Explorer: The Explorer class

Description

Package: aroma.core Class Explorer

Object ~~| ~~+--Explorer

Directly known subclasses: ChromosomeExplorer

public abstract static class Explorer extends Object

Usage

Explorer(tags="*", version="0", ...)

Arguments

Fields and Methods

Methods:

	`display`	Displays the explorer in the default browser.
	`getFullName`	-
	`getName`	Gets the name of the explorer.
	`getNames`	Gets the names of the input samples.
	`getPath`	Gets the path of the output directory.
	`getRootPath`	Gets the root path of the output directory.
	`getTags`	Gets the tags of the explorer.
	`getVersion`	-
	`nbrOfArrays`	Gets the total number of arrays.
	`process`	Generates image files, scripts and dynamic pages for the explorer.
	`setArrays`	Sets the arrays.

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

Output directory structure

The main directory of an Explorer report is reports/<name>/<subname>/. The <name> is typically the same as the name of the input data set, and the <subname> is typically the tags of ditto. This main directory is where main HTML document is stored.

For each chip type, real or "virtual" (combined), there is a subdirectory with the same name as the chip type, i.e. reports/<name>/<subname>/<chiptype>/.

For each chip type directory, there are set of subdirectories each specifying a so called image layer, e.g. an image layer showing the raw data, another containing the estimates of a model fit and so on. Path format: reports/<name>/<subname>/<chiptype>/<image layer>/. In this directory all image files are stored, e.g. PNG files.

In some cases one do not want to all input tags to become part of the subname, but instead for instance use those to name the image layer(s). In such cases one has to override the default names.