Python function to plot top ligands overlayed on a RNA velocity plot

Python function that visualizes the ligands most likely to be driving the observed RNA velocities.

Usage

plot_velocity_ligands_python(
  adata,
  color = None,
  top_n_ligands = 5,
  vector_type = "stream",
  velocity_cluster_key = "velocity_clusters",
  velocity_clusters = None,
  vkey = "velocity",
  basis = "umap",
  velocity_cluster_palette = "Spectral",
  dpi = 300,
  arrow_length = 1,
  linewidth_scale = None,
  density = 0.5,
  size = 15,
  alpha = 0.2,
  arrow_size = 1,
  figsize = None,
  label_fontsize = 10,
  cell_palette = None,
  ve_plot_cutoff = 0,
  plot_output_path = "entrain_plot.png",
  plot_negative_VE = False
)

Arguments

adata: Path to a .h5ad anndata object. Must have had entrain_velocity run on it.
color: scvelo.pl argument: Key for annotations of observations/cells or variables/genes. Use if you want dot color to denote a cell type or other annotation. Default is NULL - all cells are colored a single color denoted by argument cell_palette
top_n_ligands: Number of top ligands to include in each label.
vector_type: Whether to plot a scvelo.pl.velocity_embedding_stream() plot or a scvelo.pl.velocity_embedding_grid() plot. Default stream
velocity_cluster_key: Column name of adata.obs metadata denoting velocity clusters.
velocity_clusters: Values in adata.obs.velocity_cluster_key denoting which velocity clusters and their ligands to visualize. Defaults to NULL, in which it will plot the ligands for all positive variance explained velocity clusters
vkey: Default "velocity", scvelo.pl.velocity_embedding argument.
basis: Default "umap", scvelo.pl.velocity_embedding argument.
velocity_cluster_palette: A matplotlib color palette denoting colorscale of velocity clusters e.g., "Spectral". OR a single color in matplotlib.colors.CSS4_COLORS.keys() e.g. "black"; OR: A vector of hex codes with the same length as the number of velocity clusters being plotted e.g., c("#bfe5a0", "#9e0242", "#d8434e", "#f67b4a", "#5e4fa2").
dpi: Dpi for plotting.
arrow_length: Length of RNA velocity vectors.
linewidth_scale: Width of RNA velocity vector body.
density: Density of RNA velocity vectors.
size: scvelo.pl.velocity_embedding argument: Size of points.
alpha: Opacity of points.
arrow_size: Size of RNA velocity vector arrowhead.
figsize: Figure size. Default is c(10,10)
label_fontsize: Font size of ligand labels
cell_palette: A matplotlib color palette for annotations denoted in argument color.
ve_plot_cutoff: Whether to plot the results with VE above this limit. Default 0.0.
plot_output_path: Filename of plot to save.
plot_negative_VE: Default False. Whether to include velocity clusters with an inconclusive result.

Value

NULL. Saves a plot in working directory with name plot_output_path