plotBorder: Plots of Border Elements for Device
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Author(s) See Also

Produce box-and-whisker plot(s) of the positive and negative feature intensities for the selected device.

plotBorder(x,
           type    = c("pos", "neg"),
           qualopt = "raw",
           transfo = log2,
           range   = 0,
           names   = "namepart",
           ylim    = NULL,
           bmar    = NULL,
           las     = 2,
           dev     = "screen",
           outfile = "BorderPlot",
           w       = 800,
           h       = 540,
           ...)

`x`	object of class `QualTreeSet`.
`type`	type of border elements to be used, one of “pos”, “neg”, or both.
`qualopt`	character string specifying whether to draw boxplots for “raw”, “adjusted”, or “normalized” border intensities.
`transfo`	a valid function to transform the data, usually “log2”, or “0”.
`range`	determines how far the plot whiskers extend out from the box.
`names`	optional vector of sample names.
`ylim`	the y limits of the plot.
`bmar`	optional `list` for bottom margin and axis label magnification `cex.axis`.
`las`	the style of axis labels.
`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 `borderplot`.

Creates a boxplot of the positive and negative feature intensities for an object of class QualTreeSet.

For names=NULL full tree names will be displayed while for names="namepart" tree names will be displayed without name extension. If names is a vector of tree names, only these columns will displayed as boxplot.

For bmar=NULL the default list bmar = list(b=6, cex.axis=1.0) will be used initially. However, both bottom margin b and axis label magnification cex.axis will be adjusted depending on the number of label characters and the number of samples.

Christian Stratowa

borderplot

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