biolockj.module.report.r

Class R_PlotMds

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.report.r.R_Module

biolockj.module.report.r.R_PlotMds

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, Comparable<BioModule>

public class R_PlotMds
extends R_Module
implements ApiModule

This BioModule is used to build the R script used to generate MDS plots for each report field and each taxonomy level configured.

GUI Module Name

R Plot MDS

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	R_MDS_DISTANCE Config property: "r_PlotMds.distance" defines the distance index to use in the capscale command.
protected static String	R_MDS_NUM_AXIS Config Integer property: "r_PlotMds.numAxis" defines the number of MDS axis to report
protected static String	R_MDS_REPORT_FIELDS Config List property: "r_PlotMds.reportFields" List metadata fields to generate MDS ordination plots.

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
R_PlotMds()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Require Config."r_PlotMds.numAxis" set to integer greater than 2
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
protected String	getModulePrefix() Returns that prefix to use for property names.
protected String	getModuleRScriptName()
protected Map<String,String>	requiredRPackages()
String	version() Changes to a module class should be accompanied by a increment in version.

Methods inherited from class biolockj.module.report.r.R_Module

buildScript, calcTimeout, cleanUp, executeTask, getCustomScriptProp, getDockerImageName, getDockerImageOwner, getDockerImageTag, getFunctionLib, getFunctionLib, getModuleRScript, getTimeout, grapRUsedProps

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getWorkerScriptFunctions, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias

Field Detail

R_MDS_DISTANCE

protected static final String R_MDS_DISTANCE

Config property: "r_PlotMds.distance" defines the distance index to use in the capscale command.

See Also:

Constant Field Values

R_MDS_NUM_AXIS

protected static final String R_MDS_NUM_AXIS

Config Integer property: "r_PlotMds.numAxis" defines the number of MDS axis to report

See Also:

Constant Field Values

R_MDS_REPORT_FIELDS

protected static final String R_MDS_REPORT_FIELDS

Config List property: "r_PlotMds.reportFields"
List metadata fields to generate MDS ordination plots.

See Also:

Constant Field Values

Constructor Detail

R_PlotMds

public R_PlotMds()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Require Config."r_PlotMds.numAxis" set to integer greater than 2

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class R_Module

Throws:

Exception - thrown if missing or invalid dependencies are found

requiredRPackages

protected Map<String,String> requiredRPackages()

Overrides:

requiredRPackages in class R_Module

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns:

version

public String version()

Description copied from interface: BioModule

Changes to a module class should be accompanied by a increment in version. The is a string and open form, but using the major.minor.patch semantic versioning is recommended.

Specified by:

version in interface BioModule

Returns:

getModuleRScriptName

protected String getModuleRScriptName()

Specified by:

getModuleRScriptName in class R_Module

getModulePrefix

protected String getModulePrefix()

Description copied from class: R_Module

Returns that prefix to use for property names.

Specified by:

getModulePrefix in class R_Module

Returns: