plotVennPathway: Plot Venn diagram from multiple pathway analysis results

In RCPA: Consensus Pathway Analysis

Plot Venn diagram from multiple pathway analysis results

Description

Plot a Venn diagram from multiple pathway analysis results.

Usage

plotVennPathway(PAResults, pThreshold = 0.05, useFDR = TRUE, topToList = 10)

Arguments

PAResults	A list of data frames with the results of pathway analysis.
pThreshold	The p-value threshold to determine if a pathway is enriched.
useFDR	Use the FDR adjusted p-value instead of the raw p-value.
topToList	The number of common signifcant pathways that are used to annotate the plot.

Value

A ggplot2 object.

Examples

library(RCPA)


affyFgseaResult <- loadData("affyFgseaResult")
agilFgseaResult <- loadData("agilFgseaResult")
RNASeqFgseaResult <- loadData("RNASeqFgseaResult")
metaPAResult <- loadData("metaPAResult")

PAResults <- list(
    "Affymetrix - GSE5281" = affyFgseaResult,
    "Agilent - GSE61196" = agilFgseaResult,
    "RNASeq - GSE153873" = RNASeqFgseaResult,
    "Meta-analysis" = metaPAResult
)

PAREsultUps <- lapply(PAResults, function(df) df[df$normalizedScore > 0,])

PAREsultDowns <- lapply(PAResults, function(df) df[df$normalizedScore < 0,])

if (require("ggvenn", quietly = TRUE)){
p1 <- RCPA::plotVennPathway(PAResults, pThreshold = 0.05) +
    ggplot2::ggtitle("All Significant Pathways")
p2 <- RCPA::plotVennPathway(PAREsultUps, pThreshold = 0.05) +
    ggplot2::ggtitle("Significantly Up-regulated Pathways")
p3 <- RCPA::plotVennPathway(PAREsultDowns, pThreshold = 0.05) +
    ggplot2::ggtitle("Significantly Down-regulated Pathways")
}

RCPA documentation built on July 3, 2024, 5:08 p.m.