Object of class data frame with rows representing the proportion of
CN losses/gains across the genome (default), or actual CN values. The former
option must contain columns with the following names "chromosome", "start",
"end", "gain", and "loss", and the latter option must contain column names
"chromosome", "start", "end", "segmean", and "sample". Windows supplied must
be consistent across samples!
CN_low_cutoff
Numeric value representing the point at or below which
copy number alterations are considered losses. Only used if x represents CN
values.
CN_high_cutoff
Numeric value representing the point at or above which
copy number alterations are considered gains. Only used if x represents CN
values.
plot_title
Character string specifying the title to display on the
plot.
CN_Loss_colour
Character string specifying the colour value for copy
number losses.
CN_Gain_colour
Character string specifying the colour value for 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).
Details
cnFreq will detect the column names present in the data frame
supplied to x, and will perform one of the following actions. If "gain" and
"loss" columns are detected the raw data will be plotted, if "segmean" and
"sample" columns are detected the frequency of copy-number gains and losses
present in the cohort will be calculated and plotted. The 'plotLayer'
parameter can be used to add an additional layer to the ggplot2 graphic
(see vignette).
Value
One of the following, a dataframe containing data to be
plotted, a grob object, or a plot.
Examples
# Create data
xstart <- seq(0,4990000,length.out=500)
xloss <- rep(runif(10,0,0.6),rep(50,10))/1.5
xloss <- xloss + jitter(xloss,amount=0.002)
x <- data.frame(chromosome=rep(paste0("chr",1:5),rep(500,5)), start=xstart,
end=xstart+10000, loss=xloss, gain=(1-xloss))
# Plot the data
cnFreq(x)
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/cnFreq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cnFreq
> ### Title: Construct copy-number frequency plot
> ### Aliases: cnFreq
>
> ### ** Examples
>
> # Create data
> xstart <- seq(0,4990000,length.out=500)
> xloss <- rep(runif(10,0,0.6),rep(50,10))/1.5
> xloss <- xloss + jitter(xloss,amount=0.002)
> x <- data.frame(chromosome=rep(paste0("chr",1:5),rep(500,5)), start=xstart,
+ end=xstart+10000, loss=xloss, gain=(1-xloss))
>
> # Plot the data
> cnFreq(x)
Detected "chr" in the chromosome column of x... proceeding
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.