root.profile: ROOT Profile Plot
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Note Author(s) Examples

Creates a ROOT profile plot, i.e. a plot of parallel coordinates

1	root.profile(x, treename = "*", varlist = NULL, as.log = TRUE, globalscale = TRUE, boxes = TRUE, ylim = NULL, canvasname = "ProfilePlot", save.as = "", w = 800, h = 600)

`x`	S4 object, usually of class `DataTreeSet` or `ExprTreeSet`.
`treename`	name of tree, usually all trees present in `rootfile` of object `x`.
`varlist`	leaf name of tree, usual “fInten” or “fLevel”.
`as.log`	logical indicating if `varlist` should be drawn as logarithmic data.
`globalscale`	logical indicating if all axes should be drawn at the same scale.
`boxes`	logical indicating if box-and-whisker plots should be drawn.
`ylim`	size limits c(min,max) of `varlist`.
`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 device in pixels.
`h`	the height of the device in pixels.

Creates a ROOT profile plot for all trees treename="*" present in rootfile, or for a subset of trees. In this case varlist must be the name of one tree leaf only; for varlist=NULL leaf "fInten" will be used for class DataTreeSet and leaf "fLevel" will be used for class ExprTreeSet.

If treename is the name of one tree only then varlist can contain up to all leaves of the tree, separated by colons, e.g. varlist="fLevel:fStdev".

For boxes=TRUE the profile plot draws box-and-whisker plots and can thus be considered the equivalent of the usual boxplot.

A ROOT profile plot, i.e. a plot of parallel coordinates, is drawn in a “TreeViewer”, a graphic user interface designed to handle ROOT trees. You can activate context menus by right-clicking on items or inside the right panel.

The “TreeViewer” is explained in http://root.cern.ch/root/html/TTreeViewer.html.

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.

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

Christian Stratowa

## 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="/"))

root.profile(data.test3)

## End(Not run)