API reference

The LYNX public API is organized into themed modules under the lynx namespace.

• Model
  • lynx.model.HeteroAttnVGAE
  • lynx.dataset.HeteroDataset
  • lynx.dataset.XeniumDataset
  • lynx.config.set_model_configs
  • lynx.config.set_train_configs
• Trajectory
  • lynx.trajectory.get_curve
  • lynx.trajectory.get_tree
  • lynx.trajectory.compute_pseudotime
  • lynx.trajectory.sort_nodes
  • lynx.trajectory.prune_tree
  • lynx.trajectory.get_cell_projections
• Zonation & utilities
  • lynx.utils.get_zonations
  • lynx.utils.get_zonation_features
  • lynx.utils.get_binned_expr
  • lynx.utils.get_celltype_dynamics
  • lynx.utils.get_cluster_dynamics
  • lynx.utils.sort_fitted_expr
• Plotting
  • lynx.plot.disp_trajectory
  • lynx.plot.disp_kde_scatter
  • lynx.plot.disp_heatmap
  • lynx.plot.disp_stacked_dynamics
  • lynx.plot.disp_spatial_latents
  • lynx.plot.disp_joint_logfc
  • lynx.plot.summarize_cell_interaction
  • lynx.plot.netVisual_circle
• Association tests
  • lynx.test_assoc.test_cci
  • lynx.test_assoc.test_trajectory
  • lynx.test_assoc.get_test_associations
• IO
  • lynx.io.load_xenium
  • lynx.io.filter_cells
  • lynx.io.load_ab_stain
  • lynx.io.load_spatial_metadata
  • lynx.io.load_annot_tiffs
  • lynx.io.save_annot_tifs