plotVolcanoDE | R Documentation |
Plot volcano plot from Pathway analysis results
plotVolcanoDE(DEResult, pThreshold = 0.05, useFDR = TRUE, logFCThreshold = 1)
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. |
A ggplot2 object.
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")
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