| Previous changeset 71:0c6344d8156b (2017-06-14) Next changeset 73:156b29da2f0b (2017-06-14) |
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Commit message:
Uploaded 20170614 |
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modified:
loadandplot.xml plotwithscale.xml testandplot.xml |
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added:
._loadandplot.R ._plotwithscale.R ._testandplot.R test-data/._.DS_Store test-data/input/._Controls_regions.bed test-data/input/._Elements1_regions.bed test-data/input/._Elements2_regions.bed test-data/input/._Elements3_regions.bed test-data/input/._Feature1.bed test-data/input/._Feature2.bed test-data/input/._features.header.bed.txt test-data/input/._regions.header.txt test-data/output_loadandplot/._iwtomics.loadandplot.RData test-data/output_loadandplot/._iwtomics.loadandplot.features.txt test-data/output_loadandplot/._iwtomics.loadandplot.pdf test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.RData test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.tests.txt |
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| diff -r 0c6344d8156b -r a3bfaf944f73 ._loadandplot.R |
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| diff -r 0c6344d8156b -r a3bfaf944f73 ._plotwithscale.R |
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| diff -r 0c6344d8156b -r a3bfaf944f73 ._testandplot.R |
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| diff -r 0c6344d8156b -r a3bfaf944f73 loadandplot.xml --- a/loadandplot.xml Wed Jun 14 13:58:04 2017 -0400 +++ b/loadandplot.xml Wed Jun 14 15:20:32 2017 -0400 |
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| @@ -25,34 +25,34 @@ <![CDATA[ Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}' - #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] ) + #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] ) regionspaths='${region_paths}' - #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] ) + #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] ) regionsgalaxyids='c(${region_galaxyids})' - #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] ) + #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] ) regionsfilenames='${region_names}' - #set region_header = "${regionsheadersection.regionsheader}" + #set region_header = $regionsheadersection.regionsheader #if $region_header != "": regionsheaderfile='${region_header}' #end if - #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] ) + #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] ) featurespaths='${feature_paths}' - #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] ) + #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] ) featuresgalaxyids='c(${feature_galaxyids})' - #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] ) + #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] ) featuresfilenames='${feature_names}' - #set feature_header = "${featuresheadersection.featuresheader}" + #set feature_header = $featuresheadersection.featuresheader #if $feature_header != "": featuresheaderfile='${feature_header}' #end if - smoothing='${conditionaltype.smoothing}' + smoothing="'${conditionaltype.smoothing}'" start.are.0based='${zerobased}' #if $conditionaltype.smoothing == 'no': - alignment='${conditionaltype.alignment}' + alignment="'${conditionaltype.alignment}'" #elif $conditionaltype.smoothing == 'locpoly': - alignment='${conditionaltype.locpolyconditionalscale.alignment}' + alignment="'${conditionaltype.locpolyconditionalscale.alignment}'" #if $conditionaltype.locpolyconditionalscale.alignment == 'scale': scale='${conditionaltype.locpolyconditionalscale.scalegrid}' #end if @@ -60,14 +60,14 @@ degree='${conditionaltype.locpolydegree}' fill_gaps='${conditionaltype.fillgaps}' #elif $conditionaltype.smoothing == 'kernel': - alignment='${conditionaltype.kernelconditionalscale.alignment}' + alignment="'${conditionaltype.kernelconditionalscale.alignment}'" #if $conditionaltype.kernelconditionalscale.alignment == 'scale': scale='${conditionaltype.kernelconditionalscale.scalegrid}' #end if bandwidth='${conditionaltype.kernelbandwidth}' fill_gaps='${conditionaltype.fillgaps}' #elif $conditionaltype.smoothing == 'splines': - alignment='${conditionaltype.splinesconditionalscale.alignment}' + alignment="'${conditionaltype.splinesconditionalscale.alignment}'" #if $conditionaltype.splinesconditionalscale.alignment == 'scale': scale='${conditionaltype.splinesconditionalscale.scalegrid}' #end if @@ -78,9 +78,9 @@ average='${plotres.average}' size='${plotres.size}' - plottype='${plotres.conditionalplottype.plottype}' + plottype="'${plotres.conditionalplottype.plottype}'" #if $plotres.conditionalplottype.plottype == 'boxplot': - #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) + #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) #if $probs != "": probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})' #else: |
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| diff -r 0c6344d8156b -r a3bfaf944f73 plotwithscale.xml --- a/plotwithscale.xml Wed Jun 14 13:58:04 2017 -0400 +++ b/plotwithscale.xml Wed Jun 14 15:20:32 2017 -0400 |
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| @@ -22,19 +22,19 @@ iwtomicstests='${testids}' iwtomicsselectedfeatures='${featureids}' - #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] ) + #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] ) test_subset='${test_subset}' - #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] ) + #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] ) feature_subset='${feature_subset}' - #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] ) + #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] ) scale_subset='c(${scale_subset})' testalpha='${plotres.alpha}' average='${plotres.average}' size='${plotres.size}' - plottype='${plotres.conditionalplottype.plottype}' + plottype="'${plotres.conditionalplottype.plottype}'" #if $plotres.conditionalplottype.plottype == 'boxplot': - #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) + #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) #if $probs != "": probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})' #else: @@ -42,7 +42,7 @@ #end if #end if - groupby='${plotsum.conditionalgroupby.groupby}' + groupby="'${plotsum.conditionalgroupby.groupby}'" #if $plotsum.conditionalgroupby.groupby == "test": summaryalpha='${plotsum.conditionalgroupby.testalphaplot}' only_significant='${plotsum.conditionalgroupby.testonlysig}' |
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| diff -r 0c6344d8156b -r a3bfaf944f73 testandplot.xml --- a/testandplot.xml Wed Jun 14 13:58:04 2017 -0400 +++ b/testandplot.xml Wed Jun 14 15:20:32 2017 -0400 |
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| @@ -20,16 +20,16 @@ featureids='${featureids}' rdatafile='${rdata}' - #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] ) - #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] ) + #set region1 = ','.join( [ str( $r.region0 ) for $r in $regionssection.regions ] ) + #set region2 = ','.join( [ str( $r.region1 ) for $r in $regionssection.regions ] ) region1='c(${region1})' region2='c(${region2})' features_subset='c(${featureslist})' - statistics='${conditionalstatistics.statistics}' + statistics="'${conditionalstatistics.statistics}'" #if $conditionalstatistics.statistics == "quantile": - #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] ) + #set probabilities = ','.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] ) testprobs='c(${probabilities})' #end if @@ -38,9 +38,9 @@ testalpha='${plotres.alpha}' average='${plotres.average}' size='${plotres.size}' - plottype='${plotres.conditionalplottype.plottype}' - #if $plotres.conditionalplottype.plottype == 'boxplot': - #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) + plottype="'${plotres.conditionalplottype.plottype}'" + #if $plotres.conditionalplottype.plottype == "boxplot": + #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) #if $probs != "": probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})' #else: @@ -48,7 +48,7 @@ #end if #end if - groupby='${plotsum.conditionalgroupby.groupby}' + groupby="'${plotsum.conditionalgroupby.groupby}'" #if $plotsum.conditionalgroupby.groupby == "test": summaryalpha='${plotsum.conditionalgroupby.testalphaplot}' only_significant='${plotsum.conditionalgroupby.testonlysig}' |