plotVennDE: Plot Venn diagram from multiple DE Analysis results

In RCPA: Consensus Pathway Analysis

Plot Venn diagram from multiple DE Analysis results

Description

Plot a Venn diagram from multiple DE Analysis results.

Usage

plotVennDE(
  DEResults,
  pThreshold = 0.05,
  useFDR = TRUE,
  stat = "logFC",
  statThreshold = 0,
  topToList = 10
)

Arguments

DEResults	A list of data frames with the results of DE analysis.
pThreshold	The p-value threshold to determine if a gene is differentially expressed.
useFDR	Use the FDR adjusted p-value instead of the raw p-value.
stat	The additional statistics column to use for filtering differentially expressed genes.
statThreshold	The absolute value of the statistic threshold to use for filtering differentially expressed genes. Default is 0, which means no filtering.
topToList	The number of common DE genes that are used to annotate the plot

Value

A ggplot2 object.

Examples

library(RCPA)
library(SummarizedExperiment)

affyDEExperiment <- loadData("affyDEExperiment")
agilDEExperiment <- loadData("agilDEExperiment")
RNASeqDEExperiment <- loadData("RNASeqDEExperiment")

DEResults <- list(
    "Affymetrix - GSE5281" = rowData(affyDEExperiment),
    "Agilent - GSE61196"   = rowData(agilDEExperiment),
    "RNASeq - GSE153873"   = rowData(RNASeqDEExperiment)
)

DEResultUps <- lapply(DEResults, function(df) df[!is.na(df$logFC) & df$logFC > 0, ])

DEResultDowns <- lapply(DEResults, function(df) df[!is.na(df$logFC) & df$logFC < 0, ])

if (require("ggvenn", quietly = TRUE)){
p1 <- RCPA::plotVennDE(DEResults) + 
        ggplot2::ggtitle("All DE Genes")
p2 <- RCPA::plotVennDE(DEResultUps) +
        ggplot2::ggtitle("Up-regulated DE Genes")
p3 <- RCPA::plotVennDE(DEResultDowns) + 
        ggplot2::ggtitle("Down-regulated DE Genes")
}

RCPA documentation built on Nov. 21, 2023, 5:08 p.m.