Other arguments to plot, currently not supported at this time
collapse
Logical specifying whether or not to combine samples by unique group (see MassArrayData). If TRUE, each methylation values are averaged across all samples in each unique group. If FALSE, all samples are retained and plotted individually
bars
Logical specifying whether or not to display error bars. If TRUE (and collapse is TRUE), the median absolute deviation is calculated for each group and plotted as an error bar for each methylation value. If FALSE, no error bars are displayed
scale
Logical specifying whether or not to keep the x axis to scale. If TRUE, methylation values are plotted as a function of relative position within the amplicon sequence. If FALSE, positional information is ignored and methylation values are evenly spaced across the plot window.
sequence
Logical specifying whether or not to display the nucleotide sequence for the amplicon
labels
Logical specifying whether or not to display data labels
colors
Logical specifying whether or not to plot in color. If TRUE, colors are used. If FALSE, plotting occurs in black and white and grayscale.
main
Label/title for overall plot (default is ""
width
Numerical value specifying the display width to use for each methylation value; number corresponds to the number of base pairs to include in both directions from the methylation position (default is 1.5)
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(MassArray)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassArray/plot.MassArrayData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.MassArrayData
> ### Title: Plot MassArrayData
> ### Aliases: plot.MassArrayData
> ### Keywords: aplot
>
> ### ** Examples
>
> data(MassArray.example.data)
> plot(MassArray.example.data,collapse=FALSE,bars=FALSE,scale=FALSE)
>
>
>
>
>
> dev.off()
null device
1
>