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$genome == 'hg38',]
# Call ideoView for chromosome 1
ideoView(data, chromosome='chr1', txtSize=4)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(GenVisR)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenVisR/ideoView.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ideoView
> ### Title: Construct an ideogram
> ### Aliases: ideoView
>
> ### ** Examples
>
> # Obtain cytogenetic information for the genome of interest from attached
> # data set cytoGeno
> data <- cytoGeno[cytoGeno$genome == 'hg38',]
>
> # Call ideoView for chromosome 1
> ideoView(data, chromosome='chr1', txtSize=4)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.