root.mvaplot: ROOT M vs A Plot

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

Description

Creates a ROOT M vs A plot for a ROOT tree.

Usage

root.mvaplot(x, treename1 = character(0), treename2 = character(0),logbase = "log2", option = "P", canvasname = "MvAPlot", save.as = "", w = 540, h = 540)

Arguments

x	object of class ExprTreeSet or DataTreeSet.
treename1	name of first tree, must be present in rootfile of object x.
treename2	name of second tree, must be present in rootfile of object x.
logbase	usually “log2”, or “0”, determines if leaf data should be converted to log.
option	ROOT TGraph::PaintGraph option, usually one of “P”, “*”.
canvasname	name of ROOT canvas
save.as	graphics type for saving canvas, one of “ps”, “eps”, “pdf”, “jpg”, “gif”, “png”, “tiff”
w	the width of the canvas in pixels.
h	the height of the canvas in pixels.

Details

Creates a ROOT M vs A plot for trees treename1 and treename2 present in rootfile.

By selecting menu “File->Save->canvasname.xxx” you can save the figure as e.g. *gif, *.jpg, *.pdf, *.ps or even as C++ macro.

Alternatively, you can save the plot by setting save.as. However, this will close the canvas immediately after opening it.

Note

Always select menu item “Quit ROOT” from menu “File” to close the ROOT canvas, otherwise you are in the CINT C/C++ interpreter from ROOT. To exit CINT, you need to type “.q”.

Author(s)

Christian Stratowa

See Also

root.graph1D

Examples

## Not run: 
## first, load ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

# compute RMA
data.rma <- rma(data.test3,"Test3RMA",tmpdir="",background="pmonly",normalize=TRUE)

root.mvaplot(data.rma, "TestA1.mdp", "TestB1.mdp")

## End(Not run)

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