GenVisR (version 1.0.4)

ideoView: Construct an ideogram

Description

Given a data frame with cytogenetic information, construct an ideogram.

Usage

ideoView(x, chromosome = "chr1", txtAngle = 45, txtSize = 5, plotLayer = NULL, out = "plot")

Arguments

x

Object of class data frame with rows representing cytogenetic bands. The data frame must contain the following column names "chrom", "chromStart", "chromEnd", "name", "gieStain"

chromosome

Character string specifying which chromosome from the "chrom" column in the argument supplied to parameter x to plot.

txtAngle

Integer specifying the angle of text labeling cytogenetic bands.

txtSize

Integer specifying the size of text labeling cytogenetic bands.

plotLayer

additional ggplot2 layers for the ideogram

out

Character vector specifying the the object to output, one of "data", "grob", or "plot", defaults to "plot" (see returns).

Value

One of the following, a list of dataframes containing data to be plotted, a grob object, or a plot.

Details

ideoView is a function designed to plot cytogenetic band inforamtion. Modifications to the graphic object can be made via the `plotLayer` parameter, see vignette for details.

Examples

# Obtain cytogenetic information for the genome of interest from attached
# data set cytoGeno
data <- cytoGeno[cytoGeno$genome == 'hg38',]

# Call ideoView for chromosome 1
ideoView(data, chromosome='chr1', txtSize=4)