Explorer: The Explorer class

In aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

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

tags	A character vector of tags to be added to the output path.
version	An optional character string.
...	Not used.

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.

Author(s)

Henrik Bengtsson

aroma.core documentation built on June 25, 2024, 1:15 a.m.