Plots ligand cellwise inlfuences on a UMAP. — plot_ligand

Requires cellwise_influences to be run on obj beforehand.

Usage

plot_ligand_influences(
  obj,
  colormap = "Set1",
  reduction = "MonocleUMAP_",
  custom_colors = NULL,
  ligand_labels = TRUE,
  n_top_ligands = 5,
  label_font_size = 4,
  label_position = "endpoint"
)

Arguments

obj: A seurat object that has been analyzed with get_path_ligands or get_traj_ligands_monocle.
colormap: String denoting a brewer.pal compatible color palette.
reduction: Name of reduction to be used for plotting. Defaults to "MonocleUMAP"; the UMAP coordinates generated by the Monocle workflow.
custom_colors: Optional vector of colors to be passed to ggplot. Will override colormap parameter.
ligand_labels: Boolean. Overlay the ligand label on the plot?
n_top_ligands: Intheger denoting how many of the top ligands to overlay on the label. Default 5.
label_font_size: Font size of label. Default 4.
label_position: Where in the trajectory to place the label. Default 'endpoint', (i.e., later in pseudotime)

Value

A ggplot object with cells plotted on a UMAP with cell color corresponding to the degree of ligand influence for a particular branch.