plotVolcanoDE: Plot volcano plot from Pathway analysis results

In RCPA: Consensus Pathway Analysis

Plot volcano plot from Pathway analysis results

Description

Plot volcano plot from Pathway analysis results

Usage

plotVolcanoDE(DEResult, pThreshold = 0.05, useFDR = TRUE, logFCThreshold = 1)

Arguments

DEResult	A data frame with Pathway analysis results. The columns are ID, name, description, p.value, pFDR, size, nDE, score and normalizedScore.
pThreshold	The p-value threshold to use for the horizontal line.
useFDR	Whether to use the pFDR column instead of the p.value column.
logFCThreshold	The logFC threshold to use for the vertical line.

Value

A ggplot2 object.

Examples

library(RCPA)
library(SummarizedExperiment)

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

p1 <- RCPA::plotVolcanoDE(rowData(affyDEExperiment), logFCThreshold = 0.5) +
    ggplot2::ggtitle("Affymetrix - GSE5281")
p2 <- RCPA::plotVolcanoDE(rowData(agilDEExperiment), logFCThreshold = 0.5) +
    ggplot2::ggtitle("Agilent - GSE61196")
p3 <- RCPA::plotVolcanoDE(rowData(RNASeqDEExperiment), logFCThreshold = 0.5) +
    ggplot2::ggtitle("RNASeq - GSE153873")

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