rnavel_plot: Creates an RNA velocity projection

In Chris-Cherry/sctools: Single cell analysis tools package

Description

The function takes a loom file and Seurat object and creates a projection of RNA velocity onto a dimensional reduction of your choice. The dimensional reduction should be present in the Seurat object.

Usage

rnavel_plot(
  loom,
  ser,
  out_file,
  dr = "phate",
  cols = NULL,
  n_core = NULL,
  plot_info = NULL,
  ...
)

Arguments

loom	List of loom files as read in from process_loom.R.
ser	Seurat object containing clusters and dimensional reduction.
out_file	File name of png file to save plot.
dr	Name of dimensional reduction slot to use from Seurat object. Defaults to phate.
cols	Named vector of colors for cell clusters. If NULL then ggplot colors are generated.
n_core	Number of cores to use for velocyto.R functions. If NULL then future::availableCores will be used.
plot_info	If RNA velocity was run previously you can provide the output file to skip much of the processing time. This can be very helpful when tweaking plotting parameters.
...	Parameters to pass to velocyto.R::show.velocity.on.embedding.cor

Value

Return lists of objects containing information about rna velocity

Chris-Cherry/sctools documentation built on Jan. 25, 2022, 2:19 p.m.