.pp)

P

plot_clustermap_with_smoothing() (in module spatialmeta.pl) plot_corrcoef_stsm_inall() (in module spatialmeta.pl) plot_corrcoef_stsm_ingroup() (in module spatialmeta.pl) plot_features_trajectory() (in module spatialmeta.pl) plot_gene_corrcoef_sm_ingroup() (in module spatialmeta.pl) plot_marker_gene_metabolite() (in module spatialmeta.pl) plot_markerfeature() (in module spatialmeta.pl)

plot_metabolite_corrcoef_st_ingroup() (in module spatialmeta.pl) plot_network() (in module spatialmeta.pl) plot_newdot_sm_st() (in module spatialmeta.pl) plot_spatial_deconvolution() (in module spatialmeta.pl) plot_spot_sm_st() (in module spatialmeta.pl) plot_trajectory_with_arrows() (in module spatialmeta.pl) plot_volcano_corrcoef_gene() (in module spatialmeta.pl) plot_volcano_corrcoef_metabolite() (in module spatialmeta.pl)

R

rank_gene_and_metabolite_groups() (in module spatialmeta.pp)

read_sm_csv_as_anndata() (in module spatialmeta.pp) read_sm_imzml_as_anndata() (in module spatialmeta.pp)

S

spatial_distance_cluster() (in module spatialmeta.pp) spatial_variable() (in module spatialmeta.pp)

spatial_variable_joint_adata_sm_st() (in module spatialmeta.pp) spot_align_byknn() (in module spatialmeta.pp) spot_transform_by_manual() (in module spatialmeta.pp)

T

to_plotly() (in module spatialmeta.pl.Wrapper)

W

Wrapper() (in module spatialmeta.pl)