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Plot ligand-gene downstream regulatory relationships as a heatmap.

plot_ligand_targets_heatmap.Rd

Visualizes the NicheNet database to show regulatory relationships between a ligand and the genes they are regulating.

Usage

plot_ligand_targets_heatmap(
  adata,
  ligand_target_matrix,
  velocity_cluster,
  colorscale = "cividis",
  n_top_ligands = 5,
  n_top_genes = 10,
  filename = "ligand_target_heatmap.png",
  figsize = None,
  return_plot = True,
  rescale = False,
  coord_flip = True
)

Arguments

adata

Anndata object that has been analyzed with python function get_velocity_ligands

ligand_target_matrix

NicheNet database

velocity_cluster

String, the velocity cluster to visualize ligand-gene targets for. Only one velocity cluster can be visualized at at time.

colorscale

Name of a color palette to be passed to seaborn. Default cividis

n_top_ligands

Number of top ranked ligands to visualize. Default 5.

n_top_genes

Number of top target genes to visualize for each ligand. Default 10.

filename

Filename to save as. Default "ligand_target_heatmap.png"

figsize

Tuple to pass to matplotlib figure(). Default (10, 4).

return_plot

Boolean. If True, returns a matplotlib ax object.

rescale

Boolean. If True, rescales all regulatory potentials between 0 and 1 for each ligand. Default False because regulatory potentials are already normalized.

coord_flip

Flips the x-y axis. Default True.

Value

a matplotlib ax object, if return_plot is True.