Mercurial > repos > iuc > iwtomics_testandplot

comparison testandplot.R @ 0:800c7e974e3b draft

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planemo upload for repository https://github.com/fabio-cumbo/IWTomics4Galaxy commit 90c984bb9f803e1531fe4cb670e876809d48d205
author iuc
date Fri, 04 Aug 2017 17:51:00 -0400
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-1:000000000000 0:800c7e974e3b
1 if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
2 args=commandArgs(TRUE)
3
4 # get args names and values
5 args_values=strsplit(args,'=')
6 args_names=unlist(lapply(args_values,function(arg) arg[1]))
7 names(args_values)=args_names
8 args_values=lapply(args_values,function(arg) arg[2])
9 # read filenames
10 adjustedpvaluematrix=args_values$adjustedpvaluematrix
11 iwtomicsrespdf=args_values$iwtomicsrespdf
12 iwtomicssumpdf=args_values$iwtomicssumpdf
13 regionids=args_values$regionids
14 featureids=args_values$featureids
15 rdatafile=args_values$rdatafile
16 iwtomicsrdata=args_values$iwtomicsrdata
17 iwtomicstests=args_values$iwtomicstests
18 iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
19 # read parameters (from region1 on)
20 i_region1=which(args_names=='region1')
21 for(i in i_region1:length(args)){
22 eval(parse(text=args[[i]]))
23 }
24
25 # load RData
26 load(rdatafile)
27 # read regionids and featureids
28 regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
29 featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
30 # retrieve region1, region2 and features_subset ids and check they are in the RData
31 id_region1=regionids[region1]
32 id_region2=regionids[region2]
33 id_features_subset=featureids[features_subset]
34 if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
35 write("Wrong region ids.", stderr())
36 quit(save="no", status=10)
37 }
38 if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
39 write("Wrong feature ids.", stderr())
40 quit(save="no", status=20)
41 }
42 if(sum(duplicated(paste0(id_region1,id_region2)))){
43 write("Same test repeated multiple times.", stderr())
44 quit(save="no", status=30)
45 }
46
47 # perform test
48 tryCatch({
49 # fix repeated probs
50 if(statistics=='quantile'){
51 # fix repeated probs
52 testprobs=sort(unique(testprobs))
53 }else{
54 testprobs=0.5
55 }
56 regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset,
57 statistics=statistics,probs=testprobs,B=B)
58 # create adjustedvaluematrix output
59 for(test in seq_along(id_region1)){
60 for(id_feature in id_features_subset){
61 write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature),
62 file=adjustedpvaluematrix,append=TRUE,sep='\t')
63 pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix
64 row.names(pval)=paste('Scale',rev(seq_len(nrow(pval))))
65 write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
66 write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
67 }
68 }
69 }, error = function(err) {
70 write("Testing error.", stderr())
71 quit(save="no", status=40) #error testing
72 })
73
74 # plot test results
75 pdf(iwtomicsrespdf,width=5,height=7)
76 if(plottype=='boxplot'){
77 # fix repeated probs
78 probs=sort(unique(probs))
79 }else{
80 probs=c(0.25,0.5,0.75)
81 }
82 plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
83 dev.off()
84
85 # plot summary results
86 if(groupby!='none'){
87 pdf(iwtomicssumpdf,width=15,height=10)
88 plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE)
89 dev.off()
90 }
91
92 # create output
93 write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
94 write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
95 save(regionsFeatures_test,file=iwtomicsrdata)
96 }else{
97 write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
98 quit(save="no", status=255)
99 }