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comparison plotwithscale.xml @ 72:a3bfaf944f73 draft

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Uploaded 20170614
author fabio
date Wed, 14 Jun 2017 15:20:32 -0400
parents 39e7294c66e1
children 2bb6b44093ba
comparison
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71:0c6344d8156b 72:a3bfaf944f73
20 Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' 20 Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
21 iwtomicsrdata='${rdata}' 21 iwtomicsrdata='${rdata}'
22 iwtomicstests='${testids}' 22 iwtomicstests='${testids}'
23 iwtomicsselectedfeatures='${featureids}' 23 iwtomicsselectedfeatures='${featureids}'
24 24
25 #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] ) 25 #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
26 test_subset='${test_subset}' 26 test_subset='${test_subset}'
27 #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] ) 27 #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
28 feature_subset='${feature_subset}' 28 feature_subset='${feature_subset}'
29 #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] ) 29 #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
30 scale_subset='c(${scale_subset})' 30 scale_subset='c(${scale_subset})'
31 31
32 testalpha='${plotres.alpha}' 32 testalpha='${plotres.alpha}'
33 average='${plotres.average}' 33 average='${plotres.average}'
34 size='${plotres.size}' 34 size='${plotres.size}'
35 plottype='${plotres.conditionalplottype.plottype}' 35 plottype="'${plotres.conditionalplottype.plottype}'"
36 #if $plotres.conditionalplottype.plottype == 'boxplot': 36 #if $plotres.conditionalplottype.plottype == 'boxplot':
37 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) 37 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
38 #if $probs != "": 38 #if $probs != "":
39 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})' 39 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
40 #else: 40 #else:
41 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})' 41 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
42 #end if 42 #end if
43 #end if 43 #end if
44 44
45 groupby='${plotsum.conditionalgroupby.groupby}' 45 groupby="'${plotsum.conditionalgroupby.groupby}'"
46 #if $plotsum.conditionalgroupby.groupby == "test": 46 #if $plotsum.conditionalgroupby.groupby == "test":
47 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}' 47 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
48 only_significant='${plotsum.conditionalgroupby.testonlysig}' 48 only_significant='${plotsum.conditionalgroupby.testonlysig}'
49 #elif $plotsum.conditionalgroupby.groupby == "feature": 49 #elif $plotsum.conditionalgroupby.groupby == "feature":
50 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}' 50 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'