Mercurial > repos > iuc > iwtomics_plotwithscale

comparison plotwithscale.R @ 0:25030f0d1154 draft

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planemo upload for repository https://github.com/fabio-cumbo/IWTomics4Galaxy commit 90c984bb9f803e1531fe4cb670e876809d48d205
author iuc
date Fri, 04 Aug 2017 17:51:16 -0400
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-1:000000000000 0:25030f0d1154
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 adjustedpvalue=args_values$adjustedpvalue
11 iwtomicsrespdf=args_values$iwtomicsrespdf
12 iwtomicssumpdf=args_values$iwtomicssumpdf
13 iwtomicsrdata=args_values$iwtomicsrdata
14 iwtomicstests=args_values$iwtomicstests
15 iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
16 test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
17 feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
18 # read parameters (from test_subset on)
19 i_scale_subset=which(args_names=='scale_subset')
20 for(i in i_scale_subset:length(args)){
21 eval(parse(text=args[[i]]))
22 }
23
24 # load RData
25 load(iwtomicsrdata)
26 # read testids and featureids and check them
27 unlisted=lapply(seq_along(test_subset),
28 function(i){
29 test_subset_i=eval(parse(text=test_subset[i]))
30 feature_subset_i=eval(parse(text=feature_subset[i]))
31 test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
32 feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
33 scale_subset_i=rep(scale_subset[i],length(test_subset_i))
34 return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
35 })
36 test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
37 feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
38 scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
39 testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
40 featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
41 id_features_subset=featureids[feature_subset]
42 if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
43 write("Wrong test ids.", stderr())
44 quit(save="no", status=10)
45 }
46 if(sum(featureids!=idFeatures(regionsFeatures_test))){
47 write("Wrong feature ids.", stderr())
48 quit(save="no", status=20)
49 }
50 # retrieve test and features_subset ids
51 id_features_subset=featureids[feature_subset]
52 if(sum(duplicated(paste0(test_subset,id_features_subset)))){
53 write("Two scale thresholds selected for the same test and feature.", stderr())
54 quit(save="no", status=30)
55 }
56 # If scale_subset=0, do not change the threshold
57 default=(scale_subset==0)
58 scale_subset=scale_subset[!default]
59 test_subset=test_subset[!default]
60 id_features_subset=id_features_subset[!default]
61
62 # get scale threshold
63 scale_threshold=lapply(regionsFeatures_test@test$result,
64 function(result) unlist(lapply(result,function(feature) feature$max_scale)))
65 for(i in seq_along(test_subset)){
66 if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){
67 write("Scale threshold too high.", stderr())
68 quit(save="no", status=40)
69 }
70 scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i]
71 }
72
73 # create adjustedvalue output
74 pval=adjusted_pval(regionsFeatures_test,scale_threshold=scale_threshold)
75 for(test in seq_along(pval)){
76 for(id_feature in idFeatures(regionsFeatures_test)){
77 write(paste0('Test: ',testids[test],', on feature ',id_feature),
78 file=adjustedpvalue,append=TRUE,sep='\t')
79 pval_i=as.data.frame(t(pval[[test]][[id_feature]]))
80 row.names(pval_i)=paste('Scale',scale_threshold[[test]][[id_feature]])
81 write.table(pval_i,file=adjustedpvalue,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
82 write('',file=adjustedpvalue,append=TRUE,sep='\t')
83 }
84 }
85
86
87 # plot test results
88 pdf(iwtomicsrespdf,width=5,height=7)
89 if(plottype=='boxplot'){
90 # fix repeated probs
91 probs=sort(unique(probs))
92 }else{
93 probs=c(0.25,0.5,0.75)
94 }
95 plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,scale_threshold=scale_threshold,ask=FALSE)
96 dev.off()
97
98 # plot summary results
99 if(groupby!='none'){
100 tryCatch({
101 pdf(iwtomicssumpdf,width=15,height=10)
102 plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE)
103 dev.off()
104 }, error = function(err) {
105 if (grepl('selected features with different resolution',err$message)) {
106 write("Group by 'test' but selected features with different resolution.", stderr())
107 quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution.
108 }
109 write("Summary plot error. Please try again.", stderr())
110 quit(save="no", status=60) #error
111 })
112 }
113
114 }else{
115 write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
116 quit(save="no", status=255)
117 }