ChromosomeExplorer {aroma.core} | R Documentation |
Package: aroma.core
Class ChromosomeExplorer
Object
~~|
~~+--
Explorer
~~~~~~~|
~~~~~~~+--
ChromosomeExplorer
Directly known subclasses:
public static class ChromosomeExplorer
extends Explorer
ChromosomeExplorer(model=NULL, zooms=2^(0:7), ..., version=c("3"))
model |
A CopyNumberChromosomalModel object. |
zooms |
An positive integer vector specifying for which zoom
levels the graphics should be generated. |
... |
Not used. |
version |
The version of the Explorer HTML/Javascript generated/used. |
Methods:
display | - | |
getChromosomes | Gets the chromosomes available. | |
getFullNames | - | |
getModel | Gets the model. | |
getNames | - | |
getPath | - | |
getSampleLabels | - | |
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, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getParallelSafe, getPath, getReportPathPattern, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, nbrOfArrays, process, setAlias, setArrays, setParallelSafe, setReportPathPattern, setSubname, setup, splitByReportPathPattern
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save
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.
Henrik Bengtsson (http://www.braju.com/R/)