ChromosomeExplorer {aroma.core}

The ChromosomeExplorer class

Description

Package: aroma.core
Class ChromosomeExplorer

Object
~~|
~~+--Explorer
~~~~~~~|
~~~~~~~+--ChromosomeExplorer

Directly known subclasses:

public static class ChromosomeExplorer
extends Explorer

Usage

ChromosomeExplorer(model=NULL, zooms=2^(0:6), ...)

Arguments

model

A CopyNumberChromosomalModel object.

zooms

An positive integer vector specifying for which zoom levels the graphics should be generated.

...

Not used.

Fields and Methods

Methods:

	display	-
	getChromosomes	Gets the chromosomes available.
	getFullNames	-
	getModel	Gets the model.
	getNames	-
	getPath	-
	getZooms	-
	indexOf	-
	process	Generates image files, scripts and dynamic pages for the explorer.
	setArrays	Sets the arrays.
	setCytoband	-
	setZooms	-

Methods inherited from Explorer:
addIncludes, addIndexFile, as.character, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis

Generating PNG images

In order to get better looking graphs, but also to be able to generate bitmap images on systems without direct bitmap support, which is the case when running R in batch mode or on Unix without X11 support, images are created using the png2 device (a wrapper for bitmap() imitating png()). The png() is only used if png2(), which requires Ghostscript, does not. Note, when images are created using png2(), the images does not appear immediately, although the function call is completed, so be patient.

Author(s)

Henrik Bengtsson

See Also

CopyNumberChromosomalModel.