annotateGenePlot: Plots and annotates transcripts

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

Description

Plots the gene structure, annotates this with the target location

Usage

annotateGenePlot(txdb, target, target.colour = "red", target.size = 1,
  gene.text.size = 10, panel.spacing = grid::unit(c(0.1, 0.1, 0.1, 0.1),
  "lines"), plot.title = NULL, all.transcripts = TRUE)

Arguments

txdb	A GenomicFeatures:TxDb object
target	Location of target (GRanges)
target.colour	Colour of box indicating targt region
target.size	Thickness of box indicating target region
gene.text.size	Size for figure label
panel.spacing	Unit object, margin size
plot.title	A title for the plot. If no plot.title is supplied, the title is the list of gene ids shown (default). If plot.title == FALSE, the plot will not have a title.
all.transcripts	If TRUE (default), all transcripts of genes overlapping the target are shown, including transcripts that do not themselves overlap the target. If FALSE, only the transcripts that overlap the target are shown.

Value

A ggplot2 plot of the transcript structures

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.