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1 ceas\ \-\-\ 0\.9\.9\.7\ \(package\ version\ 1\.0\.2\)
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2 INFO\ \ \@\ .*
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3 \#\ ARGUMENTS\:\
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4 \#\ name\ \=\ ceas
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5 \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
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6 \#\ BED\ file\ \=\ .*
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7 \#\ WIG\ file\ \=\ None
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8 \#\ extra\ BED\ file\ \=\ None
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9 \#\ ChIP\ annotation\ \=\ On
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10 \#\ gene\-centered\ annotation\ \=\ \ On
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11 \#\ average\ profiling\ \=\ Off
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12 \#\ dump\ profiles\ \=\ Off
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13 \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
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14 \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
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15 \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
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16 \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
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17 \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp\
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18 INFO\ \ \@\ .*\ \#1\ read\ the\ gene\ table\.\.\.\
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19 INFO\ \ \@\ .*\ \#2\ read\ the\ bed\ file\ of\ ChIP\ regions\.\.\.\
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20 INFO\ \ \@\ .*\ \#3\ perform\ gene\-centered\ annotation\.\.\.\
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21 INFO\ \ \@\ .*\ \#4\ See\ ceas\.xls\ for\ gene\-centered\ annotation\!\
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22 INFO\ \ \@\ .*\ \#5\ read\ the\ pre\-computed\ genome\ bg\ annotation\.\.\.\
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23 INFO\ \ \@\ .*\ \#6\ perform\ ChIP\ region\ annotation\.\.\.\
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24 INFO\ \ \@\ .*\ \#7\ write\ a\ R\ script\ of\ ChIP\ region\ annotation\.\.\.\
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25
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26 R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\"
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27 Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing
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28 Platform\:\ .*
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29
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30 R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\.
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31 You\ are\ welcome\ to\ redistribute\ it\ under\ certain\ conditions\.
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32 Type\ \'license\(\)\'\ or\ \'licence\(\)\'\ for\ distribution\ details\.
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33
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34 \ \ Natural\ language\ support\ but\ running\ in\ an\ English\ locale
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35
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36 R\ is\ a\ collaborative\ project\ with\ many\ contributors\.
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37 Type\ \'contributors\(\)\'\ for\ more\ information\ and
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38 \'citation\(\)\'\ on\ how\ to\ cite\ R\ or\ R\ packages\ in\ publications\.
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39
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40 Type\ \'demo\(\)\'\ for\ some\ demos\,\ \'help\(\)\'\ for\ on\-line\ help\,\ or
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41 \'help\.start\(\)\'\ for\ an\ HTML\ browser\ interface\ to\ help\.
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42 Type\ \'q\(\)\'\ to\ quit\ R\.
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43
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44 \>\ \#\ ARGUMENTS\:\
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45 \>\ \#\ name\ \=\ ceas
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46 \>\ \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
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47 \>\ \#\ BED\ file\ \=\ .*
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48 \>\ \#\ WIG\ file\ \=\ None
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49 \>\ \#\ extra\ BED\ file\ \=\ None
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50 \>\ \#\ ChIP\ annotation\ \=\ On
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51 \>\ \#\ gene\-centered\ annotation\ \=\ \ On
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52 \>\ \#\ average\ profiling\ \=\ Off
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53 \>\ \#\ dump\ profiles\ \=\ Off
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54 \>\ \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
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55 \>\ \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
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56 \>\ \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
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57 \>\ \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
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58 \>\ \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
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59 \>\ pdf\(\"ceas\.pdf\"\,height\=11\.5\,width\=8\.5\)
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60 \>\
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61 \>\ \#\ .*
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62 \>\ \#\
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63 \>\ \#\ ChIP\ annotation
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64 \>\ \#\
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65 \>\
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66 \>\
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67 \>\ \#\
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68 \>\ \#\ Chromosomal\ Distribution
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69 \>\ \#\
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70 \>\
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71 \>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
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72 \>\ r0\<\-c\(100\.0\)
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73 \>\ r1\<\-c\(100\.0\)
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74 \>\ height\<\-rbind\(r0\,r1\)
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75 \>\ names\=c\(\"26\"\)
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76 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=TRUE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Chromosomal\ Distribution\ of\ ChIP\ Regions\"\,xlab\=\"Percentage\ \%\"\,ylab\=\"Chromosome\"\,border\=FALSE\,xlim\=c\(0\.000000\,183\.333333\)\,cex\.names\=1\)
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77 \>\ text\(x\=c\(100\.0\)\,y\=mp\[1\,\]\,label\=c\(\"100\.0\ \%\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
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78 \>\ text\(x\=c\(100\.0\)\,y\=mp\[2\,\]\,label\=c\(\"100\.0\ \%\ \(\<\=4\.9e\-324\)\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
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79 \>\ legend\(\"right\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
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80 \>\
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81 \>\ \#\
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82 \>\ \#\ Promoter\,Bipromoter\,Downstream\,\ Gene\ and\ Regions\ of\ interest
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83 \>\ \#\
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84 \>\
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85 \>\ par\(mfrow\=c\(4\,\ 1\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
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86 \>\ r0\<\-c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)
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87 \>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
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88 \>\ height\<\-rbind\(r0\,r1\)
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89 \>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
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90 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.757585\)\,cex\.names\=1\)
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91 \>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)\,label\=c\(\"1\.9\ \%\"\,\"3\.6\ \%\"\,\"5\.3\ \%\"\)\,pos\=3\,offset\=0\.2\)
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92 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
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93 \+\ \(0\.981\)\"\,\"0\.000\ \%
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94 \+\ \(0\.964\)\"\,\"0\.000\ \%
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95 \+\ \(0\.947\)\"\)\,pos\=3\,offset\=0\.2\)
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96 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
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97 \>\ r0\<\-c\(0\.03876062889120376\,\ 0\.03876062889120376\)
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98 \>\ r1\<\-c\(0\.0\,\ 0\.0\)
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99 \>\ height\<\-rbind\(r0\,r1\)
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100 \>\ names\=c\(\"\<\=2500\ bp\"\,\"\<\=5000\ bp\"\)
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101 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Bidirectional\ Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,0\.071061\)\,cex\.names\=1\)
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102 \>\ text\(x\=mp\[1\,\]\,y\=c\(0\.03876062889120376\,\ 0\.03876062889120376\)\,label\=c\(\"0\.04\ \%\"\,\"0\.04\ \%\"\)\,pos\=3\,offset\=0\.2\)
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103 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
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104 \+\ \(1\.000\)\"\,\"0\.000\ \%
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105 \+\ \(1\.000\)\"\)\,pos\=3\,offset\=0\.2\)
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106 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
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107 \>\ r0\<\-c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)
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108 \>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
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109 \>\ height\<\-rbind\(r0\,r1\)
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110 \>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
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111 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Downstream\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.131358\)\,cex\.names\=1\)
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112 \>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)\,label\=c\(\"1\.8\ \%\"\,\"3\.5\ \%\"\,\"5\.0\ \%\"\)\,pos\=3\,offset\=0\.2\)
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113 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
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114 \+\ \(0\.982\)\"\,\"0\.000\ \%
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115 \+\ \(0\.965\)\"\,\"0\.000\ \%
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116 \+\ \(0\.950\)\"\)\,pos\=3\,offset\=0\.2\)
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117 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
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118 \>\ r0\<\-c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)
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119 \>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)
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120 \>\ height\<\-rbind\(r0\,r1\)
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121 \>\ names\=c\(\"5\'UTR\"\,\"3\'UTR\"\,\"Coding\ Exon\"\,\"Intron\"\,\"All\"\)
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122 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Gene\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,43\.440571\)\,cex\.names\=1\)
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123 \>\ text\(x\=mp\[1\,\]\,y\=c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)\,label\=c\(\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.4\ \%\"\,\"19\.7\ \%\"\,\"23\.7\ \%\"\)\,pos\=3\,offset\=0\.2\)
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124 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
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125 \+\ \(0\.998\)\"\,\"0\.000\ \%
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126 \+\ \(0\.986\)\"\,\"0\.000\ \%
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127 \+\ \(0\.976\)\"\,\"0\.000\ \%
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128 \+\ \(0\.803\)\"\,\"0\.000\ \%
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129 \+\ \(0\.763\)\"\)\,pos\=3\,offset\=0\.2\)
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130 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
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131 \>\
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132 \>\ \#\
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133 \>\ \#\ Distribution\ of\ Genome\ and\ ChIP\ regions\ over\ cis\-regulatory\ element
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134 \>\ \#\ Note\ that\ the\ x\ may\ be\ modified\ for\ better\ graphics\ in\ case\ a\ value\ is\ too\ small
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135 \>\ \#\ Thus\,\ look\ at\ the\ labels\ of\ the\ pie\ chart\ to\ get\ the\ real\ percentage\ values
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136 \>\ \#\
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137 \>\
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138 \>\ par\(mfcol\=c\(2\,\ 2\)\,mar\=c\(3\,\ 3\,\ 4\,\ 2\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
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139 \>\ x\<\-c\(0\.018532\,0\.017055\,0\.016037\,0\.017830\,0\.015092\,0\.014051\,0\.010000\,0\.013833\,0\.023014\,0\.192592\,0\.670292\)
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140 \>\ pie\(x\=x\,labels\=c\(\"1\.9\ \%\"\,\"1\.7\ \%\"\,\"1\.6\ \%\"\,\"1\.8\ \%\"\,\"1\.5\ \%\"\,\"1\.4\ \%\"\,\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.3\ \%\"\,\"19\.3\ \%\"\,\"67\.0\ \%\"\)\,main\=\"Genome\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
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141 \>\ x\<\-c\(0\.000000\,1\.000000\)
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142 \>\ y\<\-c\(0\.000000\,1\.000000\)
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143 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
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144 \>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 1\.9\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 1\.7\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 1\.6\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 1\.8\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 1\.5\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 1\.4\ \%\"\,\"5\'UTR\:\ 0\.2\ \%\"\,\"3\'UTR\:\ 1\.4\ \%\"\,\"Coding\ exon\:\ 2\.3\ \%\"\,\"Intron\:\ 19\.3\ \%\"\,\"Distal\ intergenic\:\ 67\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
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145 \>\ x\<\-c\(0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,1\.000000\)
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146 \>\ pie\(x\=x\,labels\=c\(\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"100\.0\ \%\"\)\,main\=\"ChIP\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
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147 \>\ x\<\-c\(0\.000000\,1\.000000\)
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148 \>\ y\<\-c\(0\.000000\,1\.000000\)
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149 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
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150 \>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"5\'UTR\:\ 0\.000\ \%\"\,\"3\'UTR\:\ 0\.000\ \%\"\,\"Coding\ exon\:\ 0\.000\ \%\"\,\"Intron\:\ 0\.000\ \%\"\,\"Distal\ intergenic\:\ 100\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
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151 \>\
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152 \>\ \#\
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153 \>\ \#\ ChIP\ regions\ over\ the\ genome
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154 \>\ \#\
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155 \>\
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156 \>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
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157 \>\ layout\(matrix\(c\(1\,\ 0\,\ 2\,\ 2\)\,\ 2\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 5\)\)
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158 \>\ x\<\-c\(0\.000000\,2\.515610\)
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159 \>\ y\<\-c\(0\.000000\,1\.000000\)
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160 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"Distribution\ of\ Peak\ Heights\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(0\.000000\,2\.515610\)\,ylim\=c\(0\.000000\,1\.000000\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\,cex\=0\.9\)
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161 \>\ x\<\-c\(0\.000000\,2\.515610\,2\.515610\,0\.000000\)
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162 \>\ y\<\-c\(0\.000000\,0\.000000\,1\.000000\,1\.000000\)
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163 \>\ polygon\(x\,y\,col\=c\(\"black\"\)\)
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164 \>\ x\ \<\-\ c\(0\.000000\,0\.169726\,0\.339451\,0\.509177\,0\.678903\,0\.848628\,1\.018354\,1\.188079\,1\.357805\,1\.527531\,1\.697256\,1\.866982\,2\.036708\,2\.206433\,2\.376159\)
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165 \>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.800000\)
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166 \>\ lines\(x\,\ y\,xlim\=c\(0\,\ 2\.51561\)\,ylim\=c\(0\,\ 1\)\,type\=\"l\"\,col\=c\(\"cyan\"\)\,lwd\=2\)
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167 \>\ x\<\-c\(4119129\.000000\,4119130\.000000\)
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168 \>\ y\<\-c\(0\.855556\,1\.144444\)
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169 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"ChIP\ Regions\ \(Peaks\)\ over\ Chromosomes\"\,xlab\=\"Chromosome\ Size\ \(bp\)\"\,ylab\=\"Chromosome\"\,xlim\=c\(4119129\.000000\,4119130\.000000\)\,ylim\=c\(0\.855556\,1\.144444\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\)
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170 \>\ start\ \<\-\ c\(4119129\)
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171 \>\ end\ \<\-\ c\(4119130\)
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172 \>\ vals\ \<\-\ c\(2\.51561\)
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173 \>\ vals\[vals\ \>\ 2\.51561\]\ \<\-\ 2\.51561
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174 \>\ vals\[vals\ \<\ 0\]\ \<\-\ 0
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175 \>\ heights\ \<\-\ 0\.288889\ \*\ \(\(vals\ \-\ 0\)\/\(2\.51561\ \-\ 0\)\)\ \+\ 0\.855555555556
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176 \>\ for\ \(i\ in\ 1\:length\(heights\)\)\ \{
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177 \+\ \ polygon\(x\=c\(start\[i\]\,\ end\[i\]\,\ end\[i\]\,\ start\[i\]\)\,\ y\=c\(0\.855555555556\,\ 0\.855555555556\,\ heights\[i\]\,\ heights\[i\]\)\,\ col\=c\(\"\#CC0000\"\)\,\ border\=c\(\"\#CC0000\"\)\)
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178 \+\ \}
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179 \>\ mtext\(\"26\"\,side\=2\,line\=0\,outer\=FALSE\,at\=1\.0\)
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180 \>\ dev\.off\(\)
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181 null\ device\
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182 \ \ \ \ \ \ \ \ \ \ 1\
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183 \>\
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184 INFO\ \ \@\ .*\ \#\.\.\.\ cong\!\ See\ ceas\.pdf\ for\ the\ graphical\ results\ of\ CEAS\!\
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