plotMA: Plot MA plot from DE analysis results
In RCPA: Consensus Pathway Analysis

plotMA

R Documentation

Plot MA plot from DE analysis results

Description

Plot MA plot from DE analysis results

Usage

plotMA(
  DEResult,
  pThreshold = 0.05,
  useFDR = TRUE,
  logFCThreshold = 1,
  labels = NULL,
  fitMethod = "loess"
)

Arguments

`DEResult`	A data frame with DE analysis results. The columns are ID, p.value, pFDR, logFC, and aveExpr.
`pThreshold`	The p-value threshold to color significant points.
`useFDR`	Use FDR instead of p-value for significance.
`logFCThreshold`	The log2 fold change threshold to color significant points.
`labels`	named vector of labels to use for points, e.g., c("gene1" = "Gene 1", "gene2" = "Gene 2")
`fitMethod`	The method to use for fitting the loess line. If NULL then no line is drawn.

Value

A ggplot object.

Examples


library(RCPA)
library(SummarizedExperiment)

RNASeqDEExperiment <- loadData("RNASeqDEExperiment")

plotObj <- RCPA::plotMA(rowData(RNASeqDEExperiment), logFCThreshold = 0.5) + 
ggtitle("RNASeq - GSE153873")

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