EnrichmentPlot: Nonparametric analytical Rank-based Enrichment Analysis...

In califano-lab/NaRnEA: Nonparametric analytical Rank-based Enrichment Analysis - An Information Theoretic Framework for Protein Activity Measurement

Nonparametric analytical Rank-based Enrichment Analysis plotting function

Description

Nonparametric analytical Rank-based Enrichment Analysis plotting function

Usage

EnrichmentPlot(
  signature,
  association.weight,
  association.mode,
  minimum.size = 30,
  seed = 1,
  title.text = "Nonparametric analytical Rank-based Enrichment Analysis",
  x.label.text = "Nonparametric Gene Expression Signature",
  line.width = 1,
  lower.color = "blue1",
  middle.color = "grey50",
  upper.color = "red1",
  conf.int = TRUE,
  conf.level = 0.95,
  boot.num = 100,
  sig.figs = 4
)

Arguments

signature	Gene expression signature (named numeric vector)
association.weight	Association Weight values for gene set members (named numeric vector)
association.mode	Association Mode values for gene set members (named numeric vector)
minimum.size	Minimum number of gene set members. Default of 30.
seed	Random number generator seed to ensure reproducibility manner. Default of 1.
title.text	Text for title of the plot.
x.label.text	Text for x-axis label of the plot.
line.width	Line width for the gene set member segments in the nonparametric gene expression signature.
lower.color	Color for the gene set members with negative Association Mode values.
middle.color	Color for the gene set members with Association Mode values close to zero.
upper.color	Color for the gene set members with positive Association Mode values.
conf.int	Flag to compute the confidence interval for the NaRnEA Proportional Enrichment Score using a Fisher Transformation and gene set member sampling with replacement.
conf.level	Desired coverage of the confidence interval for the NaRnEA Proportional Enrichment Score. Default of 0.95.
boot.num	Number of times to sample the gene set members with replacement when estimating the confidence interval for the NaRnEA Proportional Enrichment Score. Default of 100.
sig.figs	Number of significant figures to display when plotting numerical values. Default of 4.

Value

This function returns the NaRnEA Proportional Enrichment Score (PES) with a confidence interval (if desired), the NaRnEA Normalized Enrichment Score (NES), the NaRnEA two-sided p-value of the NaRnEA, and a figure made with ggplot2 that visualizes the enrichment of the gene set members in the nonparametrically transformed differential gene expression signature.

califano-lab/NaRnEA documentation built on March 10, 2023, 7:18 p.m.