ChromosomeExplorer: The ChromosomeExplorer class
Description
Package: aroma.core
Class ChromosomeExplorer
Object
~~|
~~+--Explorer
~~~~~~~|
~~~~~~~+--ChromosomeExplorer
Directly known subclasses:
public static class ChromosomeExplorer
extends ExplorerUsage
ChromosomeExplorer(model=NULL, zooms=2^(0:6), ...)
Arguments
zooms
An positive integer vector specifying for which zoom
levels the graphics should be generated. Fields and Methods
Methods:
rll{
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, getParallelSafe, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setParallelSafe, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save, printGenerating 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() immitating 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.