MARVEL (version 1.4.0)

adhocGene.PlotSJPosition.10x: Plots the locations of specified splice junction relative to isoforms

Description

Plots the locations of specified splice junction relative to isoforms. List of isoforms are retrieved from GTF.

Usage

adhocGene.PlotSJPosition.10x(
  MarvelObject,
  coord.intron,
  coord.intron.ext = 50,
  rescale_introns = FALSE,
  show.protein.coding.only = TRUE,
  anno.label.size = 3,
  anno.colors = c("black", "gray", "red")
)

Value

An object of class S3 with new slots MarvelObject$adhocGene$SJPosition$Plot, MarvelObject$adhocGene$SJPosition$metadata, MarvelObject$adhocGene$SJPosition$exonfile, and MarvelObject$adhocGene$SJPosition$cdsfile.

Arguments

MarvelObject

Marvel object. S3 object generated from CheckAlignment.10x function.

coord.intron

Character string. Coordinates of splice junction whose splice junction will be plotted.

coord.intron.ext

Numeric value. Number of bases to extend the splice junction start and end coordinates into the exons. Helpful to enhance splice junction locations on the plot. Default is 50.

rescale_introns

Logical value. If set to TRUE, the intron length will be shorten. Helpful when introns are very long and focus visualisation of exons and splice junctions. Default is FALSE.

show.protein.coding.only

Logical value. If set to TRUE (default), only protein-coding isoforms will be displayed.

anno.label.size

Numeric value. Font size of isoform ID labels. Default is 3.

anno.colors

Vector of character strings. Colors for non-coding UTRs, coding exons, and splice junctions, respectively. Default is c("black", "gray", "red").

Examples

marvel.demo.10x <- readRDS(system.file("extdata/data",
                               "marvel.demo.10x.rds",
                               package="MARVEL")
                               )

marvel.demo.10x <- adhocGene.PlotSJPosition.10x(
                        MarvelObject=marvel.demo.10x,
                        coord.intron="chr1:100:1001",
                        rescale_introns=FALSE,
                        show.protein.coding.only=TRUE,
                        anno.label.size=1.5
                        )