plotLenIntrons: Plot length introns flanking back-spliced junctions

Description Usage Arguments Value Examples

View source: R/getPlots.R

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

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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

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# 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 July 22, 2021, 9:34 p.m.