volcanoPlot {circRNAprofiler} | R Documentation

## 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

[Package circRNAprofiler version 1.6.0 Index]