biolockj.module.report.r

Class R_PlotEffectSize

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.report.r.R_Module

biolockj.module.report.r.R_PlotEffectSize

All Implemented Interfaces:

BioModule, ScriptModule, Comparable<BioModule>

public class R_PlotEffectSize
extends R_Module

This BioModule is used to run the R script used to generate OTU-metadata fold-change-barplots for each binary report field. A pdf is created for each taxonomy level.

GUI Module Name

R Plot Effect Size

Field Summary

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

EXE_RSCRIPT, P_VAL_CUTOFF, R_COLOR_BASE, R_COLOR_HIGHLIGHT, R_COLOR_PALETTE, R_COLOR_POINT, R_DEBUG, R_FUNCTION_LIB, R_MAIN_SCRIPT, R_PCH, R_RARE_OTU_THRESHOLD, R_SAVE_R_DATA, R_TIMEOUT

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.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
R_PlotEffectSize()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() At least one of the available plot types should NOT be disabled.
List<String>	getPreRequisiteModules() Returns R_Module.getStatPreReqs() and if fold change plots are to be generated, add NormalizeTaxaTables

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

buildDockerBashScript, buildScript, executeTask, getJobParams, getMainR, getMetaMergedModule, getModuleScript, getPrimaryScript, getRTemplateDir, getStatPreReqs, getSummary, getTimeout, getWorkerScriptFunctions, writeNewScript, writePrimaryScript, writeScript

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, isValidInputModule, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.module.BioModule

cleanUp, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, isValidInputModule

Constructor Detail

R_PlotEffectSize

public R_PlotEffectSize()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

At least one of the available plot types should NOT be disabled.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class R_Module

Throws:

Exception - thrown if missing or invalid dependencies are found

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

Returns R_Module.getStatPreReqs() and if fold change plots are to be generated, add NormalizeTaxaTables

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class R_Module

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites