RCPA (version 0.2.6)

plotVolcanoDE: 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)

Value

A ggplot2 object.

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.

Examples

# \donttest{

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")

# }