plot_gene: Basic gene ploting function

In ddiez/omisc: Miscelaneous Tools for the Analysis of Omics Data

Basic gene ploting function

Description

Plots a gene from a specified assembly using Gviz package. Optionaly plots some data (e.g. read alignments). Enables zooming.

Usage

plot_gene(
  symbol,
  genome,
  tracks = NULL,
  add.data = NULL,
  add.ann = NULL,
  add.ideogram = TRUE,
  from = NULL,
  to = NULL,
  biomart = NULL,
  ylim = NULL,
  ...
)

Arguments

symbol	symbol of the gene to plot. Will be used to search using BiomartGeneRegionTrack.
genome	genome assembly (e.g. mm10 or hg38).
tracks	additional tracks to add.
add.data	list with data to be added as a DataTrack.
add.ann	annotation information.
add.ideogram	whether to add an IdeogramTrack (FALSE by default to spead up testing).
from	start genomic coordinates.
to	end genomic coordinates.
biomart	mart object (optional).
ylim	sets the limits for y-axis (default: NULL).
...	further arguments passed to plotTracks.

Value

nothing but produces a plot as side effect.

Examples

NULL

ddiez/omisc documentation built on Aug. 14, 2024, 1:19 p.m.