volcanoPlot: Plot differential circRNA expression results

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

Plot differential circRNA expression results

Description

The function volcanoPlot() generates a volcano plot with the results of the differential expression analysis.

Usage

volcanoPlot(
  res,
  log2FC = 1,
  padj = 0.05,
  title = "",
  gene = FALSE,
  geneSet = c(""),
  setxLim = FALSE,
  xlim = c(-8, 8),
  setyLim = FALSE,
  ylim = c(0, 5),
  color = "blue"
)

Arguments

res	A data frame containing the the differential expression resuls. It can be generated with getDeseqRes or getEdgerRes.
log2FC	An integer specifying the log2FC cut-off. Deafult value is 1.
padj	An integer specifying the adjusted P value cut-off. Deafult value is 0.05.
title	A character string specifying the title of the plot.
gene	A logical specifying whether to show all the host gene names of the differentially expressed circRNAs to the plot. Deafult value is FALSE.
geneSet	A character vector specifying which host gene name of the differentially expressed circRNAs to show in the plot. Multiple host gene names can be specofied. E.g. c('TTN, RyR2')
setxLim	A logical specifying whether to set x scale limits. If TRUE the value in xlim will be used. Deafult value is FALSE.
xlim	A numeric vector specifying the lower and upper x axis limits. Deafult values are c(-8 , 8).
setyLim	A logical specifying whether to set y scale limits. If TRUE the value in ylim will be used. Deafult value is FALSE.
ylim	An integer specifying the lower and upper y axis limits Deafult values are c(0, 5).
color	A string specifying the color of the differentially expressed circRNAs. Default value is "blue".

Value

A ggplot object.

Examples

# Load data frame containing detected back-spliced junctions
data("mergedBSJunctions")

pathToExperiment <- system.file("extdata", "experiment.txt",
    package ="circRNAprofiler")

# Filter circRNAs
filterdCirc <- filterCirc(
    mergedBSJunctions,
    allSamples = FALSE,
    min = 5,
    pathToExperiment)

# Find differentially expressed circRNAs
 deseqResBvsA <- getDeseqRes(
    filterdCirc,
    condition = "A-B",
    pAdjustMethod = "BH",
    pathToExperiment)

# Plot
p <- volcanoPlot(
    deseqResBvsA,
    log2FC = 1,
    padj = 0.05,
    title = "",
    setxLim = TRUE,
    xlim = c(-8 , 7.5),
    setyLim = FALSE,
    ylim = c(0 , 4),
    gene = FALSE)
p

Aufiero/circRNAprofiler documentation built on Nov. 3, 2024, 10:12 a.m.