Mercurial > repos > rnateam > locarna_pairwise

annotate test-data/archaea_relplot.scr @ 0:6a79a086fa50 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author rnateam
date Wed, 28 Dec 2016 18:53:24 -0500
parents
children f3f08a777c10
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6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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1 pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4")
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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3 rel <- read.table("mlocarna_results/results/result.bmreliability");
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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4 seqrel <- rel[[2]]
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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5 strrel <- rel[[3]]
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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7 if ("" != "") {
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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8 seq <- ""
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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9 seq <- strsplit(seq,split="")
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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10 tab <- unlist(seq)!="-"
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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12 seqrel<-seqrel[tab]
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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13 strrel<-strrel[tab]
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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14 }
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16 len<-length(seqrel)
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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18 if (0) {
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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19 seqrel<-seqrel[len:1]
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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20 strrel<-strrel[len:1]
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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21 }
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25 if (1) {
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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26 seqrel <- seqrel/1.0
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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27 }
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30 totalrel <- seqrel+strrel;
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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32 anno_space<-0.075
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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34 maxy <- max(c(1,totalrel))+anno_space*(0+1);
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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37 firstpos <- 1
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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38 lastpos <- 1+len-1
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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40 if (0) {
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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41 the_xlim <- c(lastpos,firstpos)
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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42 } else {
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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43 the_xlim <- c(firstpos,lastpos)
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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44 }
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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46 # set margin
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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47 # b, l, t, r
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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48 par(mar=c(6,2.5,1,1))
6a79a086fa50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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49
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50 # open plot (and draw threshold)
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51 plot(c(0),c(0),type="l",
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52 xlab="",ylab="",
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53 xlim=the_xlim,ylim=c(0,maxy),
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54 yaxp=c(0,1,2))
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56 ## title inside of plot
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57 legend("topleft","",bty="n")
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60 # total reliability
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61 polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,totalrel,0),col=rgb(0.8,0.8,0.9,0.5),lwd=2,border=FALSE)
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62 lines(firstpos:lastpos,totalrel,col="blue",lwd=2)
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64 # plot structure reliability
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65 polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,strrel,0),col=rgb(0.3,0.3,0.5,0.8),lwd=1,border=FALSE)
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68 ## draw other signals
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69 signals<-c();
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70 signal_sizes<-c();
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72 signal_starts <- 1:0
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74 signal_starts[1]<-1;
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75 if (0>1) {
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76 for (i in 2:0) {
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77 signal_starts[i]<-signal_starts[i-1]+signal_sizes[i-1]*2+1;
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78 }
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79 }
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80
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81 colors <- c(
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82 rgb(0.6,0.1,0.1,0.9),
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83 rgb(0.6,0.6,0.1,0.9),
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84 rgb(0.1,0.6,0.6,0.9),
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85 rgb(0.6,0.1,0.6,0.9)
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86 );
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87 colors<-c(colors,colors);
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88
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89 if (0>0) {
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90
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91 for (i in 1:0) {
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92 orientation <- signals[signal_starts[i]+signal_sizes[i]*2];
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93 sig_y <- maxy-i*anno_space;
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94
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95 for (j in 0:(signal_sizes[i]-1)) {
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96
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97 sig_x <- c(signals[signal_starts[i]+j*2],signals[signal_starts[i]+j*2+1]);
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98
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99 ## draw arrows
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100 if (orientation!=0) {
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101 the_code <- 1+(orientation+1)/2;
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102 arrows(sig_x[1],sig_y,sig_x[2],sig_y,lwd=4,col=colors[i],code=the_code,angle=20,length=0.15);
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103 } else {
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104 lines(sig_x,c(sig_y,sig_y),lwd=4,col=colors[i]);
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105 }
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106 }
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107 }
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108 }
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109
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110 #draw inferred on-signal
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111 hit_color <- rgb(0.1,0.6,0.1,0.9)
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112
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113 if (0!=1) {
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114
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115 on <- c(0,4,33,44,49);
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116 off <- c(3,20,43,48,51);
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117
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118 if (length(on)>0) {
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119 for (i in 1:length(on)) {
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120 lines(c(1+on[i],1+off[i]-1),c(maxy,maxy),lwd=7,col=hit_color);
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121 }
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122 }
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123
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124 ### draw on/off values
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125 if (0) {
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126 lines(c(1,1+len),c(0.0355791,0.0355791),lty=2,lwd=1)
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127 lines(c(1,1+len),c(0.702675,0.702675),lty=2,lwd=1)
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128 }
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129 }
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130
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131
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132 signal_names<-c();
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133
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134 if (length(signal_names)>0 || (0!=1)) {
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135 legend("bottom",c("LocARNA",signal_names),lwd=7,col=c(hit_color,colors),horiz=TRUE,inset=-0.4);
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136 # ,xpd=TRUE
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137 }