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annotate test-data/references/10-clustersStat.html @ 30:fce825ec2c84 draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 01b92e7e17eb8bc125451bf41684f512cf16d3c5-dirty
author oinizan
date Fri, 02 May 2025 07:44:22 +0000
parents 646bee69560f
children
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25
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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1 <!DOCTYPE html>
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2 <!--
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3 # Copyright (C) 2015 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 -->
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18 <html>
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19 <head>
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20 <title>FROGS Cluster stat</title>
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21 <meta charset="UTF-8">
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22 <meta name="version" content="4.2.0">
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23 <!-- CSS -->
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24 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>
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25 <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>
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26 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">
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27 <style type="text/css">
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28 #js-alert {
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29 width: 90%;
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30 margin-right: auto;
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31 margin-left: auto;
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32 }
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33 #content {
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34 width: 90%;
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35 margin-right: auto;
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36 margin-left: auto;
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37 }
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38 .clear {
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39 clear: both;
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40 height: 0px;
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41 width: 100%;
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42 float: none !important;
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43 }
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44 ul.nav-tabs {
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45 margin-bottom: 30px;
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46 }
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47 #hc-graph {
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48 height: 500px;
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49 overflow: auto;
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50 }
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51 #hc-warning {
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52 margin-top: 8px;
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53 }
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54 #hc-newick {
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55 width: 90%;
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56 position: absolute;
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57 background-color: white;
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58 border: 1px solid lightgrey;
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59 border-radius:5px;
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60 padding: 5px 5px 5px 5px;
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61 margin-top: 10px;
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62 }
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63 #dispersion {
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64 height: 1000px;
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65 }
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66 #twofigs{
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67 height: 600px;
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68 }
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69 .label-badge {
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70 position: absolute;
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71 top: -10px;
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72 left: -10px;
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73 }
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74 .badge-primary{
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75 background-color:#8EADAC;
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76 }
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77 .graph-nb {
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78 color: #95959C;
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79 font-style: italic;
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80 text-align: center;
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81 }
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82 .circle {
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83 border-style: solid;
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84 border-width: 3px;
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85 border-radius: 50px;
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86 box-shadow: 2px 2px 2px #555;
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87 border-color: #648a89;
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88 background: radial-gradient( #8EADAC, #648a89);
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89 color: white;
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90 padding: 10px;
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91 width: 180px;
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92 height: 98px;
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93 line-height: 30px;
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94 text-align: center;
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95 margin-left: auto;
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96 margin-right: auto;
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97 margin-bottom: 10px;
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98 vertical-align: middle;
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99 }
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100 .circle-value {
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101 font-weight: bold;
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102 }
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103 .d3-node {
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104 cursor: pointer;
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105 }
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106 .d3-node-dot {
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107 fill: #fff;
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108 stroke: #8EADAC;
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109 stroke-width: 3px;
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110 }
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111 .d3-collapsed-node {
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112 fill: #8EADAC;
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113 stroke: #648a89;
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114 stroke-width: 3px;
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115 }
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116 .d3-node text {
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117 font: 13px sans-serif;
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118 }
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119 .d3-link {
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120 fill: none;
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121 stroke: #648a89;
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122 stroke-width: 2px;
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123 }
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124 .page-item.active .page-link {
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125 z-index: 1;
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126 color: #fff;
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127 background-color: #8EADAC;
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128 border-color: #8EADAC;
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129 }
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130 .btn {
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131 color: #fff;
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132 border:#8EADAC;
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133 background-color: #8EADAC;
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134 }
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135 .btn:focus, .btn:active {
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136 outline: none !important;
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137 box-shadow: none !important;
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138 }
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139 .btn:hover{
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140 color: #fff;
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141 border:#648a89;
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142 background-color: #648a89;
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143 }
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144 .pb-2, .py-2 {
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145 padding-bottom: 1.5rem !important;
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146 margin-bottom: 2rem !important;
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147 margin-top: 4rem !important;
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148 }
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149 .pb-2-first{
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150 padding-bottom: 1.5rem !important;
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151 margin-bottom: 2rem !important;
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152 margin-top: 1rem !important;
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153 }
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154 .nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{
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155 color: #fff;
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156 background-color: #8EADAF;
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157 border-color: #dee2e6 #dee2e6 #fff;
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158 }
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159 a {
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160 color: #8EAEAF;
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161 }
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162 a:hover{
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163 color:#648a89;
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164 }
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165 .page-link{
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166 color: #8EAEAF;
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167 }
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168 .page-link:hover{
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169
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170 }
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171 .page-link:not(:disabled):not(.disabled) {
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172 color: #8EAEAF;
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173 }
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174 .page-item.active .page-link {
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175 color: #fff;
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176 }
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177 .highcharts-button > path{
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178 stroke:#fff !important;
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179 fill:#8EADAC !important;
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180 }
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181 g.highcharts-button{
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182 cursor:pointer !important;
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183 }
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184 g.highcharts-button:hover{
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185 color: #fff;
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186 border:#648a89;
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187 background-color: #648a89;
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188 background-color: #648a89;
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189 cursor:pointer !important;
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190 }
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191 </style>
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192 <!-- JS -->
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193 <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script>
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194 <script type="text/javascript" src="https://code.highcharts.com/8.2.0/highcharts.js"></script>
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195 <script type="text/javascript" src="https://code.highcharts.com/8.2.0/highcharts-more.js"></script>
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196 <script type="text/javascript" src="https://code.highcharts.com/8.2.0/modules/exporting.js"></script>
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197 <script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
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198 <script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script>
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199 <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.min.js" integrity="sha384-smHYKdLADwkXOn1EmN1qk/HfnUcbVRZyYmZ4qpPea6sjB/pTJ0euyQp0Mk8ck+5T" crossorigin="anonymous"></script>
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200 <script type="text/javascript">
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201 /*
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202 * d3 v3 - JavaScript d3 Library
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203 * (http://d3js.org/)
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204 */
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oinizan
parents:
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oinizan
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dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
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dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
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y(){d(),k.style("pointer-events","all").selectAll(".resize").style("display",n.empty()?"none":null),ta.select("body").style("cursor",null),L.on("mousemove.brush",null).on("mouseup.brush",null).on("touchmove.brush",null).on("touchend.brush",null).on("keydown.brush",null).on("keyup.brush",null),z(),w({type:"brushend"})}var M,x,b=this,_=ta.select(ta.event.target),w=c.of(b,arguments),k=ta.select(b),E=_.datum(),A=!/^(n|s)$/.test(E)&&l,N=!/^(e|w)$/.test(E)&&s,C=_.classed("extent"),z=W(b),q=ta.mouse(b),L=ta.select(t(b)).on("keydown.brush",i).on("keyup.brush",v);if(ta.event.changedTouches?L.on("touchmove.brush",d).on("touchend.brush",y):L.on("mousemove.brush",d).on("mouseup.brush",y),k.interrupt().selectAll("*").interrupt(),C)q[0]=f[0]-q[0],q[1]=h[0]-q[1];else if(E){var T=+/w$/.test(E),R=+/^n/.test(E);x=[f[1-T]-q[0],h[1-R]-q[1]],q[0]=f[T],q[1]=h[R]}else ta.event.altKey&&(M=q.slice());k.style("pointer-events","none").selectAll(".resize").style("display",null),ta.select("body").style("cursor",_.style("cursor")),w({type:"brushstart"}),d()}var o,a,c=E(n,"brushstart","brush","brushend"),l=null,s=null,f=[0,0],h=[0,0],g=!0,p=!0,v=Ol[0];return n.event=function(n){n.each(function(){var n=c.of(this,arguments),t={x:f,y:h,i:o,j:a},e=this.__chart__||t;this.__chart__=t,Tl?ta.select(this).transition().each("start.brush",function(){o=e.i,a=e.j,f=e.x,h=e.y,n({type:"brushstart"})}).tween("brush:brush",function(){var e=yu(f,t.x),r=yu(h,t.y);return o=a=null,function(u){f=t.x=e(u),h=t.y=r(u),n({type:"brush",mode:"resize"})}}).each("end.brush",function(){o=t.i,a=t.j,n({type:"brush",mode:"resize"}),n({type:"brushend"})}):(n({type:"brushstart"}),n({type:"brush",mode:"resize"}),n({type:"brushend"}))})},n.x=function(t){return arguments.length?(l=t,v=Ol[!l<<1|!s],n):l},n.y=function(t){return arguments.length?(s=t,v=Ol[!l<<1|!s],n):s},n.clamp=function(t){return arguments.length?(l&&s?(g=!!t[0],p=!!t[1]):l?g=!!t:s&&(p=!!t),n):l&&s?[g,p]:l?g:s?p:null},n.extent=function(t){var e,r,u,i,c;return arguments.length?(l&&(e=t[0],r=t[1],s&&(e=e[0],r=r[0]),o=[e,r],l.invert&&(e=l(e),r=l(r)),e>r&&(c=e,e=r,r=c),(e!=f[0]||r!=f[1])&&(f=[e,r])),s&&(u=t[0],i=t[1],l&&(u=u[1],i=i[1]),a=[u,i],s.invert&&(u=s(u),i=s(i)),u>i&&(c=u,u=i,i=c),(u!=h[0]||i!=h[1])&&(h=[u,i])),n):(l&&(o?(e=o[0],r=o[1]):(e=f[0],r=f[1],l.invert&&(e=l.invert(e),r=l.invert(r)),e>r&&(c=e,e=r,r=c))),s&&(a?(u=a[0],i=a[1]):(u=h[0],i=h[1],s.invert&&(u=s.invert(u),i=s.invert(i)),u>i&&(c=u,u=i,i=c))),l&&s?[[e,u],[r,i]]:l?[e,r]:s&&[u,i])},n.clear=function(){return n.empty()||(f=[0,0],h=[0,0],o=a=null),n},n.empty=function(){return!!l&&f[0]==f[1]||!!s&&h[0]==h[1]},ta.rebind(n,c,"on")};var Hl={n:"ns-resize",e:"ew-resize",s:"ns-resize",w:"ew-resize",nw:"nwse-resize",ne:"nesw-resize",se:"nwse-resize",sw:"nesw-resize"},Ol=[["n","e","s","w","nw","ne","se","sw"],["e","w"],["n","s"],[]],Il=ac.format=gc.timeFormat,Yl=Il.utc,Zl=Yl("%Y-%m-%dT%H:%M:%S.%LZ");Il.iso=Date.prototype.toISOString&&+new Date("2000-01-01T00:00:00.000Z")?Jo:Zl,Jo.parse=function(n){var t=new Date(n);return isNaN(t)?null:t},Jo.toString=Zl.toString,ac.second=Ft(function(n){return new cc(1e3*Math.floor(n/1e3))},function(n,t){n.setTime(n.getTime()+1e3*Math.floor(t))},function(n){return n.getSeconds()}),ac.seconds=ac.second.range,ac.seconds.utc=ac.second.utc.range,ac.minute=Ft(function(n){return new cc(6e4*Math.floor(n/6e4))},function(n,t){n.setTime(n.getTime()+6e4*Math.floor(t))},function(n){return n.getMinutes()}),ac.minutes=ac.minute.range,ac.minutes.utc=ac.minute.utc.range,ac.hour=Ft(function(n){var t=n.getTimezoneOffset()/60;return new cc(36e5*(Math.floor(n/36e5-t)+t))},function(n,t){n.setTime(n.getTime()+36e5*Math.floor(t))},function(n){return n.getHours()}),ac.hours=ac.hour.range,ac.hours.utc=ac.hour.utc.range,ac.month=Ft(function(n){return n=ac.day(n),n.setDate(1),n},function(n,t){n.setMonth(n.getMonth()+t)},function(n){return n.getMonth()}),ac.months=ac.month.range,ac.months.utc=ac.month.utc.range;var Vl=[1e3,5e3,15e3,3e4,6e4,3e5,9e5,18e5,36e5,108e5,216e5,432e5,864e5,1728e5,6048e5,2592e6,7776e6,31536e6],Xl=[[ac.second,1],[ac.second,5],[ac.second,15],[ac.second,30],[ac.minute,1],[ac.minute,5],[ac.minute,15],[ac.minute,30],[ac.hour,1],[ac.hour,3],[ac.hour,6],[ac.hour,12],[ac.day,1],[ac.day,2],[ac.week,1],[ac.month,1],[ac.month,3],[ac.year,1]],$l=Il.multi([[".%L",function(n){return n.getMilliseconds()}],[":%S",function(n){return n.getSeconds()}],["%I:%M",function(n){return n.getMinutes()}],["%I %p",function(n){return n.getHours()}],["%a %d",function(n){return n.getDay()&&1!=n.getDate()}],["%b %d",function(n){return 1!=n.getDate()}],["%B",function(n){return n.getMonth()}],["%Y",Ne]]),Bl={range:function(n,t,e){return ta.range(Math.ceil(n/e)*e,+t,e).map(Ko)},floor:y,ceil:y};Xl.year=ac.year,ac.scale=function(){return Go(ta.scale.linear(),Xl,$l)};var Wl=Xl.map(function(n){return[n[0].utc,n[1]]}),Jl=Yl.multi([[".%L",function(n){return n.getUTCMilliseconds()}],[":%S",function(n){return n.getUTCSeconds()}],["%I:%M",function(n){return n.getUTCMinutes()}],["%I %p",function(n){return n.getUTCHours()}],["%a %d",function(n){return n.getUTCDay()&&1!=n.getUTCDate()}],["%b %d",function(n){return 1!=n.getUTCDate()}],["%B",function(n){return n.getUTCMonth()}],["%Y",Ne]]);Wl.year=ac.year.utc,ac.scale.utc=function(){return Go(ta.scale.linear(),Wl,Jl)},ta.text=At(function(n){return n.responseText}),ta.json=function(n,t){return Nt(n,"application/json",Qo,t)},ta.html=function(n,t){return Nt(n,"text/html",na,t)},ta.xml=At(function(n){return n.responseXML}),"function"==typeof define&&define.amd?define(ta):"object"==typeof module&&module.exports&&(module.exports=ta),this.d3=ta}();
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210 </script>
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211 <script type="text/javascript">
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212 /*
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213 * Node 0.1.0 - JavaScript Node Library
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214 *
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215 * Copyright (c) 2015 Escudie Frederic
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216 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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217 */
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218 var Node=function(e,t,n,r){if(this.name=e,this.parent=t,this.children=new Array,null!=n)for(var i=0;i<n.length;i++)this.addChild(n[i]);this.metadata=new Array,null!=r&&(this.metadata=r)};Node.fromNewick=function(e){for(var t=new Array,n=0;n<e.length;n++){var r=e[n];if("("==r)t.push("(");else if(")"==r){for(var i=new Node(null,null,null,null);"("!=t[t.length-1];)i.addChild(t.pop());t.pop(),t.push(i)}else if(","==r);else if(";"==r);else if(":"==r){for(var h="";","!=e[n+1]&&")"!=e[n+1]&&";"!=e[n+1];)n++,h+=e[n];t[t.length-1].metadata.dist=h}else{'"'==r?(stop_markers=['"'],n++):stop_markers=[",",")",":",";"];for(var o=e[n];-1==stop_markers.indexOf(e[n+1]);)n++,o+=e[n];-1!=stop_markers.indexOf('"')&&n++;var l=new Node(o,null,null,null);t.push(l)}}return t[0]},Node.prototype.toNewick=function(){},Node.prototype.toJson=function(){var e={name:null!=this.name?this.name:""};if(this.hasChild()){for(var t=new Array,n=0;n<this.children.length;n++)t.push(this.children[n].toJson());e.children=t}return e},Node.prototype.getLeavesNames=function(){var e=new Array;if(this.hasChild())for(var t=0;t<this.children.length;t++)for(var n=this.children[t].getLeavesNames(),r=0;r<n.length;r++)e.push(n[r]);else e.push(this.name);return e},Node.prototype.nbLeaves=function(){var e=0;if(this.hasChild())for(var t=0;t<this.children.length;t++)e+=this.children[t].nbLeaves();else e=1;return e},Node.prototype.maxDepth=function(){var e=0;if(this.hasChild())for(var t=0;t<this.children.length;t++)e=Math.max(e,this.children[t].maxDepth());return 1+e},Node.prototype.toAsciiTree=function(e){null==e&&(e=0);var t="--- "+(null!=this.name?this.name:"ancestor")+" ";e+=t.length;for(var n=0;n<this.children.length;n++)t+="\n"+Array(e).join(" ")+"\\"+this.children[n].toAsciiTree(e);return t},Node.prototype.toString=function(){var e="Node: "+this.name;return e+="\n Parent="+(null!=this.parent?this.parent.name:"-"),e+=this.hasChild()?"\n Children="+Object.keys(this.children).join(", "):"\n Children=-"},Node.prototype.hasChild=function(e){if(null==e)return this.children.length>0;for(var t=!1,n=0;n<this.children.length&&!t;n++)e==this.children[n]&&(t=!0);return t},Node.prototype.getChild=function(e){if(!this.hasChild(e))throw this.name+" doesn't have child named '"+e+"'.";return this.children[e]},Node.prototype.getParent=function(){return this.parent},Node.prototype.addChild=function(e){null==e.parent&&(e.parent=this),this.children.push(e)};
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219 </script>
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220 <script type="text/javascript">
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221 /*
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222 * HTMLTable.js 0.1.0 - HTMLTable Library
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223 *
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224 * Copyright (c) 2015 Escudie Frederic
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225 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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226 */
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227 function HTMLtable(e){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)if(!r[i][f]){var m=g.exec(v[s].innerHTML);null!=m&&(void 0===m[1]&&(m[1]=""),v[s].innerHTML=a+m[1]+l),s++}}},this.toCSV=function(){for(var e="",l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)r[g][v]||(e+=o[i].innerHTML,i++),e+=a;e=e.substr(0,e.length-1)+"\n"}return e},l(),g()}var in_array=function(e,t){for(var r in t)if(t[r]==e)return!0;return!1};
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228
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229 /*
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230 * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library
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231 *
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232 * Copyright (c) 2015 Escudie Frederic
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233 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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234 */
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235 !function(t){t.fn.datatableExport=function(a){var e={anchor_id:t(this).attr("id"),table_id:null,csv_separator:";",omitted_columns:[]},n=t.extend(e,a);if(!t(this).length)throw"The element where the datatableExport is called does not exist.";if(void 0==n.anchor_id)throw"The datatableExport plugin must be called on an element with id.";if(null==n.table_id)throw"You must set the table_id parameter in datatableExport plugin.";if(!t("#"+n.table_id))throw"The datatable '#"+n.table_id+"' cannot be retieve in DOM.";return this.each(function(){var a=t(this);a.on("click",function(){t.fn.datatableExport.csv(n.anchor_id,n.table_id,n.csv_separator,n.omitted_columns)})})},t.fn.datatableExport.cleanCellMarkup=function(a,e){t.parseHTML(e);t("#"+a).append('<div class="hidden data-tmp">'+e+"</div>"),t("#"+a+" .data-tmp").find("input").each(function(){var a="";a=t(this).is(":checkbox")?t(this).is(":checked")?"true":"false":t(this).val(),t(this).replaceWith(a)});var n=t("#"+a+" .data-tmp").text();return t("#"+a+" .data-tmp").remove(),n},t.fn.datatableExport.csv=function(a,e,n,i){var l="",r=t("#"+e).DataTable(),d=t("#"+e+" thead")[0],o=new HTMLtable(d.cloneNode(!0));o.deleteColumns(i),l+=o.toCSV();var c=r.rows().data();t.each(c,function(e,n){for(var r="",d=0;d<n.length;d++)-1==t.inArray(d,i)&&(r+='"'+t.fn.datatableExport.cleanCellMarkup(a,n[d])+'";');""!=r&&(r=r.slice(0,-1)),l+=r+"\n"}),t("#"+a+"-extract-csv").length||t("#"+a).append('<a id="'+a+'-extract-csv" href="data:text/csv;charset=UTF-8,'+encodeURI(l)+'" download="data.csv" style="display:none;"></a>'),t("#"+a+"-extract-csv")[0].click()}}(jQuery);
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236 </script>
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237 <script type="text/javascript">
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238 //HC global var
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239 var linkage_data = null ;
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240 var d3_tree = null ;
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241 var diagonal = null ;
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242 var svg_layout = null ;
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243 var node_id = 0 ;
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244
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245 /**
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246 * Draw/update linkage tree.
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247 */
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248 function update_linkage_nodes(source) {
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249 var duration = d3.event && d3.event.altKey ? 5000 : 500;
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250
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251 // Compute the new tree layout.
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252 var nodes = d3_tree.nodes(linkage_data).reverse();
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253
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254 // Normalise for fixed-depth.
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255 nodes.forEach(function(d) { d.y = d.depth * 100; });
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256
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257 // Update the nodes.
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258 var node = svg_layout.selectAll("g.d3-node")
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259 .data(nodes, function(d) { return d.id || (d.id = ++node_id); });
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260
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261 // Enter any new nodes at the parent's previous position.
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262 var nodeEnter = node.enter().append("svg:g")
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263 .attr("class", "d3-node")
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264 .attr("transform", function(d) { return "translate(" + source.y0 + "," + source.x0 + ")"; })
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265 .on("click", function(d) { toggle(d); });
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266
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267 nodeEnter.append("svg:circle")
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268 .attr("r", 1e-6)
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269 .attr("class", function(d) { return d._children ? "d3-collapsed-node" : "d3-node-dot"; });
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270
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271 nodeEnter.append("svg:text")
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272 .attr("x", function(d) { return d.children || d._children ? -10 : 10; })
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273 .attr("dy", ".35em")
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274 .attr("text-anchor", function(d) { return d.children || d._children ? "end" : "start"; })
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275 .text(function(d) { return d.name; })
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276 .style("fill-opacity", 1e-6);
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277
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278 // Transition nodes to their new position.
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279 var nodeUpdate = node.transition()
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280 .duration(duration)
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281 .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; });
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282
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283 nodeUpdate.select("circle")
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284 .attr("r", 6)
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285 .attr("class", function(d) { return d._children ? "d3-collapsed-node" : "d3-node-dot"; });
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286
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287 nodeUpdate.select("text")
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288 .style("fill-opacity", 1);
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289
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290 // Transition exiting nodes to the parent's new position.
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291 var nodeExit = node.exit().transition()
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292 .duration(duration)
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293 .attr("transform", function(d) { return "translate(" + source.y + "," + source.x + ")"; })
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294 .remove();
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295
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296 nodeExit.select("circle")
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297 .attr("r", 1e-6);
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298
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299 nodeExit.select("text")
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300 .style("fill-opacity", 1e-6);
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301
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302 // Update the links
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303 var link = svg_layout.selectAll("path.d3-link")
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304 .data( d3_tree.links(nodes), function(d) { return d.target.id; } );
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305
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306 // Enter any new links at the parent's previous position.
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307 link.enter().insert("svg:path", "g")
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308 .attr("class", "d3-link")
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309 .attr("d", function(d) {
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310 var o = {x: source.x0, y: source.y0};
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311 return diagonal({source: o, target: o});
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312 })
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313 .transition()
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314 .duration(duration)
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315 .attr("d", diagonal);
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316
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317 // Transition links to their new position.
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318 link.transition()
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319 .duration(duration)
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320 .attr("d", diagonal);
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321
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322 // Transition exiting nodes to the parent's new position.
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323 link.exit().transition()
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324 .duration(duration)
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325 .attr("d", function(d) {
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326 var o = {x: source.x, y: source.y};
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327 return diagonal({source: o, target: o});
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328 })
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329 .remove();
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330
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331 // Stash the old positions for transition.
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332 nodes.forEach(function(d) {
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333 d.x0 = d.x;
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334 d.y0 = d.y;
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335 });
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336 }
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337
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338 /**
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339 * Hide/Unhide children's node when toggle on node in linkage view.
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340 */
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341 function toggle( d ) {
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342 //Hide/Unhide attributes
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343 if (d.children) {
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344 d._children = d.children;
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345 d.children = null;
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346 } else {
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347 d.children = d._children;
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348 d._children = null;
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349 }
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350 //Update node and her children in SVG
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351 update_linkage_nodes(d);
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352 }
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353 </script>
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354
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355 <script type="text/javascript">
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356 /**
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357 * Returns the string representation of the number.
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358 * @param pValue {Float} The number to process.
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359 * @return {String} The string representation (example: 12856892.11111 => 12,856,892.11).
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360 */
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361 var numberDisplay = function( pValue ){
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362 var new_val = "" ;
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363 if( ("" + pValue + "").indexOf(".") != -1 ){
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364 new_val = pValue.toFixed(2).replace(/(\d)(?=(\d{3})+\b)/g, '$1,');
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365 } else {
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366 new_val = pValue.toFixed().replace(/(\d)(?=(\d{3})+\b)/g, '$1,');
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367 }
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368 return new_val ;
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369 }
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370
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371 /**
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372 * Returns the HTML table representation of the data.
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373 * @param pTitle {String} The title of the table.
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374 * @param pCategories {Array} The title of each column.
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375 * @param pData {Array} 2D matrix with row and column data.
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376 * @return {String} The HTML table representation.
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377 */
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378 var table = function( pTitle, pCategories, pData ) {
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379 // Header
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380 var table_header = '' ;
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381 var table_header_line = "" ;
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382 for(var idx = 0 ; idx < pCategories.length ; idx++){
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383 table_header_line += " <th>" + pCategories[idx] + "</th>\n" ;
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384 }
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385 table_header += " <tr>\n" + table_header_line + " </tr>\n" ;
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386 table_header = " <thead>\n" + table_header + " </thead>\n" ;
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387
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388 // Body
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389 var table_body = '' ;
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390 for(var data_idx = 0 ; data_idx < pData.length ; data_idx++){
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391 var table_body_row = "" ;
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392 for(var category_idx = 0 ; category_idx < pCategories.length ; category_idx++){
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393 if( typeof pData[data_idx][category_idx] === "number" ) {
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394 table_body_row += " <td>" + numberDisplay(pData[data_idx][category_idx]) + "</td>\n" ;
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395 } else {
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396 table_body_row += " <td>" + pData[data_idx][category_idx] + "</td>\n" ;
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397 }
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398 }
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399 table_body += " <tr>\n" + table_body_row + " </tr>\n" ;
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400 }
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401 table_body = " <tbody>\n" + table_body + " </tbody>\n" ;
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402
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403 return '<table class="table table-striped table-bordered">\n' + table_header + table_body + "</table>\n" ;
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404 }
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405
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406 /**
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407 * Returns hash use to init HightChart object (without 'type').
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408 * @param pTitle {String} The title of the chart.
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409 * @param pXTitle {String} The xAxis title.
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410 * @param pYTitle {String} The yAxis title.
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411 * @param pXCategories {Array} The title of each category (x scale labels).
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412 * @param pData {Array} The HightChart series.
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413 * @return {Hash} The hash.
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414 * @warning This method use HightChart xAxis.categories.
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415 */
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416 var chartplot = function( pTitle, pXTitle, pYTitle, pXCategories, pData ) {
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417 var chart = {
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418 title: {
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419 text: pTitle
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420 },
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421 xAxis: {},
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422 yAxis: {
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423 title: {
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424 text: pYTitle
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425 }
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426 },
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427 series: pData,
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428 credits: {
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429 enabled: false
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430 }
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431 }
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diff changeset
432 if( pXCategories != null ){
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433 chart['xAxis']['categories'] = pXCategories ;
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434 }
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diff changeset
435 if( pXTitle != null ){
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436 chart['xAxis']['title'] = { text: pXTitle } ;
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437 }
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diff changeset
438 if( pData.length <= 1 ) {
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439 chart['legend'] = {'enabled': false};
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440 } else {
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441 chart['legend'] = {'enabled': true};
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442 }
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443 return chart ;
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444 }
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445 /**
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446 * Returns hash use to init HightChart boxplot.
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447 * @param pTitle {String} The title of the chart.
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448 * @param pXTitle {String} The xAxis title.
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449 * @param pYTitle {String} The yAxis title.
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450 * @param pXCategories {Array} x scale labels.
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451 * @param pData {Array} The HightChart series.
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452 * @return {Hash} Parameters to use in Highchart's constructor.
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453 */
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454 var boxplot_param = function(pTitle, pXTitle, pYTitle, pXCategories, pData) {
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455 var chart = chartplot( pTitle, null, pYTitle, pXCategories, pData );
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456 chart['chart'] = { type: 'boxplot', zoomType: 'y',selectionMarkerFill: "rgb(222,159,115,0.25)" };
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457 chart['yAxis']['min'] = 0 ;
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458 chart['exporting'] = {buttons: {contextButton: { symbol: 'download' }}};
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459 chart['navigation'] = {
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460 buttonOptions: {
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461 theme: {
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462 r: 4,
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463 fill:'#8EADAC',
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464 states: {
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465 hover: {
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466 fill: 'rgb(100, 138, 137)',
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467 stroke:'#8EADAC'
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468 },
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469 select: {
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470 stroke: '#8EADAC',
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471 fill: 'rgb(100, 138, 137)',
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472 }
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473 }
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474 }
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475 }
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476 };
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477 return chart ;
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478 };
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479
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diff changeset
480 /**
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481 * Returns hash use to init HightChart area.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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482 * @param pTitle {String} The title of the chart.
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483 * @param pXTitle {String} The xAxis title.
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484 * @param pYTitle {String} The yAxis title.
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485 * @param pXCategories {Array} x scale labels.
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486 * @param pData {Array} The HightChart series.
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487 * @return {Hash} Parameters to use in Highchart's constructor.
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488 */
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489 var areaplot_param = function(pTitle, pXTitle, pYTitle, pXCategories, pData) {
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490 var x_max = 0 ;
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491 for( var series_idx = 0 ; series_idx < pData.length ; series_idx++ ){
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492 for( var val_idx = 0 ; val_idx < pData[series_idx].length ; val_idx++ ){
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493 x_max = Math.max(parseInt(pData[series_idx][val_idx][0]), parseInt(x_max));
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494 }
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495 }
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496 var chart = chartplot( pTitle, pXTitle, pYTitle, pXCategories, pData );
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497 chart['chart'] = {
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498 type: 'area',
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499 zoomType:"x",
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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500 selectionMarkerFill: "rgb(222,159,115,0.25)"
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501 };
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502 chart['xAxis']['tickInterval'] = Math.max(1, parseInt(x_max/10));
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503 chart['plotOptions'] = {
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504 area: {
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505 marker: {
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506 enabled: true,
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507 symbol: 'circle',radius:4,
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508 }
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509 }
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510 };
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diff changeset
511 return chart ;
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512 }
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513
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514 /**
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515 * Returns hash use to init HightChart line.
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516 * @param pTitle {String} The title of the chart.
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517 * @param pXTitle {String} The xAxis title.
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518 * @param pYTitle {String} The yAxis title.
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519 * @param pXCategories {Array} x scale labels.
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520 * @param pData {Array} The HightChart series.
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521 * @return {Hash} Parameters to use in Highchart's constructor.
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522 */
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diff changeset
523 var lineplot_param = function(pTitle, pXTitle, pYTitle, pXCategories, pData) {
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524 var chart = chartplot( pTitle, pXTitle, pYTitle, pXCategories, pData );
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diff changeset
525 chart['chart'] = {
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526 type: 'line'
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527 };
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528 chart['yAxis']['min'] = 0 ;
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529 chart['legend'] = {'enabled': true};
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530 chart['plotOptions'] = {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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531 area: {
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diff changeset
532 marker: {
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parents:
diff changeset
533 enabled: true,
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parents:
diff changeset
534 symbol: 'circle',radius:4,
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parents:
diff changeset
535 }
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parents:
diff changeset
536 }
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diff changeset
537 };
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parents:
diff changeset
538 return chart ;
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parents:
diff changeset
539 }
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parents:
diff changeset
540
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parents:
diff changeset
541 var get_dispersion = function( values, counts ) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
542 var dispersion = new Array();
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
543
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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diff changeset
544 // Unstack list
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diff changeset
545 unstacked_list = new Array();
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
546 for( var idx = 0 ; idx < values.length ; idx++ ){
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parents:
diff changeset
547 for( var nb_add = 0 ; nb_add < counts[idx] ; nb_add++ ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
548 unstacked_list.push( values[idx] );
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diff changeset
549 }
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diff changeset
550 }
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parents:
diff changeset
551
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parents:
diff changeset
552 // Process metrics
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parents:
diff changeset
553 var nb_elt = unstacked_list.length ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
554 dispersion['min'] = unstacked_list[0] ;
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parents:
diff changeset
555 dispersion['max'] = unstacked_list[nb_elt - 1];
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
556 if( nb_elt % 2 == 0 ) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
557 dispersion['median'] = unstacked_list[(nb_elt/2) -1] ;
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diff changeset
558 } else {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
559 dispersion['median'] = (unstacked_list[parseInt((nb_elt/2) -1)] + unstacked_list[parseInt(nb_elt/2)])/2 ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
560 }
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parents:
diff changeset
561 // Deciles
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
562 for( var idx = 1 ; idx <= 9 ; idx++ ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
563 if( idx != 5 ) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
564 dispersion[idx + '_decile'] = unstacked_list[Math.floor(idx*(nb_elt/10) + 0.5) -1] ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
565 } else {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
566 dispersion['5_decile'] = dispersion['median'] ;
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oinizan
parents:
diff changeset
567 }
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parents:
diff changeset
568 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
569 // Quartiles
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
570 dispersion['lower_quartile'] = unstacked_list[Math.floor((nb_elt/4) + 0.5) -1] ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
571 dispersion['upper_quartile'] = unstacked_list[Math.floor((3*(nb_elt/4)) + 0.5) -1] ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
572
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
573 return dispersion ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
574 };
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parents:
diff changeset
575
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parents:
diff changeset
576 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
577 //
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
578 // Nav templates
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
579 //
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
580 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
581 var cluster_distrib_load = function( container_id ) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
582 // Radializes colors
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
583 Highcharts.setOptions({
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
584 colors : ['#8EADAC', '#DE9F73'] ,
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parents:
diff changeset
585 });
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oinizan
parents:
diff changeset
586 Highcharts.SVGRenderer.prototype.symbols.download = function (x, y, w, h) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
587 var path = [
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oinizan
parents:
diff changeset
588 // Arrow stem
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
589 'M', x + w * 0.5, y,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
590 'L', x + w * 0.5, y + h * 0.7,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
591 // Arrow head
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
592 'M', x + w * 0.3, y + h * 0.5,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
593 'L', x + w * 0.5, y + h * 0.7,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
594 'L', x + w * 0.7, y + h * 0.5,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
595 // Box
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
596 'M', x, y + h * 0.9,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
597 'L', x, y + h,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
598 'L', x + w, y + h,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
599 'L', x + w, y + h * 0.9
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
600 ];
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
601 return path;
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parents:
diff changeset
602 };
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
603 /* Radial gradient ?*/
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
604 /*
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
605 Highcharts.getOptions().colors = Highcharts.map(Highcharts.getOptions().colors, function (color) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
606 return {
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parents:
diff changeset
607 radialGradient: { cx: 0.5, cy: 0.3, r: 0.7 },
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oinizan
parents:
diff changeset
608 stops: [
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parents:
diff changeset
609 [0, color],
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
610 [1, Highcharts.Color(color).brighten(-0.1).get('rgb')] // darken
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
611 ]
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parents:
diff changeset
612 };
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613 });
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parents:
diff changeset
614 */
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parents:
diff changeset
615 var dispersion = get_dispersion( clusters_sizes, series[0]['data'] );
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diff changeset
616
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diff changeset
617 // Nb clusters and nb sequences
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parents:
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618 var nb_clusters = 0 ;
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parents:
diff changeset
619 var nb_sequences = 0 ;
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parents:
diff changeset
620 for( var clusters_sizes_idx = 0 ; clusters_sizes_idx < clusters_sizes.length ; clusters_sizes_idx++ ){
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parents:
diff changeset
621 nb_clusters += series[0]['data'][clusters_sizes_idx] ;
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parents:
diff changeset
622 nb_sequences += ( series[0]['data'][clusters_sizes_idx] * clusters_sizes[clusters_sizes_idx] );
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623 }
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parents:
diff changeset
624 $('#nb-clusters').append( '' +
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diff changeset
625 '<div class="circle">' +
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parents:
diff changeset
626 ' <span class="circle-title">Clusters</span>' +
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parents:
diff changeset
627 ' <br />' +
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parents:
diff changeset
628 ' <span class="circle-value">' + numberDisplay(nb_clusters) + '</span>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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parents:
diff changeset
629 '</div>'
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parents:
diff changeset
630 );
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parents:
diff changeset
631 $('#nb-sequences').append( '' +
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parents:
diff changeset
632 '<div class="circle">' +
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parents:
diff changeset
633 ' <span class="circle-title">Sequences</span>' +
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634 ' <br />' +
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635 ' <span class="circle-value">' + numberDisplay(nb_sequences) + '</span>' +
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636 '</div>'
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637 );
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638
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diff changeset
639 // Boxplot
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640 var boxplot_series = [{
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641 'name': "Cluster size",
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642 'data': [[dispersion['min'],
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643 dispersion['lower_quartile'],
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644 dispersion['median'],
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diff changeset
645 dispersion['upper_quartile'],
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diff changeset
646 dispersion['max']]]
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647 }];
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648 $('#' + container_id).append( '<div id="dispersion"></div>' );
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649 $('#dispersion').append( '<h2 class="pb-2 mt-4 mb-2 border-bottom">Clusters size summary</h2>');
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650 $('#dispersion').append( '<p>The cluster size is the sum of the abundances of the sequences grouped in a cluster.</p>');
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651 $('#dispersion').append('<div id="twofigs" class="row"></div>');
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652 $('#twofigs').append( '<div class="col-12 col-md-8"" style="height:100%;">' );
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653 $('#dispersion div').last().highcharts( boxplot_param("Clusters size distribution", null, "Cluster size", ["All"], boxplot_series) );
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654
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diff changeset
655 // Deciles
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656 var decile_data = [
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657 ["Min", dispersion['min']],
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658 [1, dispersion['1_decile']],
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659 [2, dispersion['2_decile']],
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660 [3, dispersion['3_decile']],
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661 [4, dispersion['4_decile']],
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662 ["Median", dispersion['5_decile']],
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663 [6, dispersion['6_decile']],
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664 [7, dispersion['7_decile']],
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665 [8, dispersion['8_decile']],
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666 [9, dispersion['9_decile']],
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667 ["Max", dispersion['max']]
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668 ];
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669 $('#twofigs').append( '<div class="col-12 col-md-4"">' );
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670 $('#dispersion div').last().append( table("Clusters size distribution (decile)", ["Decile", "Value"], decile_data) );
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671
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672 // Details
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673 var cluster_sum = 0 ;
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674 for( var idx=0 ; idx < clusters_sizes.length ; idx++ ){
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675 cluster_sum += series[0]['data'][idx] ;
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676 }
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677 var distrib_data = new Array();
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678 for( var idx=0 ; idx < clusters_sizes.length ; idx++ ){
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679 var cluster_prct = Math.round((series[0]['data'][idx]/cluster_sum)*10000)/100 ;
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680 distrib_data.push([ clusters_sizes[idx], series[0]['data'][idx], cluster_prct ]);
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681 }
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682 $('#dispersion').append( '<h2 class="pb-2 mt-4 mb-2 border-bottom">Clusters size details</h2>');
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683 $('#dispersion').append( '<div class="col-md-12"></div>' );
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diff changeset
684 //$('#dispersion div').last().append( '<h1 class="page-header">Clusters size details<h1/>' );
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685 $('#dispersion div').last().append( table("Clusters size", ["Cluster size", "Number of cluster", "% of all clusters"], distrib_data) );
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686 $('#dispersion table').last().prop( 'id', 'dispersion-table' );
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687 $('#' + container_id + ' table').last().DataTable({
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diff changeset
688 dom: "<'#dispersion-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" +
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diff changeset
689 "<'row'<'col-sm-12'tr>>" +
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690 "<'row'<'col-sm-5'i><'col-sm-7'p>>"
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691 //"sDom": '<"top"<"#dispersion-csv-export"><"clear">lf>rt<"bottom"ip><"clear">'
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692 });
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693 $('#dispersion-csv-export').addClass( 'dataTables_filter' );
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694 $('#dispersion-csv-export').html( '<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>' );
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695 $('#dispersion-csv-export').datatableExport({
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696 'table_id': "dispersion-table"
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697 });
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698 }
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699
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700 var sample_table_load = function( container_id ){
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701 var table_data = new Array();
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702 for( sample in samples_distrib ){
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703 table_data.push([
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diff changeset
704 sample,
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705 samples_distrib[sample]['shared_observations'] + samples_distrib[sample]['own_observations'],
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diff changeset
706 samples_distrib[sample]['shared_observations'],
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diff changeset
707 samples_distrib[sample]['own_observations'],
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708 samples_distrib[sample]['shared_seq'] + samples_distrib[sample]['own_seq'],
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diff changeset
709 samples_distrib[sample]['shared_seq'],
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diff changeset
710 samples_distrib[sample]['own_seq'],
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711 ])
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712 }
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713 $('#' + container_id).html( table("Samples information", ["Sample", "Total clusters", "Shared clusters", "Own clusters", "Total sequences", "Shared sequences", "Own sequences"], table_data) );
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diff changeset
714 $('#' + container_id + ' table').prop( 'id', 'samples-table' );
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diff changeset
715 $('#' + container_id + ' table').DataTable({
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diff changeset
716 dom: "<'#samples-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" +
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diff changeset
717 "<'row'<'col-sm-12'tr>>" +
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718 "<'row'<'col-sm-5'i><'col-sm-7'p>>"
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parents:
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719 //"sDom": '<"top"<"#samples-csv-export"><"clear">lf>rt<"bottom"ip><"clear">'
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720 });
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721 $('#samples-csv-export').addClass( 'dataTables_filter' );
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722 $('#samples-csv-export').html( '<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>' );
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723 $('#samples-csv-export').datatableExport({
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724 'table_id': "samples-table"
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725 });
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726 }
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727
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728 var hierarchical_clustering_load = function( container_id ) {
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diff changeset
729 var tree = Node.fromNewick( newick );
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
730 var leaves_names = tree.getLeavesNames();
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
731 var leaf_name_length = 0 ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
732 for( var idx = 0 ; idx < leaves_names.length ; idx++ ) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
733 leaf_name_length = Math.max( leaf_name_length, leaves_names[idx].length );
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
734 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
735 var width = tree.maxDepth() * 95 + (leaf_name_length * 8) ; // nb_link * width_link + text_length
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
736 var height = 50 + tree.nbLeaves() * 40 ; //margin_top + nb_terminal_nodes + height_nodes
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
737
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
738 // Display tree
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
739 linkage_data = tree.toJson();
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
740 d3_tree = null ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
741 diagonal = null ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
742 svg_layout = null ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
743 node_id = 0 ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
744
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
745 d3_tree = d3.layout.cluster()
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
746 .size([height, width]);
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
747
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
748 diagonal = d3.svg.diagonal()
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
749 .projection(function(d) { return [d.y, d.x]; });
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
750 $('#' + container_id).append('<div style="margin-left:auto;margin-right:auto;"></div>');
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
751 svg_layout = d3.select('#' + container_id + ' div').append("svg:svg")
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
752 .attr("width", width)
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
753 .attr("height", height)
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
754 .append("svg:g")
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
755 .attr("transform", "translate(20,20)");
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
756
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
757 linkage_data.x0 = height / 2;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
758 linkage_data.y0 = 0;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
759
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
760 update_linkage_nodes(linkage_data);
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
761
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
762 // Display warnings
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
763 var excluded_samples = $.grep(
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
764 Object.keys(samples_distrib),
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
765 function(el){ return $.inArray(el, leaves_names) == -1 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
766 );
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
767 if( excluded_samples.length > 0 ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
768 $('#' + container_id).append( '' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
769 '<div id="hc-warning" class="alert alert-warning alert-dismissible">' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
770 ' <span>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
771 ' <span class="glyphicon glyphicon-exclamation-sign"></span>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
772 ' Excluded because they have no sequence: ' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
773 ' </span>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
774 ' <span>' + excluded_samples.sort().join(", ") + '</span>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
775 '</div>'
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
776 );
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
777 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
778
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
779 // Display newick
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
780 $('#' + container_id).append( '' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
781 '<div id="hc-newick">' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
782 ' <span class="badge badge-primary label-badge">Newick</span>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
783 ' <span>' + newick + '</span>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
784 '</div>'
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
785 );
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
786 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
787
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
788 var sequence_distrib_load = function( container_id ) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
789 var series_cumulative = new Array() ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
790 for( var series_idx = 0 ; series_idx < series.length ; series_idx++ ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
791 series_cumulative.push({
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
792 'name': series[series_idx]['name'],
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
793 'data': new Array(),
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
794 'pointStart': 1
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
795 });
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
796 var sum = 0 ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
797 var previous_cumulative_count = 0 ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
798 for( var val_idx = 0 ; val_idx < series[series_idx]['data'].length ; val_idx++ ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
799 var current_count = series[series_idx]['data'][val_idx] * clusters_sizes[val_idx] ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
800 var cumulative_count = previous_cumulative_count + current_count ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
801 series_cumulative[series_idx]['data'].push( [clusters_sizes[val_idx], cumulative_count] );
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
802 previous_cumulative_count = cumulative_count ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
803 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
804 sum_series[series[series_idx]['name']] = previous_cumulative_count ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
805 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
806 for( var series_idx = 0 ; series_idx < series.length ; series_idx++ ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
807 for( var val_idx = 0 ; val_idx < series[series_idx]['data'].length ; val_idx++ ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
808 var current_prct = (series_cumulative[series_idx]['data'][val_idx][1] / sum_series[series[series_idx]['name']])*100 ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
809 series_cumulative[series_idx]['data'][val_idx][1] = Math.round(current_prct*100)/100 ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
810 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
811 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
812 var seq_by_depth = areaplot_param("Cumulative sequences proportion by cluster size", "Cluster size", "% sequences", null, series_cumulative);
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
813 seq_by_depth['tooltip'] = {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
814 formatter:function() {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
815 tooltip_head = '<b>Clusters with size <= ' + numberDisplay(this.x) + '</b>' ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
816 tooltip_body = '' ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
817 for( var i=0 ; i<this.points.length ; i++) {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
818 var pcnt = (this.points[i].point.y / sum_series[this.points[i].series.name]) * 100;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
819 tooltip_body += '<tr>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
820 '<td style="color:' + this.points[i].series.color +'">' + this.points[i].series.name + ' : </td>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
821 '<td> ' + this.points[i].point.y + '% </td>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
822 '<td> sequences</td>' +
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
823 '</tr>' ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
824 }
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
825 return tooltip_head + '<table>' + tooltip_body + '</table>' ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
826 },
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
parents:
diff changeset
827 shared: true,
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diff changeset
828 useHTML: true
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829 };
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830 $('#' + container_id).append('<div></div>');
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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diff changeset
831 $('#' + container_id).highcharts( seq_by_depth );
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832 $('#' + container_id).append('<p class="graph-nb">N.B.: Select area to zoom in.</p>');
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833 }
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834
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835
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836 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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837 //
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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838 // Data
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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839 //
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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840 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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841 var clusters_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15] ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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842 var series = [{
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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843 'name': "All",
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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844 'data': [2, 2, 5, 8, 6, 8, 4, 7, 3, 1, 3, 1]
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845 }];
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846 var sum_series = new Array() ;
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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847 var samples_distrib = {"01_subsample": {"shared_seq": 92, "shared_observations": 36, "own_seq": 8, "own_observations": 3}, "02_subsample": {"shared_seq": 90, "shared_observations": 37, "own_seq": 10, "own_observations": 3}, "03_subsample": {"shared_seq": 99, "shared_observations": 40, "own_seq": 1, "own_observations": 1}} ;
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848 var newick = "((01_subsample,(02_subsample,03_subsample):0.410):0.470);" ;
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849
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850
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851 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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852 //
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853 // Main
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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854 //
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855 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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856 $(function() {
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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857 // Remove alert
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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858 $('#js-alert').remove();
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859 $('#content').removeClass("hidden");
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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860
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861 // Load active tab
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862 cluster_distrib_load( "cluster-distrib" );
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863
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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864 // Add tab listener
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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865 $('.nav-tabs a').click(function (e) {
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866 e.preventDefault();
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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867 $(this).tab('show');
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868 if( $(this).attr('href') == "#sequence-distrib" && $('#sequence-distrib').hasClass('disabled') ){
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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869 $('#sequence-distrib').removeClass("disabled");
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870 sequence_distrib_load( "sequence-distrib" );
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871 } else if( $(this).attr('href') == "#samples-distrib" && $('#samples-distrib').hasClass('disabled') ){
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872 $('#samples-distrib').removeClass("disabled");
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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873 sample_table_load( "samples-distrib-table" );
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874 hierarchical_clustering_load( "samples-distrib-hc" );
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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875 }
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876 })
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877 });
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878 </script>
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879 </head>
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880 <body>
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881 <p id="js-alert" class="alert alert-warning">
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882 javascript is needed to display data.<br />
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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883 If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
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884 </p>
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885
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886 <div id="content" class="hidden">
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887 <ul class="nav nav-tabs">
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888 <li class="nav-item active"><a class="nav-link active" href="#cluster-distrib">Clusters distribution</a></li>
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889 <li class="nav-item active"><a class="nav-link" href="#sequence-distrib">Sequences distribution</a></li>
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890 <li class="nav-item active"><a class="nav-link" href="#samples-distrib">Samples distribution</a></li>
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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891 </ul>
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892 <div class="tab-content">
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893 <div id="cluster-distrib" role="tabpanel" class="tab-pane active">
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894 <div class="row">
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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895 <div class="col-md-2"></div>
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896 <div id="nb-clusters" class="col-sm-6 col-md-4"></div>
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897 <div id="nb-sequences" class="col-sm-6 col-md-4"></div>
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898 <div class="col-md-2"></div>
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899 </div>
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900 </div>
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901 <div id="sequence-distrib" role="tabpanel" class="tab-pane disabled"></div>
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902 <div id="samples-distrib" role="tabpanel" class="tab-pane disabled">
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903 <div>
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904 <h2 class="pb-2 mt-4 mb-2 border-bottom">Sequences count</h2>
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905 <div id="samples-distrib-table"></div>
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906 </div>
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907 <div>
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908 <h2 class="pb-2 mt-4 mb-2 border-bottom">Hierarchical clustering</h2>
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909 <div id="samples-distrib-hc"></div>
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910 </div>
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911 </div>
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912 </div>
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913 </div>
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914 </body>
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915 </html>