Plot Density Estimate for Device

Description

Plot the density estimates for each sample for the selected device.

Usage

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plotDensity(x,
            which      = "",
            size       = 0,
            transfo    = log2,
            ylab       = "density",
            xlab       = "log intensity",
            names      = "namepart",
            type       = "l",
            col        = 1:6,
            lty        = 1:5,
            add.legend = FALSE,
            dev        = "screen",
            outfile    = "DensityPlot",
            w          = 540,
            h          = 540,
            verbose    = TRUE,
            ...) 

Arguments

x

object of class DataTreeSet or ExprTreeSet.

which

type of probes to be used, for details see validData.

size

length of sequence to be generated as subset.

transfo

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

xlab

a title for the x axis.

ylab

a title for the y axis.

names

optional vector of sample names.

type

type for the plot.

col

colors to use for the different arrays.

lty

line types to use for the different arrays.

add.legend

logical, if TRUE then a legend will be drawn.

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.

verbose

logical, if TRUE print status information.

...

optional arguments to be passed to plot.

Details

Plots the non-parametric density estimates for each sample.

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 callplot.

Author(s)

Christian Stratowa

See Also

hist

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