API

• Plotting functions
  • Basic plotting
    • voyagerpy.plotting.draw_graph
    • voyagerpy.plotting.grouped_violinplot
    • voyagerpy.plotting.imshow
    • voyagerpy.plotting.plot_bin2d
    • voyagerpy.plotting.plot_fitline
    • voyagerpy.plotting.scatter
    • voyagerpy.plotting.simple_violinplot
  • Special plotting
    • voyagerpy.plotting.elbow_plot
    • voyagerpy.plotting.moran_plot
    • voyagerpy.plotting.plot_barcode_data
    • voyagerpy.plotting.plot_barcode_histogram
    • voyagerpy.plotting.plot_barcodes_bin2d
    • voyagerpy.plotting.plot_correlogram
    • voyagerpy.plotting.plot_dim_loadings
    • voyagerpy.plotting.plot_expression
    • voyagerpy.plotting.plot_features_bin2d
    • voyagerpy.plotting.plot_features_histogram
    • voyagerpy.plotting.plot_local_result
    • voyagerpy.plotting.plot_moran_mc
    • voyagerpy.plotting.plot_pca
    • voyagerpy.plotting.plot_spatial_feature
    • voyagerpy.plotting.spatial_reduced_dim
  • Helper functions
    • voyagerpy.plotting.plot.configure_subplots
    • voyagerpy.plotting.plot.configure_violins
    • voyagerpy.plotting.plot.contour_plot
    • voyagerpy.plotting.plot.plot_single_barcode_data
    • voyagerpy.plotting.plot.subplots_single_colorbar
• Spatial functions
  • Tissue segmentation
    • voyagerpy.spatial.detect_tissue_threshold
    • voyagerpy.spatial.get_approx_tissue_boundary
    • voyagerpy.spatial.get_tissue_boundary
    • voyagerpy.spatial.get_tissue_contour_score
  • Geometries
    • voyagerpy.spatial.get_geom
    • voyagerpy.spatial.get_spot_coords
    • voyagerpy.spatial.get_visium_spots
    • voyagerpy.spatial.set_geometry
    • voyagerpy.spatial.to_points
    • voyagerpy.spatial.to_spatial_weights
  • Image transformation
    • voyagerpy.spatial.apply_transforms
    • voyagerpy.spatial.cancel_transforms
    • voyagerpy.spatial.mirror_img
    • voyagerpy.spatial.rollback_transforms
    • voyagerpy.spatial.rotate_img90
  • Metrics and neighbours
    • voyagerpy.spatial.compute_spatial_lag
    • voyagerpy.spatial.local_moran
    • voyagerpy.spatial.losh
    • voyagerpy.spatial.moran
  • Graphs
    • voyagerpy.spatial.compute_correlogram
    • voyagerpy.spatial.compute_higher_order_neighbors
    • voyagerpy.spatial.get_default_graph
    • voyagerpy.spatial.set_default_graph
• Utils
  • Highly variable genes
    • voyagerpy.utils.model_gene_var
    • voyagerpy.utils.get_top_hvgs
  • Marker genes
    • voyagerpy.utils.find_markers
    • voyagerpy.utils.get_marker_genes
    • voyagerpy.utils.get_p_clusters
    • voyagerpy.utils.get_stat_clusters
  • Utility functions
    • voyagerpy.utils.add_per_cell_qcmetrics
    • voyagerpy.utils.add_per_gene_qcmetrics
    • voyagerpy.utils.get_scale
    • voyagerpy.utils.is_highres
    • voyagerpy.utils.is_lowres
    • voyagerpy.utils.kurtosis
    • voyagerpy.utils.log_norm_counts
    • voyagerpy.utils.scale