biolockj.module.report.r

Class R_CalculateStats

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.report.r.R_Module

biolockj.module.report.r.R_CalculateStats

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, Comparable<BioModule>

public class R_CalculateStats
extends R_Module
implements ApiModule

This BioModule is used to build the R script used to generate taxonomy statistics and plots.

GUI Module Name

R Statistics Calculator

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	ADJ_PVAL_ATTRIBUTE This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "ATTRIBUTE"
protected static String	ADJ_PVAL_GLOBAL This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "GLOBAL"
protected static String	ADJ_PVAL_LOCAL This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "LOCAL"
protected static String	ADJ_PVAL_TAXA This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "TAXA"
protected static String	P_VALS_NP Non parametric p-value identifier: "nonParametricPvals"
protected static String	P_VALS_NP_ADJ Non parametric adjusted p-value identifier: "adjNonParPvals"
protected static String	P_VALS_PAR Parametric p-value identifier: "parametricPvals"
protected static String	P_VALS_PAR_ADJ Parametric adjusted p-value identifier: "adjParPvals"
protected static String	R_ADJ_PVALS_SCOPE Config String property: "r_CalculateStats.pAdjustScope" defines R p.adjust( n ) parameter.
protected static String	R_PVAL_ADJ_METHOD Config String property: "r_CalculateStats.pAdjustMethod" defines p.adjust( method ) parameter.
protected static String	R_SQUARED_VALS R^2 identifier: "rSquaredVals"

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_CalculateStats()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Validate configuration file properties used to build the R report: super.checkDependencies() Require "r_CalculateStats.pAdjustScope" Require "r_CalculateStats.pAdjustMethod"
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()
static File	getStatsFile(BioModule module, String level, Boolean isParametric, Boolean isAdjusted) Get the stats file for the given fileType and taxonomy level.
static String	getSuffix(Boolean isParametric, Boolean isAdjusted) Get the file name suffix used to specify types of statistics.
static boolean	isStatsFile(File file) Analyze file name for key strings to determine if file is a stats file output by this module.
protected Map<String,String>	requiredRPackages()

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, version

Field Detail

ADJ_PVAL_ATTRIBUTE

protected static final String ADJ_PVAL_ATTRIBUTE

This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "ATTRIBUTE"

See Also:

Constant Field Values

ADJ_PVAL_GLOBAL

protected static final String ADJ_PVAL_GLOBAL

This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "GLOBAL"

See Also:

Constant Field Values

ADJ_PVAL_LOCAL

protected static final String ADJ_PVAL_LOCAL

This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "LOCAL"

See Also:

Constant Field Values

ADJ_PVAL_TAXA

protected static final String ADJ_PVAL_TAXA

This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "TAXA"

See Also:

Constant Field Values

P_VALS_NP

protected static final String P_VALS_NP

Non parametric p-value identifier: "nonParametricPvals"

See Also:

Constant Field Values

P_VALS_NP_ADJ

protected static final String P_VALS_NP_ADJ

Non parametric adjusted p-value identifier: "adjNonParPvals"

See Also:

Constant Field Values

P_VALS_PAR

protected static final String P_VALS_PAR

Parametric p-value identifier: "parametricPvals"

See Also:

Constant Field Values

P_VALS_PAR_ADJ

protected static final String P_VALS_PAR_ADJ

Parametric adjusted p-value identifier: "adjParPvals"

See Also:

Constant Field Values

R_ADJ_PVALS_SCOPE

protected static final String R_ADJ_PVALS_SCOPE

Config String property: "r_CalculateStats.pAdjustScope" defines R p.adjust( n ) parameter. There are 4 supported options:

1. "GLOBAL" n = number of all pVal tests for all fields and all taxonomy levels
2. "ATTRIBUTE" n = number of all pVal tests for 1 field at all taxonomy levels
3. "TAXA" n = number of all pVal tests for all fields at 1 taxonomy level
4. "LOCAL" n = number of all pVal tests for 1 field at 1 taxonomy level

See Also:

Constant Field Values

R_PVAL_ADJ_METHOD

protected static final String R_PVAL_ADJ_METHOD

Config String property: "r_CalculateStats.pAdjustMethod" defines p.adjust( method ) parameter. p.adjust.methods = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")

See Also:

Constant Field Values

R_SQUARED_VALS

protected static final String R_SQUARED_VALS

R^2 identifier: "rSquaredVals"

See Also:

Constant Field Values

Constructor Detail

R_CalculateStats

public R_CalculateStats()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Validate configuration file properties used to build the R report:

• super.checkDependencies()
• Require "r_CalculateStats.pAdjustScope"
• Require "r_CalculateStats.pAdjustMethod"

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

getStatsFile

public static File getStatsFile(BioModule module,
                                String level,
                                Boolean isParametric,
                                Boolean isAdjusted)
                         throws Exception

Get the stats file for the given fileType and taxonomy level.

Parameters:

module - Calling module

level - Taxonomy level

isParametric - Boolean TRUE to query for parametric file

isAdjusted - Boolean TRUE to query for adjusted p-value file

Returns:

File Table of statistics or null

Throws:

Exception - if errors occur

getSuffix

public static String getSuffix(Boolean isParametric,
                               Boolean isAdjusted)
                        throws Exception

Get the file name suffix used to specify types of statistics.

Parameters:

isParametric - boolean get the Parametric rather than the non-parametric suffix. If null, get the r-squared suffix.

isAdjusted - boolean get the adjusted rather than the non-adjusted suffix

Returns:

file name suffix

Throws:

Exception - if errors occur

isStatsFile

public static boolean isStatsFile(File file)

Analyze file name for key strings to determine if file is a stats file output by this module.

Parameters:

file - Ambiguous file

Returns:

TRUE if file name is formatted as if output by this 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:

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: