MvA Scatter Plot for Device

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Description

Produce scatter plots of M values vs A values of the samples for the selected device.

Usage

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plotMA(x,
       transfo = log2,
       method  = "median",
       names   = "namepart",
       ylim    = c(-6, 6),
       xlab    = "A",
       ylab    = "M",
       pch     = ".",
       mar     = c(3, 3, 2, 1),
       dev     = "screen",
       outfile = "MvAPlot",
       w       = 540,
       h       = 540,
       ...)

Arguments

x

object of class ExprTreeSet.

transfo

a valid function to transform the data, usually “log2”, or “0”.

method

method to compute M, “mean” or “median”.

names

optional vector of sample names.

ylim

range for the plotted M values.

xlab

a title for the x axis.

ylab

a title for the y axis.

pch

either an integer specifying a symbol or a single character to be used in plotting points.

mar

plot margin.

dev

graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.

outfile

the name of the output file.

w

the width of the device in pixels.

h

the height of the device in pixels.

...

optional arguments to be passed to plot.

Details

Produces M vs A plots for slot data for an object of class ExprTreeSet for the selected graphics device.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as M vs A plot.

Author(s)

Christian Stratowa

See Also

mvaplot

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