plotLenIntrons {circRNAprofiler} | R Documentation

## Plot length introns flanking back-spliced junctions

### Description

The function plotLenIntrons() generates vertical boxplots for comparison of length of introns flanking the back-spliced junctions (e.g. detected Vs randomly selected).

### Usage

    plotLenIntrons(
      annotatedFBSJs,
      annotatedBBSJs,
      df1Name = "foreground",
      df2Name = "background",
      title = "",
      setyLim = FALSE,
      ylim = c(0, 8)
    )

### Arguments

`annotatedFBSJs` | A data frame with the annotated back-spliced junctions (e.g. detected). It can be generated with `annotateBSJs`. These act as foreground back-spliced junctions.
`annotatedBBSJs` | A data frame with the annotated back-spliced junctions (e.g. randomly selected). It can generated with `annotateBSJs`. These act as background back-spliced junctions.
`df1Name` | A string specifying the name of the first data frame. This will be displayed in the legend of the plot. Deafult value is "foreground".
`df2Name` | A string specifying the name of the first data frame. This will be displayed in the legend of the plot. Deafult value is "background".
`title` | A character string specifying the title of the plot.
`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, 8).

### Value

A ggplot object.

### Examples

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

    # Load short version of the gencode v19 annotation file
    data("gtf")

    # Annotate the first 10 back-spliced junctions
    annotatedFBSJs <- annotateBSJs(mergedBSJunctions[1:10, ], gtf)

    # Get random back-spliced junctions
    randomBSJunctions <- getRandomBSJunctions( gtf, n = 10, f = 10)

    # Annotate random back-spliced junctions
    annotatedBBSJs <- annotateBSJs(randomBSJunctions, gtf, isRandom = TRUE)

    # Plot
    p <- plotLenIntrons(
        annotatedFBSJs,
        annotatedBBSJs,
        df1Name = "foreground",
        df2Name = "background",
        title = "")
    p

[Package circRNAprofiler version 1.8.0 Index]