plot.NES: GSEA analyses NES plotter

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

GSEA analyses NES plotter

Description

Plotting of a bar plot indicating the Normalized Enrichment Score (NES) of a gsea result. Bars will have different colors by positive or negative enrichment and transparency proportional to their p-value.

Usage

## S3 method for class 'NES'
plot(
  gsea.object,
  pos.NES.label = "+NES",
  neg.NES.label = "-NES",
  pos.NES.color = "steelblue",
  neg.NES.color = "orange",
  string.pattern.to.remove = "HALLMARK|GOBP",
  alpha.range = c(0.3, 1),
  add.counts = TRUE,
  perc.bleeding.x = 8,
  axes.text.size = 10,
  title = "NES enrichments"
)

Arguments

gsea.object	A gseaResult object as generate by clusterprofiler.
pos.NES.label	String for the label of sets enriched in the group with positive ranking feature scores. Default: "+NES".
neg.NES.label	String for the label of sets enriched in the group with negative ranking feature scores. Default: "-NES".
pos.NES.color	String for the color of sets enriched in the group with positive ranking feature scores. Default: "steelblue".
neg.NES.color	String for the color of sets enriched in the group with negative ranking feature scores. Default: "orange".
string.pattern.to.remove	String with a regular expression of a pattern to be removed from the set names. Default: "HALLMARK|GOBP".
alpha.range	Numeric vector of length 2 indicating minimum and maximum value for the transparency. Individual values must be a number between 0 and 1. Default: c(0.3, 1).
add.counts	Logic value to indicate whether add labels with the set size counts. Default: "TRUE".
perc.bleeding.x	Numeric value indicating the percentage of the full x.axis range to add on the left on the right. Useful when labels are falling outside for the x-max. Default: 8 (%).
axes.text.size	Numeric value indicating the font size of the axis text. Default: 10.
title	String indicating the title of the plot. Default: "NES enrichments".

Value

A ggplot object.

sebastian-gregoricchio/Rseb documentation built on May 15, 2024, 5:45 a.m.