VizAnnotatedMarkers: Visualize an annotated marker list

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

Description

VizAnnotatedMarkers creates Seurat FeaturePlots (and other visualizations) for lists of marker genes associated with a given annotation.

Usage

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

Arguments

scrna	Seurat object.
marker.df	Dataframe with two columns named "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.
heatmap	Boolean indicating whether to create a Seurat Heatmap 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.
heatmap.params	List of keyword arguments to be passed to Seurat DoHeatmap. features and assay are already defined and will throw an error if passed.
...	Arguments to be passed to Seurat FeaturePlot. cols, features, reduction, and ncol are already defined and will throw an error if passed.

Details

Plots for each annotation 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.