Function reference • entrain

Entrain R Functions

cellwise_influences(): Evaluates where ligands are most strongly driving trajectory dynamics.

choose_path(): Choose cells along the path of a principal graph. Modified from Monocle3 function choose_graph_segments to allow for selection of multiple branches and zooming in.

cells_between_vertices(): Get cells between nodes.

draw_entrain_circos(): Draw circos plot of Entrain ligands.

entrain_cluster_velocities(): Cluster the velocity matrix

entrain_velocity(): Identify ligands responsible for observed velocity vectors.

get_expressed_genes(): Determine expressed genes of a cell type.

get_expressed_ligands(): Determine expressed ligands of a list of cell types

get_path_ligands(): Core function for Entrain ligand assignment that is agnostic to the trajectory inference algorithm used.

get_senders_interactive(): Interactive selection of sender clusters.

get_traj_ligands_monocle(): Identify ligands responsible for trajectory dynamics using Monocle graph learning.

intersect_genes(): Intersect seurat object genes

intersect_seurat_adata(): Subset cells in Seurat and Anndata objects such that they have identical cellIDs.

plot_covarying_genes_heatmap(): Heatmap plot of top trajectory gene covariances.

plot_covarying_genes_scatter(): Scatter plot of top trajectory covarying genes.

plot_ligand_influences(): Plots ligand cellwise inlfuences on a UMAP.

plot_ligand_targets(): Plots a heatmap of ligand-target regulatory potentials extracted from NicheNet.

plot_ligand_targets_heatmap(): Plot ligand-gene downstream regulatory relationships as a heatmap.

plot_ligand_trajectories(): Plots ligand influences and variance explained scores on a Monocle trajectory plot.

plot_sender_influence_velocity(): Plot sender influences overlayed on a RNA velocity plot

plot_velocity_clusters(): Plot top ligands overlayed on a RNA velocity plot

plot_velocity_ligand_targets(): Plots a heatmap of ligand-target regulatory potentials extracted from NicheNet.

plot_velocity_ligands(): Plot top ligands overlayed on a RNA velocity plot

plot_velocity_likelihoods_heatmap(): Plot velocity likelihoods as a heatmap.

velocity_ligand_importance_heatmap(): Velocity Ligand Importance Heatmap

Entrain Python Functions for Velocity and Spatial analysis

Functions in the accompanying Spatial-Entrain Python package for spatial transcriptomics and velocity. To use the below functions, install entrain-spatial.

get_velocity_ligands_spatial(): Spatial Velocity Entrain Analysis

get_velocity_ligands(): Velocity Entrain Analysis

velocity_label_transfer(): Velocity Label Transfer

plot_velocity_ligands_python(): Python function to plot top ligands overlayed on a RNA velocity plot

plot_influence_proportions(): Python function to plot relative influence for each spatially adjacent cell type.

plot_likelihoods_heatmap(): Plot velocity likelihoods as a heatmap.

plot_ligand_importance_heatmap(): Velocity Ligand Importance Heatmap