plotDensity: Plot Density Estimate for Device

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

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

Usage

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

xps documentation built on Nov. 8, 2020, 6 p.m.