Mercurial > repos > fabio > iwtomics

comparison plotwithscale.R @ 74:2bb6b44093ba draft

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Uploaded 20170619
author fabio
date Mon, 19 Jun 2017 12:08:59 -0400
parents 1e677d6b1aaf
children
comparison
equal deleted inserted replaced
73:156b29da2f0b 74:2bb6b44093ba
38 scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset)) 38 scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
39 testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE)) 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)) 40 featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
41 id_features_subset=featureids[feature_subset] 41 id_features_subset=featureids[feature_subset]
42 if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){ 42 if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
43 write("Wrong test ids.", stderr())
43 quit(save="no", status=10) 44 quit(save="no", status=10)
44 stop('Wrong test ids')
45 } 45 }
46 if(sum(featureids!=idFeatures(regionsFeatures_test))){ 46 if(sum(featureids!=idFeatures(regionsFeatures_test))){
47 write("Wrong feature ids.", stderr())
47 quit(save="no", status=20) 48 quit(save="no", status=20)
48 stop('Wrong feature ids')
49 } 49 }
50 # retrieve test and features_subset ids 50 # retrieve test and features_subset ids
51 id_features_subset=featureids[feature_subset] 51 id_features_subset=featureids[feature_subset]
52 if(sum(duplicated(paste0(test_subset,id_features_subset)))){ 52 if(sum(duplicated(paste0(test_subset,id_features_subset)))){
53 write("Two scale thresholds selected for the same test and feature.", stderr())
53 quit(save="no", status=30) 54 quit(save="no", status=30)
54 stop('Two scale thresholds selected for the same test and feature.')
55 } 55 }
56 # If scale_subset=0, do not change the threshold 56 # If scale_subset=0, do not change the threshold
57 default=(scale_subset==0) 57 default=(scale_subset==0)
58 scale_subset=scale_subset[!default] 58 scale_subset=scale_subset[!default]
59 test_subset=test_subset[!default] 59 test_subset=test_subset[!default]
62 # get scale threshold 62 # get scale threshold
63 scale_threshold=lapply(regionsFeatures_test@test$result, 63 scale_threshold=lapply(regionsFeatures_test@test$result,
64 function(result) unlist(lapply(result,function(feature) feature$max_scale))) 64 function(result) unlist(lapply(result,function(feature) feature$max_scale)))
65 for(i in seq_along(test_subset)){ 65 for(i in seq_along(test_subset)){
66 if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){ 66 if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){
67 write("Scale threshold too high.", stderr())
67 quit(save="no", status=40) 68 quit(save="no", status=40)
68 stop('Scale threshold too high.')
69 } 69 }
70 scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i] 70 scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i]
71 } 71 }
72 72
73 # create adjustedvalue output 73 # create adjustedvalue output
101 pdf(iwtomicssumpdf,width=15,height=10) 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) 102 plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE)
103 dev.off() 103 dev.off()
104 }, error = function(err) { 104 }, error = function(err) {
105 if (grepl('selected features with different resolution',err$message)) { 105 if (grepl('selected features with different resolution',err$message)) {
106 write("Group by 'test' but selected features with different resolution.", stderr())
106 quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution. 107 quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution.
107 stop(err)
108 } 108 }
109 write("Summary plot error. Please try again.", stderr())
109 quit(save="no", status=60) #error 110 quit(save="no", status=60) #error
110 stop(err)
111 }) 111 })
112 } 112 }
113 113
114 }else{ 114 }else{
115 write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
115 quit(save="no", status=255) 116 quit(save="no", status=255)
116 stop("Missing IWTomics package")
117 } 117 }