_pkgdown.yml

url: https://theimagelab.github.io/entrain/, https://github.com/theimagelab/entrain
template:
  bootstrap: 5
  bootswatch: flatly


reference:
- title: Entrain R Functions
- contents:
  - cellwise_influences
  - choose_path
  - cells_between_vertices
  - draw_entrain_circos
  - entrain_cluster_velocities
  - entrain_velocity
  - get_expressed_genes
  - get_expressed_ligands
  - get_path_ligands
  - get_senders_interactive
  - get_traj_ligands_monocle
  - intersect_genes
  - intersect_seurat_adata
  - plot_covarying_genes_heatmap
  - plot_covarying_genes_scatter
  - plot_ligand_influences
  - plot_ligand_targets
  - plot_ligand_targets_heatmap
  - plot_ligand_trajectories
  - plot_sender_influence_velocity
  - plot_velocity_clusters
  - plot_velocity_ligand_targets
  - plot_velocity_ligands
  - plot_velocity_likelihoods_heatmap
  - velocity_ligand_importance_heatmap 
- title: Entrain Python Functions for Velocity and Spatial analysis
  desc:  Functions in the accompanying Spatial-Entrain Python package for spatial transcriptomics and velocity. To use the below functions, install `entrain-spatial`.
- contents:
  - get_velocity_ligands_spatial
  - get_velocity_ligands
  - velocity_label_transfer
  - plot_velocity_ligands_python
  - plot_influence_proportions
  - plot_likelihoods_heatmap
  - plot_ligand_importance_heatmap