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:

BioModule, ScriptModule, Comparable<BioModule>

public class R_PlotMds
extends R_Module

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.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_PlotMds()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Require Config."r_PlotMds.numAxis" set to integer greater than 2

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

buildDockerBashScript, buildScript, executeTask, getJobParams, getMainR, getMetaMergedModule, getModuleScript, getPreRequisiteModules, 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

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