MassArray (version 1.24.0)

plot.MassArrayData: Plot MassArrayData

Description

Function to generate graphical output for methylation data in a MassArrayData object

Usage

"plot"(x, ..., collapse = TRUE, bars = TRUE, scale = TRUE, sequence = TRUE, labels = TRUE, colors = TRUE, main = position(x), width = 1.5)

Arguments

x

Object of class MassArrayData

...

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)

See Also

See Also MassArrayData

Examples

data(MassArray.example.data)
plot(MassArray.example.data,collapse=FALSE,bars=FALSE,scale=FALSE)