RCPA (version 0.2.6)

plotVolcanoPathway: 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")
)

Value

A ggplot2 object.

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.

Examples

# \donttest{
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")

# }