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Plots ligand influences and variance explained scores on a Monocle trajectory plot.

plot_ligand_trajectories.Rd

Requires get_path_ligands or get_traj_ligands_monocle to be run on dataset beforehand. Specifically for plotting Entrain results analyzed on a Monocle trajectory.

Usage

plot_ligand_trajectories(
  obj,
  color_cells_by = "pseudotime",
  n_top_ligands = 5,
  trajectory_graph_color = "grey70",
  group_label_size = 5,
  trajectory_graph_segment_size = 1,
  cell_size = 0.6,
  label_groups_by_cluster = FALSE,
  label_font_size = 4,
  cds = NULL
)

Arguments

obj

A seurat object that has been analyzed with get_path_ligands or get_traj_ligands_monocle.

color_cells_by

Argument for monocle3::plot_cells(). A column in colData(obj@misc$entrain$monocle_cds) or colData(cds) denoting how to color the cells. Default pseudotime

n_top_ligands

Number of top ligands to write on each plot label.

trajectory_graph_color

Parameters to be passed to Monocle plot_cells function.

group_label_size

Parameters to be passed to Monocle plot_cells function.

trajectory_graph_segment_size

Parameters to be passed to Monocle plot_cells function.

cell_size

Parameters to be passed to Monocle plot_cells function.

label_groups_by_cluster

Argument for monocle3::plot_cells(). Default FALSE.

label_font_size

Argument for monocle3::plot_cells(). Default 4.

cds

Optional cell_data_set object to use instead of the default cds at obj@misc$entrain$monocle_cds

Value

a ggplot object with cells, trajectories, and ligand labels plotted on a UMAP.