VizEnrichments: Visualize GO/pathway enrichments

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

Description

VizEnrichments creates barcharts for enrichments returned by RunEnrichr. Two plots will be created for each library - one ranked by adj. p-value, the other by Enrichr's combined score metrics.

Usage

VizEnrichments(enrichments, outdir = NULL, n.terms = 10,
  remove.insig = TRUE, adj.p.thresh = 0.05, colors = c("grey",
  "darkred"))

Arguments

enrichments	Named list containing enrichment results as returned by RunEnrichr.
outdir	Path to the output directory, will save plots as properly-sized PDFs if set. Otherwise, they will be printed.
n.terms	Number of terms to place on plot.
remove.insig	Boolean indicating whether terms that don't meet the adj.p.thresh should be removed from the plots.
adj.p.thresh	Value indicating adjusted p-value threshold to filter terms.
colors	Vector of two colors to use for coloring bars. First will be low, second will be high.

Details

Plots will be saved in a PDF named by library if outdir is set.

Author(s)

Jared Andrews

See Also

RunEnrichr for running enrichment analysis.

Examples

genes <- c("CD8A", "GZMA", "GZMK", "GZMB", "CD4", "CD3E", "GNLY")
libs <- c("Reactome_2016", "KEGG_2019_HUMAN")
terms <- RunEnrichr(genes, libraries = libs)

VizEnrichments(enrichments = terms)

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