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Class RgenDemo

java.lang.Object
  |
  +--RgenDemo
public class RgenDemo
extends java.lang.Object

Class RgenDemo - generate a R demo script based on the current RLO genRbits that are set. The client-specific demo bits are defined in the R_GENR_xxxx constants.

These R snippets are for simple generation purposes - NOT for serious analysis of the array data. We expect that some people could use them as a basis for more sophisticated analyses. 

 ----------------------------------------------------------------
   NOTE: these methods are under construction and have not
   been validated..... 
   (PFL)
 ----------------------------------------------------------------

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:
$Date: 2003/06/27 19:02:47 $ $Revision: 1.48 $
Author:
P. Lemkin (NCI-Frederick); G. Thornwall (SAIC-Frederick); W.G. Alvord and Lubomirski (CSS/DMS/NCI-Frederick), Frederick, MD; S. Sundaram, SRA/BIMAS/CIT-NIH.
See Also:
MAExplorer Home, Reval, MJAReval

Field Summary
private  boolean addAnovaFlag
          RLO GenR test to add to R script: R_GENR_ANOVA
private  boolean addBoxplotFlag
          RLO GenR test to add to R script: R_GENR_BOXPLOT
private  boolean addCorFlag
          RLO GenR test to add to R script: R_GENR_COR
private  boolean addDensityFlag
          RLO GenR test to add to R script: R_GENR_DENSITY
private  boolean addHistFlag
          RLO GenR test to add to R script: R_GENR_HIST
private  boolean addLoessFlag
          RLO GenR test to add to R script: R_GENR_LOESS
private  boolean addPlotFlag
          RLO GenR test to add to R script: R_GENR_PLOT
private  boolean addSummaryFlag
          RLO GenR test to add to R script: R_GENR_SUMMARY
private  boolean addTtestFlag
          RLO GenR test to add to R script: R_GENR_TTEST
private  java.lang.String clientStateThrFile
          Input file for current RLO, if lookupRdataTypeDBvalue("State-thresholds")
private  java.lang.String clientStateValuesFile
          Input file for current RLO, if lookupRdataTypeDBvalue("Stat-flags-names")
private  java.lang.String curCondSetDataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("Cur-cond-list")
private  java.lang.String curHPdataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("Cur-HP")
private  java.lang.String curOclDataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("Cur-OCL")
private  java.lang.String f1SampleName
          F1 sample name if used
private  java.lang.String f2SampleName
          F2 sample name if used
private  java.lang.String geneAnnotationFile
          Input file for current RLO, if lookupRdataTypeDBvalue("Annotation")
private  int genRbits
          Data R generation processing bits: RB_GENR_xxxx
private  int[] getOutputDataTypes
          Output types [0:nOutputFiles-1] if any
private  java.lang.String hpEPlistDataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("HP-E-list")
private  java.lang.String hpXsetDataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("HP-X-set")
private  java.lang.String hpXYdataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("Cur-HP-XY")
private  java.lang.String hpXYsetDataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("HP-XY-sets")
private  java.lang.String hpYsetDataFile
          Input file for current RLO, if lookupRdataTypeDBvalue("HP-Y-set")
(package private)  int[] inputDataTypes
          R_DATA_TYPE_xxxx type of input file if any
private  boolean is1DdataFlag
           
private  boolean is1DsetDataFlag
           
private  boolean is2DdataFlag
           
private  boolean is2DsetDataFlag
           
private  boolean isOCLdataFlag
          Data category flag: OCL data - cur Ordered Condition Lists of samples.
private  boolean isPseudoDataFlag
           
private  java.lang.String jpgFile
          Current JPEG file for current RLO, if specified
(package private)  MaeJavaAPI mja
           
(package private)  MJAcondition mjaCondition
           
(package private)  MJAeval mjaEval
           
(package private)  MJAfilter mjaFilter
           
(package private)  MJAproperty mjaProperty
           
(package private)  MJAreport mjaReport
           
(package private)  MJAReval mjaReval
          instance of Reval
(package private)  MJAsampleList mjaSampleList
           
(package private)  MJAstate mjaState
           
(package private)  MJAutil mjaUtil
           
(package private)  MJAReval mr
           
(package private)  int nInputFiles
          # of input files if any, 0 if none
private  int nOutputFiles
          Number of output files if any
private  int nR2Client
          Number of output Action files if any
(package private) static int nUseGenRCB
          Rscript generation GUI for DEMO only: # of entries
private  int objAction
           
private  java.lang.String objName
           
private  int oldCurRLOid
          OLD RLO prior to creating R script
private  java.lang.String[] outputDataFileNames
          Output files [0:nOutputFiles-1] if any
private  java.lang.String pdfFile
          Current PDF file for current RLO, if specified
private  java.lang.String pngFile
          Current PNG file for current RLO, if specified
private  int processBits
          Data processing bits: RB_PB_xxxx
private  java.lang.String psFile
          Current Postscript file for current RLO, if specified
private  float pValueThreshold
           
(package private) static int R_GENR_ANOVA
          Generate R script bit: add anova() to generated R script
(package private) static int R_GENR_BOXPLOT
          Generate R script bit: add boxplot() plot to generated R script
(package private) static int R_GENR_COR
          Generate R script bit: add cor() to generated R script
(package private) static int R_GENR_DEMO
          Generate R script bit: This defines the RLO as a Demonstration script
(package private) static int R_GENR_DENSITY
          Generate R script bit: add density() plot to generated R script
(package private) static int R_GENR_HIST
          Generate R script bit: add hist() plot to generated R script
(package private) static int R_GENR_LOESS
          Generate R script bit: add loess(x,y) to generated R script
(package private) static int R_GENR_PLOT
          Generate R script bit: add plot(samples table) plot to generated R script
(package private) static int R_GENR_PSEUDO_DATA
          Generate R script bit: Generate pseudo data
(package private) static int R_GENR_SUMMARY
          Generate R script bit: add summary() to generated R script
(package private) static int R_GENR_TTEST
          Generate R script bit: add ttest() to generated R script
private  java.lang.String[] r2ClientFileNames
          Output Action file names [0:nR2Client-1] if any
private  java.lang.String[] r2ClientObjNames
          Output Action Object names [0:nR2Client-1] if any
private  int[] r2ClientObjTypes
          Output Action Object type [0:nR2Client-1] if any
private  int rloID
          RLO to use
(package private)  java.lang.String Rscript
          The complete generated .R script
private  java.lang.String RscriptName
          Current Rscript file for current RLO
(package private)  Rtest rt
          Rtest instance
(package private)  java.lang.String sMsg
          Return string.
private  java.lang.String sTitle
          Title is the "Method: current RLO menu name
private  java.lang.String svgFile
          Current SVG file for current RLO, if specified
private  java.lang.String tabDelimReportFile
           
private  java.lang.String tTestFct
          Optional t-test function code if required by addTtestFlag
private  boolean useF1F2dataFlag
          get x and y data from separate channels if lookupProcessBitsDBvalue("Use-F1-F2-channels") is set
(package private) static int[] useGenRbit
          Rscript generation GUI for DEMO only: add separate method generators
(package private) static java.lang.String[] useGenRname
          Rscript generation GUI for DEMO only: add separate method generators
private  boolean usingNgenesFlag
          optional flag that we defined nGenes in R if the analysis involves the nGenes R variable.
private  boolean verticallyStackedFlag
          Check if vertical stacking if processBits lookupProcessBitsDBvalue("Use-vert-stacked-data") is set
 
Constructor Summary
RgenDemo(Rtest rt)
          RgenDemo() - Constructor
 
Method Summary
(package private)  java.lang.String createClientDemoRscript(int rloID)
          createClientDemoRscript() - create Demo R script in {MAExplorer installation}/R/ folder based on the RLO file specifications and the genRbits field.
(package private)  java.lang.String genClientEpilogue()
          genClientEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.
(package private)  java.lang.String genClientReaderPrologue()
          genClientReaderPrologue() - generate client dependent Reader prologue R script to read data commands.
private  java.lang.String genDataANOVA()
          genDataANOVA() - generate data ANOVA commands [TODO] debug...
private  java.lang.String genDataBoxplot()
          genDataBoxplot() - generate data boxplot commands
private  java.lang.String genDataCorrelation()
          genDataCorrelation() - generate data Correlation tables commands
private  java.lang.String genDataDensity()
          genDataDensity() - generate data density plots commands
private  java.lang.String genDataHistogram()
          genDataHistogram() - generate data histogram plot commands
private  java.lang.String genDataLoess()
          genDataLoess() - generate data loess commands
private  java.lang.String genDataScatterplots()
          genDataScatterplots() - generate data scatterplots commands
private  java.lang.String genDataSummary()
          genDataSummary() - generate data summary commands
private  java.lang.String genDataTtest()
          genDataTtest() - generate data t-test commands
(package private)  java.lang.String genDemoPart2ClientPrologue()
          genDemoPart2ClientPrologue() - generate the demo part 2 client- dependent prologue to set global R vars from data frame just read in.
(package private)  java.lang.String genRbits2String(int rloID)
          genRbits2String() - create string representing the genRbits of the current RLayOut (RLO) of the instance
(package private)  boolean initClientStateFromRLO(int rloID)
          initClientStateFromRLO() - init create script state prior to generating R scripts.
 boolean isClientGenRmethodLegal(int genRmethod)
          isClientGenRmethodLegal() - test if specified Gen R method is legal for this data types for the current RLO.
private  boolean isInputDataType(int idType)
          isInputDataType() - test if specified input data type is used in this RLO.
 int setupClientDemoRLOdb()
          setupClientDemoRLOdb() - create MJARevalr analyses[0:nAnalyses-1] database.
 
Methods inherited from class java.lang.Object
, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait
 

Field Detail

R_GENR_DEMO

static final int R_GENR_DEMO
Generate R script bit: This defines the RLO as a Demonstration script

R_GENR_PSEUDO_DATA

static final int R_GENR_PSEUDO_DATA
Generate R script bit: Generate pseudo data

R_GENR_HIST

static final int R_GENR_HIST
Generate R script bit: add hist() plot to generated R script

R_GENR_DENSITY

static final int R_GENR_DENSITY
Generate R script bit: add density() plot to generated R script

R_GENR_LOESS

static final int R_GENR_LOESS
Generate R script bit: add loess(x,y) to generated R script

R_GENR_PLOT

static final int R_GENR_PLOT
Generate R script bit: add plot(samples table) plot to generated R script

R_GENR_BOXPLOT

static final int R_GENR_BOXPLOT
Generate R script bit: add boxplot() plot to generated R script

R_GENR_SUMMARY

static final int R_GENR_SUMMARY
Generate R script bit: add summary() to generated R script

R_GENR_TTEST

static final int R_GENR_TTEST
Generate R script bit: add ttest() to generated R script

R_GENR_ANOVA

static final int R_GENR_ANOVA
Generate R script bit: add anova() to generated R script

R_GENR_COR

static final int R_GENR_COR
Generate R script bit: add cor() to generated R script

rt

Rtest rt
Rtest instance

mja

MaeJavaAPI mja

mjaCondition

MJAcondition mjaCondition

mjaEval

MJAeval mjaEval

mjaFilter

MJAfilter mjaFilter

mjaProperty

MJAproperty mjaProperty

mjaReport

MJAreport mjaReport

mjaSampleList

MJAsampleList mjaSampleList

mjaState

MJAstate mjaState

mjaUtil

MJAutil mjaUtil

mjaReval

MJAReval mjaReval
instance of Reval

mr

MJAReval mr

oldCurRLOid

private int oldCurRLOid
OLD RLO prior to creating R script

rloID

private int rloID
RLO to use

pValueThreshold

private float pValueThreshold

RscriptName

private java.lang.String RscriptName
Current Rscript file for current RLO

pdfFile

private java.lang.String pdfFile
Current PDF file for current RLO, if specified

jpgFile

private java.lang.String jpgFile
Current JPEG file for current RLO, if specified

pngFile

private java.lang.String pngFile
Current PNG file for current RLO, if specified

psFile

private java.lang.String psFile
Current Postscript file for current RLO, if specified

svgFile

private java.lang.String svgFile
Current SVG file for current RLO, if specified

curHPdataFile

private java.lang.String curHPdataFile
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-HP")

hpXYdataFile

private java.lang.String hpXYdataFile
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-HP-XY")

hpXYsetDataFile

private java.lang.String hpXYsetDataFile
Input file for current RLO, if lookupRdataTypeDBvalue("HP-XY-sets")

hpXsetDataFile

private java.lang.String hpXsetDataFile
Input file for current RLO, if lookupRdataTypeDBvalue("HP-X-set")

hpYsetDataFile

private java.lang.String hpYsetDataFile
Input file for current RLO, if lookupRdataTypeDBvalue("HP-Y-set")

hpEPlistDataFile

private java.lang.String hpEPlistDataFile
Input file for current RLO, if lookupRdataTypeDBvalue("HP-E-list")

curCondSetDataFile

private java.lang.String curCondSetDataFile
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-cond-list")

curOclDataFile

private java.lang.String curOclDataFile
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-OCL")

geneAnnotationFile

private java.lang.String geneAnnotationFile
Input file for current RLO, if lookupRdataTypeDBvalue("Annotation")

clientStateThrFile

private java.lang.String clientStateThrFile
Input file for current RLO, if lookupRdataTypeDBvalue("State-thresholds")

clientStateValuesFile

private java.lang.String clientStateValuesFile
Input file for current RLO, if lookupRdataTypeDBvalue("Stat-flags-names")

nInputFiles

int nInputFiles
# of input files if any, 0 if none

inputDataTypes

int[] inputDataTypes
R_DATA_TYPE_xxxx type of input file if any

outputDataFileNames

private java.lang.String[] outputDataFileNames
Output files [0:nOutputFiles-1] if any

getOutputDataTypes

private int[] getOutputDataTypes
Output types [0:nOutputFiles-1] if any

nOutputFiles

private int nOutputFiles
Number of output files if any

r2ClientFileNames

private java.lang.String[] r2ClientFileNames
Output Action file names [0:nR2Client-1] if any

r2ClientObjNames

private java.lang.String[] r2ClientObjNames
Output Action Object names [0:nR2Client-1] if any

r2ClientObjTypes

private int[] r2ClientObjTypes
Output Action Object type [0:nR2Client-1] if any

nR2Client

private int nR2Client
Number of output Action files if any

tabDelimReportFile

private java.lang.String tabDelimReportFile

objName

private java.lang.String objName

objAction

private int objAction

isPseudoDataFlag

private boolean isPseudoDataFlag

is1DdataFlag

private boolean is1DdataFlag

is2DdataFlag

private boolean is2DdataFlag

is1DsetDataFlag

private boolean is1DsetDataFlag

is2DsetDataFlag

private boolean is2DsetDataFlag

isOCLdataFlag

private boolean isOCLdataFlag
Data category flag: OCL data - cur Ordered Condition Lists of samples.

verticallyStackedFlag

private boolean verticallyStackedFlag
Check if vertical stacking if processBits lookupProcessBitsDBvalue("Use-vert-stacked-data") is set

useF1F2dataFlag

private boolean useF1F2dataFlag
get x and y data from separate channels if lookupProcessBitsDBvalue("Use-F1-F2-channels") is set

processBits

private int processBits
Data processing bits: RB_PB_xxxx

genRbits

private int genRbits
Data R generation processing bits: RB_GENR_xxxx

f1SampleName

private java.lang.String f1SampleName
F1 sample name if used

f2SampleName

private java.lang.String f2SampleName
F2 sample name if used

addSummaryFlag

private boolean addSummaryFlag
RLO GenR test to add to R script: R_GENR_SUMMARY

addHistFlag

private boolean addHistFlag
RLO GenR test to add to R script: R_GENR_HIST

addDensityFlag

private boolean addDensityFlag
RLO GenR test to add to R script: R_GENR_DENSITY

addPlotFlag

private boolean addPlotFlag
RLO GenR test to add to R script: R_GENR_PLOT

addLoessFlag

private boolean addLoessFlag
RLO GenR test to add to R script: R_GENR_LOESS

addBoxplotFlag

private boolean addBoxplotFlag
RLO GenR test to add to R script: R_GENR_BOXPLOT

addTtestFlag

private boolean addTtestFlag
RLO GenR test to add to R script: R_GENR_TTEST

addAnovaFlag

private boolean addAnovaFlag
RLO GenR test to add to R script: R_GENR_ANOVA

addCorFlag

private boolean addCorFlag
RLO GenR test to add to R script: R_GENR_COR

tTestFct

private java.lang.String tTestFct
Optional t-test function code if required by addTtestFlag

usingNgenesFlag

private boolean usingNgenesFlag
optional flag that we defined nGenes in R if the analysis involves the nGenes R variable.

sTitle

private java.lang.String sTitle
Title is the "Method: current RLO menu name

useGenRname

static java.lang.String[] useGenRname
Rscript generation GUI for DEMO only: add separate method generators

useGenRbit

static int[] useGenRbit
Rscript generation GUI for DEMO only: add separate method generators

nUseGenRCB

static int nUseGenRCB
Rscript generation GUI for DEMO only: # of entries

Rscript

java.lang.String Rscript
The complete generated .R script

sMsg

java.lang.String sMsg
Return string. OK if null, else contains the problem
Constructor Detail

RgenDemo

public RgenDemo(Rtest rt)
RgenDemo() - Constructor
Parameters:
rt - is the Rtest
mja - is the MaejavaAPI instance
Method Detail

setupClientDemoRLOdb

public int setupClientDemoRLOdb()
setupClientDemoRLOdb() - create MJARevalr analyses[0:nAnalyses-1] database. This specifies, for each analysis, the MAExplorer data to extract to input files to be read by R when the R script is run. It also specifies the output files created by R that we should read after the R eval is finished. 
 Notes
 1. Add new analyses here. 
 2. We could fill in this database from an external disk database of 
    R-layouts as ".rlo" files that describes the analysis methods.
 3. You must put the .R script files in the {MAExplorer installation}/R 
    directory
 4. If there are input files, they will be created and saved in the
    {project}/Temp/ directory

 5. The output files will appear in the {project}/Report directory
    if any are created.
Returns:
number of analyses in DB if succeed in building this database
See Also:
createClientDemoRscript(int), MJAReval.readPermanentRLOdatabase(boolean), MJAReval.addRLO(java.lang.String, java.lang.String, java.lang.String, java.lang.String[], int[], int, int, java.lang.String[], int[], java.lang.String[], java.lang.String[], int[], java.lang.String), MJAReval.getNbrAnalyses()

createClientDemoRscript

java.lang.String createClientDemoRscript(int rloID)
createClientDemoRscript() - create Demo R script in {MAExplorer installation}/R/ folder based on the RLO file specifications and the genRbits field.
[NOTES]
  • that this demo .R script is shares the {MAExplorer installation}/R/ directory that has the fixed .R scripts distributed with MAExplorer. Therefore, care must be taken to name them differently.
  • Just because a genRbit is enabled, it will not necessarily generate that option. Rather, the data must support the option AND the genRbits must be enabled.
  • The genRbits are defined as R_GENR_xxxx constants.

    Returns:
    null if succeed and wrote out the demo script, else error message
    See Also:
    MJAReval.getRscriptBasePath(), MJAReval.setCurrentRLO(int), MJAreport.writeTextToFile(java.lang.String, java.lang.String), MJAutil.cvtBackslash2Fwdslash(java.lang.String), genDataANOVA(), genDataBoxplot(), genDataCorrelation(), genDataDensity(), #genEpilogue, genDataHistogram(), genDataLoess(), genDataScatterplots(), genDataSummary(), genDataTtest(), initClientStateFromRLO(int)

    • isClientGenRmethodLegal

    public boolean isClientGenRmethodLegal(int genRmethod)
    isClientGenRmethodLegal() - test if specified Gen R method is legal for this data types for the current RLO. We do this by testing input file specs to match methods available in the GenRtest code generators.

    [NOTE] keep this up to date or it won't offer the right choices

    Parameters:
    genRmethod - indexes the useGenRbit[] table.
    Returns:
    true if it is legal
    See Also:
    MJAreport#getInputDataTypes, isInputDataType(int)

    isInputDataType

    private boolean isInputDataType(int idType)
    isInputDataType() - test if specified input data type is used in this RLO. Note: we must set up the local inputDataTypes[0:nInputFiles-1] data.
    Parameters:
    idType - is the input data type to test for membership in inputDataTypes[0:nInputFiles-1].
    Returns:
    true if it is

    initClientStateFromRLO

    boolean initClientStateFromRLO(int rloID)
    initClientStateFromRLO() - init create script state prior to generating R scripts. This state can then be used by the generators for prologue, epilogue, and demo genXXXX code generators based on based on the RLO file specifications and the genRbits field.

    Parameters:
    rloID - to init
    Returns:
    true if succeed
    See Also:
    MJAReval.getAllProcessBits(), MJAReval.getAllGenRbits(), MJAReval.getCurrentRLOid(), MJAReval.getRLOinputFile(int, int), MJAReval.getRLOoutFile(int, int), MJAReval.getCurrentRLORscriptName(), MJAReval.getOutputDataFileNames(), MJAReval.getOutputDataTypes(), MJAReval.getSetR2ClientFileNames(), MJAReval.getSetR2ClientObjNames(), MJAReval.getSetR2ClientObjTypes(), MJAReval.setCurrentRLO(int), MJAReval.setCurrentRLO(int)

    genClientReaderPrologue

    java.lang.String genClientReaderPrologue()
    genClientReaderPrologue() - generate client dependent Reader prologue R script to read data commands. Generate the Rscript.
    Returns:
    Rscript if OK, else null. Then sMsg contains error message
    See Also:
    MJAReval.getCurrentRLOmenuName(), MJAcondition.getCurCondition(), MJAcondition.getCurOCL(), MJAsampleList.getCurrent_HP_name(boolean), MJAutil.cvtBackslash2Fwdslash(java.lang.String)

    genDemoPart2ClientPrologue

    java.lang.String genDemoPart2ClientPrologue()
    genDemoPart2ClientPrologue() - generate the demo part 2 client- dependent prologue to set global R vars from data frame just read in.
    Returns:
    null if nothing generated, else return additional R code

    genClientEpilogue

    java.lang.String genClientEpilogue()
    genClientEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.

    If tabDelimReportFile exists and an objAction is specified, then it will write out the following R object with write.table(). 

     lookupR2ClientActionDBvalue objAction   R object to write
 =========                               =================
 "Gene-set"                              genesActionList
 "Gene-set-pValues"                      genesActionList
 "Gene-set-clusters"                     genesActionList
 "Gene-set-dataFilter"                   genesActionList
 "Gene-set-normalization")               genesActionList
 "Condition-list"                        condActionList
 "OCL"                                   oclActionList
 "Map-normalization"                     mapActionList
 "Map-2Dplot-overlay"                    mapActionList
 "Poly-normalization"                    polyActionList
    [TODO] needs work...
    Returns:
    Rscript if OK, else null. Then sMsg contains error message

    genDataSummary

    private java.lang.String genDataSummary()
    genDataSummary() - generate data summary commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataHistogram

    private java.lang.String genDataHistogram()
    genDataHistogram() - generate data histogram plot commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataDensity

    private java.lang.String genDataDensity()
    genDataDensity() - generate data density plots commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataScatterplots

    private java.lang.String genDataScatterplots()
    genDataScatterplots() - generate data scatterplots commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataLoess

    private java.lang.String genDataLoess()
    genDataLoess() - generate data loess commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataBoxplot

    private java.lang.String genDataBoxplot()
    genDataBoxplot() - generate data boxplot commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataTtest

    private java.lang.String genDataTtest()
    genDataTtest() - generate data t-test commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataANOVA

    private java.lang.String genDataANOVA()
    genDataANOVA() - generate data ANOVA commands [TODO] debug...
    Returns:
    R script if OK, else null and sMsg contains error message

    genDataCorrelation

    private java.lang.String genDataCorrelation()
    genDataCorrelation() - generate data Correlation tables commands
    Returns:
    R script if OK, else null and sMsg contains error message

    genRbits2String

    java.lang.String genRbits2String(int rloID)
    genRbits2String() - create string representing the genRbits of the current RLayOut (RLO) of the instance
    Parameters:
    rloID - is the index of the RLO to convert
    Returns:
    string representing the RLO genRbits
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