Welcome to spatialMETA’s documentation!
spatialMETA is a method for integrating spatial multi-omics data. spatialMETA aligns ST and SM to a unified resolution, integrates single or multiple sample data to identify cross-modal spatial patterns, and offers extensive visualization and analysis functions.
Contents
- Installation
- Tutorials
- API
AnnDataSTAnnDataSMAnnDataJointSMST- Data
- Preprocessing
read_sm_csv_as_anndata()get_mz_reference()read_sm_imzml_as_anndata()merge_sm_pos_neg()calculate_qc_metrics_sm()filter_cells_sm()filter_metabolites_sm()new_spot_sample()spot_align_byknn()joint_adata_sm_st()normalize_total_joint_adata_sm_st()spatial_variable_joint_adata_sm_st()spatial_variable()rank_gene_and_metabolite_groups()corrcoef_stsm_inall()corrcoef_stsm_ingroup()spatial_distance_cluster()calculate_dot_df()metabolite_annotation()merge_and_assign_var_data()calculate_metabolite_enrichment()add_obs_to_adata()add_hvf_to_jointadata()calculate_scale_factor()spot_transform_by_manual()
- Model
- Plotting
make_colormap()create_fig()create_subplots()plot_spot_sm_st()plot_newdot_sm_st()plot_markerfeature()plot_marker_gene_metabolite()plot_corrcoef_stsm_inall()plot_corrcoef_stsm_ingroup()plot_spatial_deconvolution()plot_gene_corrcoef_sm_ingroup()plot_metabolite_corrcoef_st_ingroup()plot_volcano_corrcoef_gene()plot_volcano_corrcoef_metabolite()plot_trajectory_with_arrows()plot_clustermap_with_smoothing()plot_features_trajectory()plot_network()Wrapper()to_plotly()