VizAnnotatedMarkers: Visualize an annotated marker list

Description Usage Arguments Details Author(s)

View source: R/viz.R

Description

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

Usage

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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.