plotLenIntrons: Plot length introns flanking back-spliced junctions

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

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

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