# HG changeset patch
# User iuc
# Date 1501883476 14400
# Node ID 25030f0d115413a68fa6946c54b59f8920cd8d58
planemo upload for repository https://github.com/fabio-cumbo/IWTomics4Galaxy commit 90c984bb9f803e1531fe4cb670e876809d48d205
diff -r 000000000000 -r 25030f0d1154 loadandplot.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.R Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,144 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+ args=commandArgs(TRUE)
+
+ # get args names and values
+ args_values=strsplit(args,'=')
+ args_names=unlist(lapply(args_values,function(arg) arg[1]))
+ names(args_values)=args_names
+ args_values=lapply(args_values,function(arg) arg[2])
+ # read filenames
+ outrdata=args_values$outrdata
+ outregions=args_values$outregions
+ outfeatures=args_values$outfeatures
+ outpdf=args_values$outpdf
+ regionspaths=unlist(strsplit(args_values$regionspaths,'\\|'))
+ if("regionsheaderfile" %in% args_names){
+ # the file regionsheaderfile must contain as first column the (unique) regionsfilenames,
+ # as second column the corresponding ids and as third column the names
+ tryCatch({
+ regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+ regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|'))
+ if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
+ write("IWTomics message: Not all region files are present in the first column of header file for regions.", stderr())
+ quit(save="no", status=11)
+ }
+ id_regions=regionsheader[regionsfilenames,1]
+ name_regions=regionsheader[regionsfilenames,2]
+ }, error = function(err) {
+ write("IWTomics message: An error has occurred reading the header file for regions. Please try again.", stderr())
+ quit(save="no", status=10) #error on header file
+ })
+ }else{
+ eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
+ id_regions=paste0('data_',regionsgalaxyids)
+ name_regions=paste0('data_',regionsgalaxyids)
+ }
+ featurespaths=unlist(strsplit(args_values$featurespaths,'\\|'))
+ if("featuresheaderfile" %in% args_names){
+ # the file featuresheaderfile must contain as first column the (unique) featuresfilenames,
+ # as second column the corresponding ids and as third column the names
+ tryCatch({
+ featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+ featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|'))
+ if(length(setdiff(featuresfilenames,row.names(featuresheader)))) {
+ write("IWTomics message: Not all feature files are present in the first column of header file for features.", stderr())
+ quit(save="no", status=21)
+ }
+ id_features=featuresheader[featuresfilenames,1]
+ name_features=featuresheader[featuresfilenames,2]
+ }, error = function(err) {
+ write("IWTomics message: An error has occurred reading the header file for features. Please try again.", stderr())
+ quit(save="no", status=20) #error on header file
+ })
+ }else{
+ eval(parse(text=args[[which(args_names=='featuresgalaxyids')]]))
+ id_features=paste0('data_',featuresgalaxyids)
+ name_features=paste0('data_',featuresgalaxyids)
+ }
+ # read parameters (from smoothing on)
+ i_smoothing=which(args_names=='smoothing')
+ for(i in i_smoothing:length(args)){
+ eval(parse(text=args[[i]]))
+ }
+
+ # load data
+ tryCatch({
+ regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment,
+ id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based)
+ }, error = function(err) {
+ if(grepl('invalid format',err$message)){
+ write("IWTomics message: Not enough columns in input file.", stderr())
+ quit(save="no", status=31) # error, not enough columns in input file
+ }else if(grepl('duplicated regions',err$message)){
+ write("IWTomics message: Duplicated regions in region file.", stderr())
+ quit(save="no", status=32) # error, duplicated regions in region file
+ }else if(grepl('duplicated windows',err$message)){
+ write("IWTomics message: Duplicated windows in feature file.", stderr())
+ quit(save="no", status=33) # error, duplicated windows in feature file
+ }else if(grepl('overlapping windows',err$message)){
+ write("IWTomics message: Overlapping windows in feature file.", stderr())
+ quit(save="no", status=34) # error, overlapping windows in feature file
+ }else if(grepl('not all regions in datasets',err$message)){
+ write("IWTomics message: Windows in feature files do not cover all regions in region files.", stderr())
+ quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
+ }else if(grepl('ifferent size windows',err$message)){
+ write("IWTomics message: All windows in a feature file must have the same size.", stderr())
+ quit(save="no", status=36) # error, all windows in a feature files must have the same size
+ }
+ #error loading data
+ write("IWTomics message: An error has occurred reading the data. Please try again.", stderr())
+ quit(save="no", status=30)
+ })
+
+ # smooth data
+ if(smoothing!='no'){
+ tryCatch({
+ if(smoothing=='locpoly'){
+ dist_knots=10
+ }else if(smoothing=='kernel'){
+ degree=3
+ dist_knots=10
+ }else if(smoothing=='splines'){
+ bandwidth=5
+ }
+ if(alignment=='scale'){
+ if(scale==0){
+ regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+ bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+ }else{
+ regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+ bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale)
+ }
+ }else{
+ regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+ bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+ }
+ }, error = function(err) {
+ write("IWTomics message: An error has occurred smoothing the data. Please try again.", stderr())
+ quit(save="no", status=40) #error on smoothing
+ })
+ }
+
+ # plot data
+ pdf(outpdf,width=10,height=8)
+ if(plottype=='boxplot'){
+ # fix repeated probs
+ probs=sort(unique(probs))
+ }else{
+ probs=c(0.25,0.5,0.75)
+ }
+ plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+ dev.off()
+
+ # create output
+ #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)),
+ #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)),
+ #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ save(regionsFeatures,file=outrdata)
+}else{
+ write("IWTomics message: Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
+ quit(save="no", status=255)
+}
\ No newline at end of file
diff -r 000000000000 -r 25030f0d1154 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,105 @@
+
+ 1.0.0
+
+
+ bioconductor-iwtomics
+
+
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+
+
+ 10.1080/10485252.2017.1306627
+
+ @MANUAL{
+ iwtomics,
+ author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.},
+ title = {IWTomics: Interval-Wise Testing for Omics Data},
+ note = {R package version 1.0.0},
+ year = {2017}
+ }
+
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diff -r 000000000000 -r 25030f0d1154 plotwithscale.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/plotwithscale.R Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,117 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+ args=commandArgs(TRUE)
+
+ # get args names and values
+ args_values=strsplit(args,'=')
+ args_names=unlist(lapply(args_values,function(arg) arg[1]))
+ names(args_values)=args_names
+ args_values=lapply(args_values,function(arg) arg[2])
+ # read filenames
+ adjustedpvalue=args_values$adjustedpvalue
+ iwtomicsrespdf=args_values$iwtomicsrespdf
+ iwtomicssumpdf=args_values$iwtomicssumpdf
+ iwtomicsrdata=args_values$iwtomicsrdata
+ iwtomicstests=args_values$iwtomicstests
+ iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+ test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
+ feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
+ # read parameters (from test_subset on)
+ i_scale_subset=which(args_names=='scale_subset')
+ for(i in i_scale_subset:length(args)){
+ eval(parse(text=args[[i]]))
+ }
+
+ # load RData
+ load(iwtomicsrdata)
+ # read testids and featureids and check them
+ unlisted=lapply(seq_along(test_subset),
+ function(i){
+ test_subset_i=eval(parse(text=test_subset[i]))
+ feature_subset_i=eval(parse(text=feature_subset[i]))
+ test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
+ feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
+ scale_subset_i=rep(scale_subset[i],length(test_subset_i))
+ return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
+ })
+ test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
+ feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
+ scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
+ testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ id_features_subset=featureids[feature_subset]
+ if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
+ write("Wrong test ids.", stderr())
+ quit(save="no", status=10)
+ }
+ if(sum(featureids!=idFeatures(regionsFeatures_test))){
+ write("Wrong feature ids.", stderr())
+ quit(save="no", status=20)
+ }
+ # retrieve test and features_subset ids
+ id_features_subset=featureids[feature_subset]
+ if(sum(duplicated(paste0(test_subset,id_features_subset)))){
+ write("Two scale thresholds selected for the same test and feature.", stderr())
+ quit(save="no", status=30)
+ }
+ # If scale_subset=0, do not change the threshold
+ default=(scale_subset==0)
+ scale_subset=scale_subset[!default]
+ test_subset=test_subset[!default]
+ id_features_subset=id_features_subset[!default]
+
+ # get scale threshold
+ scale_threshold=lapply(regionsFeatures_test@test$result,
+ function(result) unlist(lapply(result,function(feature) feature$max_scale)))
+ for(i in seq_along(test_subset)){
+ if(scale_threshold[[test_subset[i]]][id_features_subset[i]]
+ on Test Scale
+
+ macros.xml
+
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diff -r 000000000000 -r 25030f0d1154 test-data/input/Controls_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Controls_regions.bed Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,35 @@
+chr1 91399892 91499892
+chr1 116447079 116547079
+chr2 231381109 231481109
+chr3 47386633 47486633
+chr3 99195712 99295712
+chr3 116765114 116865114
+chr3 134345017 134445017
+chr4 68064019 68164019
+chr4 137465811 137565811
+chr4 173293016 173393016
+chr5 59044110 59144110
+chr5 94592763 94692763
+chr5 108436006 108536006
+chr5 110836898 110936898
+chr5 146661073 146761073
+chr6 99727306 99827306
+chr7 88291325 88391325
+chr7 120999784 121099784
+chr8 126860366 126960366
+chr8 127636547 127736547
+chr11 41362564 41462564
+chr11 101741527 101841527
+chr12 15210277 15310277
+chr13 91106037 91206037
+chr13 91518822 91618822
+chr13 98959030 99059030
+chr15 39087176 39187176
+chr17 58542142 58642142
+chr18 12199823 12299823
+chr20 8173704 8273704
+chr21 16255112 16355112
+chr21 45089115 45189115
+chrX 23898983 23998983
+chrX 37029585 37129585
+chrX 103593349 103693349
diff -r 000000000000 -r 25030f0d1154 test-data/input/Elements1_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Elements1_regions.bed Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,25 @@
+chr2 49960150 50060150
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+chr3 140326750 140426750
+chr4 41772201 41872201
+chr4 70629719 70729719
+chr4 109340735 109440735
+chr5 15025389 15125389
+chr5 43028888 43128888
+chr5 58231354 58331354
+chr5 91277761 91377761
+chr5 119464508 119564508
+chr6 85309170 85409170
+chr6 85762072 85862072
+chr6 134621363 134721363
+chr6 147470164 147570164
+chr7 77195798 77295798
+chr7 77880914 77980914
+chr7 114805399 114905399
+chr10 46350885 46450885
+chr10 67833078 67933078
+chr12 27722692 27822692
+chr12 95518506 95618506
+chr12 117863466 117963466
+chr14 100464166 100564166
+chrX 29266748 29366748
diff -r 000000000000 -r 25030f0d1154 test-data/input/Elements2_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Elements2_regions.bed Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,20 @@
+chr1 65942901 66042901
+chr1 117128102 117228102
+chr1 190338169 190438169
+chr2 227365478 227465478
+chr6 50856764 50956764
+chr6 135703067 135803067
+chr7 38228726 38328726
+chr7 51115898 51215898
+chr7 150325760 150425760
+chr8 25475691 25575691
+chr9 73374609 73474609
+chr11 55092625 55192625
+chr11 86581661 86681661
+chr12 12795284 12895284
+chr12 48151882 48251882
+chr12 83109951 83209951
+chr15 31430278 31530278
+chr15 65610815 65710815
+chr17 40766223 40866223
+chr20 17245048 17345048
diff -r 000000000000 -r 25030f0d1154 test-data/input/Elements3_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Elements3_regions.bed Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,28 @@
+chr1 49721616 49821616
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+chr2 73790843 73890843
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+chr5 58501529 58601529
+chr5 152853250 152953250
+chr6 136085023 136185023
+chr6 147019529 147119529
+chr7 14192964 14292964
+chr7 125519883 125619883
+chr8 77652872 77752872
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+chr21 15966609 16066609
diff -r 000000000000 -r 25030f0d1154 test-data/input/Feature1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Feature1.bed Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,5400 @@
+chr1 91399892 91401892 0.914729028492568
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diff -r 000000000000 -r 25030f0d1154 test-data/input/Feature2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/Feature2.bed Fri Aug 04 17:51:16 2017 -0400
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diff -r 000000000000 -r 25030f0d1154 test-data/input/features.header.bed.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/features.header.bed.txt Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,2 @@
+Feature1.bed ftr1 Feature 1
+Feature2.bed ftr2 Feature 2
\ No newline at end of file
diff -r 000000000000 -r 25030f0d1154 test-data/input/regions.header.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input/regions.header.txt Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,4 @@
+Elements1_regions.bed elem1 Elements 1
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\ No newline at end of file
diff -r 000000000000 -r 25030f0d1154 test-data/output_loadandplot/iwtomics.loadandplot.RData
Binary file test-data/output_loadandplot/iwtomics.loadandplot.RData has changed
diff -r 000000000000 -r 25030f0d1154 test-data/output_loadandplot/iwtomics.loadandplot.features.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_loadandplot/iwtomics.loadandplot.features.txt Fri Aug 04 17:51:16 2017 -0400
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diff -r 000000000000 -r 25030f0d1154 test-data/output_loadandplot/iwtomics.loadandplot.pdf
Binary file test-data/output_loadandplot/iwtomics.loadandplot.pdf has changed
diff -r 000000000000 -r 25030f0d1154 test-data/output_loadandplot/iwtomics.loadandplot.regions.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 25030f0d1154 test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt Fri Aug 04 17:51:16 2017 -0400
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+Test: elem1 vs control, on feature ftr1
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+Test: elem3 vs control, on feature ftr2
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diff -r 000000000000 -r 25030f0d1154 test-data/output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf
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diff -r 000000000000 -r 25030f0d1154 test-data/output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf
Binary file test-data/output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf has changed
diff -r 000000000000 -r 25030f0d1154 test-data/output_testandplot/iwtomics.testandplot.RData
Binary file test-data/output_testandplot/iwtomics.testandplot.RData has changed
diff -r 000000000000 -r 25030f0d1154 test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,312 @@
+Test: elem1 vs control, on feature ftr1
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+
+Test: elem2 vs control, on feature ftr1
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+Scale 11 0.81 0.81 0.82 0.853 0.883 0.949 0.89 0.89 0.89 0.89 0.941 0.941 0.89 0.89 0.89 0.89 0.895 0.878 0.842 0.818 0.813 0.774 0.562 0.07 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 10 0.778 0.778 0.802 0.838 0.883 0.949 0.883 0.883 0.883 0.883 0.941 0.941 0.883 0.88 0.88 0.88 0.895 0.878 0.839 0.798 0.756 0.732 0.528 0.064 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 9 0.743 0.743 0.763 0.827 0.883 0.949 0.883 0.883 0.883 0.883 0.941 0.941 0.883 0.88 0.88 0.88 0.895 0.878 0.805 0.737 0.708 0.708 0.517 0.051 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 8 0.724 0.724 0.724 0.782 0.866 0.949 0.875 0.875 0.875 0.88 0.941 0.941 0.88 0.88 0.88 0.88 0.895 0.858 0.75 0.697 0.697 0.697 0.499 0.038 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 7 0.71 0.71 0.71 0.731 0.826 0.949 0.861 0.861 0.861 0.88 0.941 0.941 0.863 0.863 0.863 0.863 0.895 0.801 0.695 0.685 0.685 0.685 0.436 0.029 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 6 0.681 0.671 0.671 0.695 0.78 0.949 0.823 0.823 0.823 0.88 0.941 0.941 0.859 0.82 0.82 0.824 0.895 0.74 0.667 0.667 0.667 0.632 0.349 0.023 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 5 0.681 0.622 0.63 0.669 0.759 0.949 0.822 0.767 0.813 0.88 0.941 0.941 0.859 0.801 0.756 0.824 0.895 0.74 0.653 0.634 0.608 0.545 0.306 0.015 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 4 0.681 0.622 0.588 0.655 0.759 0.949 0.822 0.734 0.787 0.88 0.941 0.941 0.859 0.773 0.738 0.824 0.895 0.74 0.638 0.569 0.564 0.545 0.278 0.009 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 3 0.681 0.622 0.588 0.599 0.759 0.949 0.822 0.726 0.706 0.88 0.941 0.941 0.859 0.672 0.738 0.824 0.895 0.74 0.567 0.512 0.564 0.545 0.234 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 2 0.681 0.622 0.5 0.5 0.717 0.949 0.822 0.578 0.586 0.784 0.941 0.941 0.759 0.534 0.611 0.824 0.895 0.662 0.45 0.47 0.564 0.545 0.158 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+Scale 1 0.681 0.553 0.434 0.417 0.582 0.949 0.66 0.476 0.513 0.664 0.889 0.868 0.592 0.461 0.487 0.708 0.895 0.512 0.342 0.402 0.564 0.494 0.074 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
+
diff -r 000000000000 -r 25030f0d1154 test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf
Binary file test-data/output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf has changed
diff -r 000000000000 -r 25030f0d1154 test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_testandplot/iwtomics.testandplot.selectedfeatures.txt Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,1 @@
+ftr1 ftr2
diff -r 000000000000 -r 25030f0d1154 test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf
Binary file test-data/output_testandplot/iwtomics.testandplot.summaryplot.pdf has changed
diff -r 000000000000 -r 25030f0d1154 test-data/output_testandplot/iwtomics.testandplot.tests.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_testandplot/iwtomics.testandplot.tests.txt Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,1 @@
+elem1 vs control elem2 vs control elem3 vs control
diff -r 000000000000 -r 25030f0d1154 testandplot.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testandplot.R Fri Aug 04 17:51:16 2017 -0400
@@ -0,0 +1,99 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+ args=commandArgs(TRUE)
+
+ # get args names and values
+ args_values=strsplit(args,'=')
+ args_names=unlist(lapply(args_values,function(arg) arg[1]))
+ names(args_values)=args_names
+ args_values=lapply(args_values,function(arg) arg[2])
+ # read filenames
+ adjustedpvaluematrix=args_values$adjustedpvaluematrix
+ iwtomicsrespdf=args_values$iwtomicsrespdf
+ iwtomicssumpdf=args_values$iwtomicssumpdf
+ regionids=args_values$regionids
+ featureids=args_values$featureids
+ rdatafile=args_values$rdatafile
+ iwtomicsrdata=args_values$iwtomicsrdata
+ iwtomicstests=args_values$iwtomicstests
+ iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+ # read parameters (from region1 on)
+ i_region1=which(args_names=='region1')
+ for(i in i_region1:length(args)){
+ eval(parse(text=args[[i]]))
+ }
+
+ # load RData
+ load(rdatafile)
+ # read regionids and featureids
+ regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ # retrieve region1, region2 and features_subset ids and check they are in the RData
+ id_region1=regionids[region1]
+ id_region2=regionids[region2]
+ id_features_subset=featureids[features_subset]
+ if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
+ write("Wrong region ids.", stderr())
+ quit(save="no", status=10)
+ }
+ if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
+ write("Wrong feature ids.", stderr())
+ quit(save="no", status=20)
+ }
+ if(sum(duplicated(paste0(id_region1,id_region2)))){
+ write("Same test repeated multiple times.", stderr())
+ quit(save="no", status=30)
+ }
+
+ # perform test
+ tryCatch({
+ # fix repeated probs
+ if(statistics=='quantile'){
+ # fix repeated probs
+ testprobs=sort(unique(testprobs))
+ }else{
+ testprobs=0.5
+ }
+ regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset,
+ statistics=statistics,probs=testprobs,B=B)
+ # create adjustedvaluematrix output
+ for(test in seq_along(id_region1)){
+ for(id_feature in id_features_subset){
+ write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature),
+ file=adjustedpvaluematrix,append=TRUE,sep='\t')
+ pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix
+ row.names(pval)=paste('Scale',rev(seq_len(nrow(pval))))
+ write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+ write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
+ }
+ }
+ }, error = function(err) {
+ write("Testing error.", stderr())
+ quit(save="no", status=40) #error testing
+ })
+
+ # plot test results
+ pdf(iwtomicsrespdf,width=5,height=7)
+ if(plottype=='boxplot'){
+ # fix repeated probs
+ probs=sort(unique(probs))
+ }else{
+ probs=c(0.25,0.5,0.75)
+ }
+ plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+ dev.off()
+
+ # plot summary results
+ if(groupby!='none'){
+ pdf(iwtomicssumpdf,width=15,height=10)
+ plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE)
+ dev.off()
+ }
+
+ # create output
+ write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ save(regionsFeatures_test,file=iwtomicsrdata)
+}else{
+ write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
+ quit(save="no", status=255)
+}
\ No newline at end of file