spatialMETA
  • Installation
  • Tutorials
    • 1. Preprocess
    • 2. Alignment
    • 3. Reassignment
    • 4. Integration
      • 4.1 Vertical Integration for SM and ST Data
      • 4.2 Vertical and Horizontal Integration for SM and ST Data
      • 4.3 Horizontal Integration for SM Data
    • 5. Analysis & Visualization
  • API
    • AnnDataST
    • AnnDataSM
    • AnnDataJointSMST
    • Data
      • list_datasets()
      • load_adata()
      • load_imzML_and_ibd()
      • load_Vicari_2024_msi()
    • 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
      • Alignment Model for ST and SM
      • Integration Model for ST and SM
      • Integration Model for SM Only
    • 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()
spatialMETA
  • Overview: module code

All modules for which code is available

  • spatialmeta.data._dataloader
  • spatialmeta.model._alignment_module
  • spatialmeta.model._model
  • spatialmeta.model._moe
  • spatialmeta.plotting._plotting
  • spatialmeta.plotting.core.wrapper
  • spatialmeta.preprocess._metabolite_annotation
  • spatialmeta.preprocess._preprocess
  • spatialmeta.preprocess._simple
  • spatialmeta.util._classes

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