plotVolcanoPathway: 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

plotVolcanoPathway(
  PAResult,
  xAxis = c("normalizedScore", "score"),
  yAxis = c("-log10(pFDR)", "-log10(p.value)"),
  pThreshold = 0.05,
  label = "name",
  IDsToLabel = NULL,
  topToLabel = 10,
  sideToLabel = c("both", "left", "right")
)

Arguments

PAResult	A data frame with Pathway analysis results. The columns are ID, name, description, p.value, pFDR, pathwaySize, nDE, score and normalizedScore.
xAxis	The column to use for the x-axis.
yAxis	The column to use for the y-axis.
pThreshold	The p-value threshold to use for the horizontal line.
label	The column to use for the labels. Default is "name".
IDsToLabel	A vector of IDs to label. When NULL, the top pathways are labeled. Default is NULL.
topToLabel	The number of top pathways to label when IDsToLabels is NULL.
sideToLabel	The side of the plot to label.

Value

A ggplot2 object.

Examples

library(RCPA)
affyFgseaResult <- loadData("affyFgseaResult")
agilFgseaResult <- loadData("agilFgseaResult")
RNASeqFgseaResult <- loadData("RNASeqFgseaResult")
metaPAResult <- loadData("metaPAResult")

p1 <- RCPA::plotVolcanoPathway(affyFgseaResult, sideToLabel = "left")
p2 <- RCPA::plotVolcanoPathway(agilFgseaResult, sideToLabel = "left")
p3 <- RCPA::plotVolcanoPathway(RNASeqFgseaResult, sideToLabel = "left")
p4 <- RCPA::plotVolcanoPathway(metaPAResult, sideToLabel = "left")

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