ideoView {GenVisR} | R Documentation

## 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).

### 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.

### Value

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

### 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)

[Package GenVisR version 1.8.1 Index]