Object of class data frame with rows representing copy-number
segment calls. The data frame must contain columns with the following names
"chromosome", "start", "end", "segmean", "sample".
y
Object of class data frame with rows representing chromosome
boundaries for a genome assembly. The data frame must contain columns with
the following names "chromosome", "start", "end" (optional: see details).
genome
Character string specifying a valid UCSC genome (see details).
plot_title
Character string specifying title to display on the plot.
CN_Loss_colour
Character string specifying the colour value of copy
number losses.
CN_Gain_colour
Character string specifying the colour value of copy
number gains.
x_title_size
Integer specifying the size of the x-axis title.
y_title_size
Integer specifying the size of the y-axis title.
facet_lab_size
Integer specifying the size of the faceted labels
plotted.
plotLayer
Valid ggplot2 layer to be added to the plot.
out
Character vector specifying the the object to output, one of
"data", "grob", or "plot", defaults to "plot" (see returns).
CNscale
Character string specifying if copy number calls supplied are
relative (i.e.copy neutral == 0) or absolute (i.e. copy neutral ==2). One of
"relative" or "absolute"
Details
cnSpec requires the location of chromosome boundaries for a given
genome assembly in order to ensure the entire chromosome space is plotted.
As a convenience this information is available to cnSpec for
the following genomes "hg19", "hg38", "mm9", "mm10", "rn5" and can be
retrieved by supplying one of the afore mentioned assemblies via the 'genome'
parameter. If a genome assembly is supplied to the 'genome' parameter and is
unrecognized cnSpec will attempt to query the UCSC MySQL database for the
required information. If chromosome boundary locations are unavailable for
a given assembly or if it is desireable to plot a specific region
encapsulating the copy number data these boundaries can be supplied to the
'y' paramter which has priority of the parameter 'genome'.
The 'plotLayer' parameter can be used to add an additional layer to the
ggplot2 graphic (see vignette).
Value
One of the following, a list of dataframes containing data to be
plotted, a grob object, or a plot.
Examples
cnSpec(LucCNseg, genome="hg19")
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/cnSpec.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cnSpec
> ### Title: Construct copy-number cohort plot
> ### Aliases: cnSpec
>
> ### ** Examples
>
> cnSpec(LucCNseg, genome="hg19")
genome specified is preloaded, retrieving data...
>
>
>
>
>
> dev.off()
null device
1
>