VizScoredSets: Visualize scored gene modules

In j-andrews7/EZscRNA: Simple Convenience Functions for High-Level scRNA-Seq Analysis

Description

VizScoredSets creates Seurat FeaturePlots for scored gene sets.

Usage

VizScoredSets(scrna, marker.df, outdir, idents = "default", vln = NULL,
  ridge = NULL, dot = NULL, vln.params = NULL, ridge.params = NULL,
  dot.params = NULL, ...)

Arguments

scrna	Seurat object.
marker.df	Dataframe with the two columns called "Set" and "Marker". The "Set" column should contain a cell or process-type (e.g. Tcell, Bcell, Exhaustion markers, etc.) while the "Marker" column contains the comma-delimited gene symbols associated with it.
outdir	Path to output directory.
idents	String or character vector containing meta.data columns to use as cell identities across all plots. Multiple can be provided - plots will be generated for each.
vln	Boolean indicating whether to create Seurat VlnPlots for each set. Splits by cell idents.
ridge	Boolean indicating whether to create Seurat RidgePlots for each set. Splits by cell idents.
dot	Boolean indicating whether to create Seurat DotPlots for each set. Splits by cell idents.
vln.params	List of keyword arguments to be passed to VlnPlot. features are already defined and will throw an error if passed.
ridge.params	List of keyword arguments to be passed to Seurat RidgePlot. features are already defined and will throw an error if passed.
dot.params	List of keyword arguments to be passed to Seurat DotPlot. features are already defined and will throw an error if passed.
...	Arguments to be passed to FeaturePlot. cols, features, reduction, and ncol are already defined and will throw an error if passed.

Details

Plots for each scored gene set will be output to a PDF that will be dynamically sized and named based on the name and number of markers for the set. New directories will be created for each set in the output directory.

Author(s)

Jared Andrews

j-andrews7/EZscRNA documentation built on Feb. 24, 2020, 10:37 a.m.