Scatter plot of top trajectory covarying genes. — plot_covarying_genes

Recovers the expression of the top genes that covary with pseudotime and plots it as a scatter plot.

Usage

plot_covarying_genes_scatter(
  obj,
  path = paths[1],
  n_top_genes = 10,
  color_key = NULL,
  nrow = 5,
  ncol = 2,
  metric = "Covariances"
)

obj: A seurat object that has been analyzed with get_path_ligands or get_traj_ligands_monocle.
path: Name of list element in obj@misc$entrain$paths corresponding to the trajectory path that you wish to visualize.
n_top_genes: Number of top importance target genes to visualize. Default 10.
color_key: A column name in obj@meta.data corresponding to a label you wish to color by e.g., a cluster label.
nrow: Number of rows for the facet plot grid.
ncol: Number of columns for the facet plot grid.
metric: One of "Covariances" or "Correlations". Default "Covariances". Determines whether to use pseudotime covariance or pseudotime correlation in the calculation of TRAINing genes.

A ggplot2 plot object.