Mercurial > repos > frogs > frogs_3_1_0
view test-data/references/06-affiliation.html @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
| author | frogs |
|---|---|
| date | Thu, 28 Feb 2019 10:14:49 -0500 |
| parents | |
| children |
line wrap: on
line source
<!DOCTYPE html> <!-- # Copyright (C) 2015 INRA # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> <html> <head> <title>FROGS Affiliation</title> <meta charset="UTF-8"> <meta name="version" content="1.0.2"> <!-- CSS --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link> <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet"></link> <style type="text/css"> #js-alert { width: 90%; margin-right: auto; margin-left: auto; } #content { width: 90%; margin-right: auto; margin-left: auto; } .clear { clear: both; height: 0px; width: 100%; float: none !important; } ul.nav-tabs { margin-bottom: 30px; } .page-item.active .page-link { z-index: 1; color: #fff; background-color: #8EADAC; border-color: #8EADAC; outline: none !important; box-shadow: none !important; } .btn { color: #fff; border:#8EADAC; background-color: #8EADAC; } .btn:focus, .btn:active { outline: none !important; box-shadow: none !important; } .btn:hover:enabled{ color: #fff; border:#648a89; background-color: #648a89; cursor:pointer !important; } .pb-2, .py-2 { padding-bottom: 1.5rem !important; margin-bottom: 2rem !important; margin-top: 4rem !important; } .pb-2-first{ padding-bottom: 1.5rem !important; margin-bottom: 2rem !important; margin-top: 1rem !important; } /* ##### THEME FOR CHECKBOXES ##### */ .container { position: relative; padding-left: 0px; margin-bottom: 15px; cursor: pointer; -webkit-user-select: none; -moz-user-select: none; -ms-user-select: none; user-select: none; } /* Hide the browser's default checkbox */ .container input { position: absolute; opacity: 0; cursor: pointer; } /* Create a custom checkbox */ .checkmark { position: absolute; top: 0; left: 0; height: 20px; width: 20px; background-color: #8EADAC; border-radius: 5px; opacity:0.65; } /* On mouse-over, add a grey background color */ .container:hover input ~ .checkmark { background-color: #648a89; } /* When the checkbox is checked, add a blue background */ .container input:checked ~ .checkmark { background-color: #8EADAC; opacity:1; } /* Create the checkmark/indicator (hidden when not checked) */ .checkmark:after { content: ""; position: absolute; display: none; } /* Show the checkmark when checked */ .container input:checked ~ .checkmark:after { display: block; } /* Style the checkmark/indicator */ .container .checkmark:after { left: 7px; top: 3px; width: 6px; height: 10px; border: solid white; border-width: 0 3px 3px 0; -webkit-transform: rotate(45deg); -ms-transform: rotate(45deg); transform: rotate(45deg); } .highcharts-button > path{ stroke:#fff !important; fill:#8EADAC !important; } g.highcharts-button{ cursor:pointer !important; } g.highcharts-button:hover{ color: #fff; border:#648a89; background-color: #648a89; background-color: #648a89; cursor:pointer !important; } <!-- .selectpicker{ background-color:rgb(100, 138, 137,0.25); border-color:#8EADAC; } .selectpicker:hover{ background-color:rgb(100, 138, 137,0.25); border-color:#8EADAC; } --> option{ color:green } option:active, option:hover { outline: none !important; } /* make it red instead (with with same width and style) */ option:active, option:hover { box-shadow:red !important; outline-color: red !important; } select { -webkit-border-radius:25px; -moz-border-radius:25px; border-radius:25px; } select:hover { background-color:gren; } option:hover { background-color:yellow; } option { -webkit-border-radius:25px; -moz-border-radius:25px; border-radius:25px; color:blue; background-color:yellow; } </style> <!-- JS --> <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script> <script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script> <script type="text/javascript" src="https://code.highcharts.com/4.1.4/modules/exporting.js"></script> <script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script> <script type="text/javascript" src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap4.min.js"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.11.0/umd/popper.min.js" integrity="sha384-b/U6ypiBEHpOf/4+1nzFpr53nxSS+GLCkfwBdFNTxtclqqenISfwAzpKaMNFNmj4" crossorigin="anonymous"></script> <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.min.js" integrity="sha384-smHYKdLADwkXOn1EmN1qk/HfnUcbVRZyYmZ4qpPea6sjB/pTJ0euyQp0Mk8ck+5T" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.12.4/js/bootstrap-select.min.js"></script> <script type="text/javascript"> /* * HTMLTable.js 0.1.0 - HTMLTable Library * * Copyright (c) 2015 Escudie Frederic * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license. */ 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}; /* * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library * * Copyright (c) 2015 Escudie Frederic * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license. */ !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); </script> <script type="text/javascript"> Highcharts.SVGRenderer.prototype.symbols.download = function (x, y, w, h) { var path = [ // Arrow stem 'M', x + w * 0.5, y, 'L', x + w * 0.5, y + h * 0.7, // Arrow head 'M', x + w * 0.3, y + h * 0.5, 'L', x + w * 0.5, y + h * 0.7, 'L', x + w * 0.7, y + h * 0.5, // Box 'M', x, y + h * 0.9, 'L', x, y + h, 'L', x + w, y + h, 'L', x + w, y + h * 0.9 ]; return path; }; /** * Returns the string representation of the number. * @param pValue {Float} The number to process. * @return {String} The string representation (example: 12856892.11111 => 12,856,892.11). */ var numberDisplay = function( pValue ){ var new_val = "" ; if( ("" + pValue + "").indexOf(".") != -1 ){ new_val = pValue.toFixed(2).replace(/(\d)(?=(\d{3})+\b)/g, '$1,'); } else { new_val = pValue.toFixed().replace(/(\d)(?=(\d{3})+\b)/g, '$1,'); } return new_val ; } /** * Returns the HTML table representation of the data. * @param pTitle {String} The title of the table. * @param pCategories {Array} The title of each column. * @param pData {Array} 2D matrix with row and column data. * @return {String} The HTML table representation. */ var table = function( pTitle, pCategories, pData ) { // Header var table_header = '' ; var table_header_line = "" ; for(var idx = 0 ; idx < pCategories.length ; idx++){ table_header_line += " <th>" + pCategories[idx] + "</th>\n" ; } table_header += " <tr>\n" + table_header_line + " </tr>\n" ; table_header = " <thead>\n" + table_header + " </thead>\n" ; // Body var table_body = '' ; for(var data_idx = 0 ; data_idx < pData.length ; data_idx++){ var table_body_row = "" ; for(var category_idx = 0 ; category_idx < pCategories.length ; category_idx++){ if( typeof pData[data_idx][category_idx] === "number" ) { table_body_row += " <td>" + numberDisplay(pData[data_idx][category_idx]) + "</td>\n" ; } else { table_body_row += " <td>" + pData[data_idx][category_idx] + "</td>\n" ; } } table_body += " <tr>\n" + table_body_row + " </tr>\n" ; } table_body = " <tbody>\n" + table_body + " </tbody>\n" ; return '<table class="table table-striped table-bordered">\n' + table_header + table_body + "</table>\n" ; } // couleur des diapos : bleu #8EADAC, vert : #A2A32F, orange1 #C6792B , taupe #9A866C, orange pastel : #DE9F73 var histogram_param = function( pTitle, pYTitle, pCategories, pSeries, unity ) { var param = { chart: { type: 'column' }, colors : [ '#8EADAC', '#DE9F73' ] , exporting:{buttons: {contextButton: { symbol: 'download' }}}, buttons: {contextButton: {menuItems: ['downloadPNG', 'downloadSVG']}}, navigation: { buttonOptions: { theme: { r: 4, fill:'#8EADAC', states: { hover: { fill: 'rgb(100, 138, 137)', stroke:'#8EADAC' }, select: { stroke: '#8EADAC', fill: 'rgb(100, 138, 137)', } } } } }, title: { text: pTitle }, xAxis: { categories: pCategories, crosshair: true, crosshair: { color: "rgb(142,173,172,0.25)" } }, yAxis: { min: 0, title: { text: pYTitle } }, tooltip: { headerFormat: '<span style="font-size:10px">{point.key}</span><table>', pointFormat: '<tr><td style="color:{series.color};padding:0">{series.name}: </td>' + '<td style="padding:0"><b>{point.y} ' + unity + '</b></td></tr>', footerFormat: '</table>', shared: true, useHTML: true }, plotOptions: { column: { pointPadding: 0.2, borderWidth: 0 } }, credits: { enabled: false }, series: pSeries }; return param ; } /** * Returns hash use to init HightChart object (without 'type'). * @param pTitle {String} The title of the chart. * @param pXTitle {String} The xAxis title. * @param pYTitle {String} The yAxis title. * @param pXCategories {Array} The title of each category (x scale labels). * @param pData {Array} The HightChart series. * @return {Hash} The hash. * @warning This method use HightChart xAxis.categories. */ // couleur des diapos : bleu #8EADAC, vert : #A2A32F, orange1 #C6792B , taupe #9A866C, orange pastel : #DE9F73 var chartplot = function( pTitle, pXTitle, pYTitle, pXCategories, pData ) { var chart = { title: { text: pTitle }, colors : [ '#8EADAC', '#DE9F73' ] , exporting:{buttons: {contextButton: { symbol: 'download' }}}, buttons: {contextButton: {menuItems: ['downloadPNG', 'downloadSVG']}}, navigation: { buttonOptions: { theme: { r: 4, fill:'#8EADAC', states: { hover: { fill: 'rgb(100, 138, 137)', stroke:'#8EADAC' }, select: { stroke: '#8EADAC', fill: 'rgb(100, 138, 137)', } } } } }, xAxis: {}, yAxis: { title: { text: pYTitle } }, series: pData, credits: { enabled: false } } if( pXCategories != null ){ chart['xAxis']['categories'] = pXCategories ; } if( pXTitle != null ){ chart['xAxis']['title'] = { text: pXTitle } ; } if( pData.length <= 1 ) { chart['legend'] = {'enabled': false}; } else { chart['legend'] = {'enabled': true}; } return chart ; } var pie_param = function( pTitle, pData, unity ) { var series = [{ type: 'pie', name: unity, data: pData }] var plot = chartplot( pTitle, null, null, null, series ); plot['tooltip'] = { pointFormat: '{series.name}: <b>{point.percentage:.1f}%</b>' }; plot['plotOptions'] = { pie: { allowPointSelect: true, cursor: 'pointer', dataLabels: { enabled: true, format: '<b>{point.name}</b>: {point.y:,.0f}', style: { color: (Highcharts.theme && Highcharts.theme.contrastTextColor) || 'black' } } } }; return plot ; }; $(function() { var global_results = {"nb_clstr_with_affi": 86, "nb_clstr": 86, "nb_seq_ambiguous": [0, 0, 0, 0, 0, 0, 0, 0], "nb_seq": 45574, "nb_clstr_ambiguous": [0, 0, 0, 0, 0, 0, 0, 0], "nb_seq_with_affi": 45574} ; var sample_results = {"02": {"nb_seq": 15140, "nb_seq_with_affi": 15140, "nb_clstr_with_affi": 86, "nb_clstr": 86}, "03": {"nb_seq": 15167, "nb_seq_with_affi": 15167, "nb_clstr_with_affi": 86, "nb_clstr": 86}, "01": {"nb_seq": 15267, "nb_seq_with_affi": 15267, "nb_clstr_with_affi": 86, "nb_clstr": 86}} ; var taxonomy_ranks = ["Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species"] ; // Remove alert $('#js-alert').remove(); $('#content').removeClass("hidden"); // Display summary var std_color = Highcharts.getOptions().colors ; Highcharts.getOptions().colors = Highcharts.map(Highcharts.getOptions().colors, function (color) { return { radialGradient: { cx: 0.5, cy: 0.3, r: 0.7 }, stops: [ [0, color], [1, Highcharts.Color(color).brighten(-0.3).get('rgb')] // darken ] }; }); var pie_series = [ ["With affiliation", global_results["nb_clstr_with_affi"]], ["Without affiliation", (global_results["nb_clstr"] - global_results["nb_clstr_with_affi"])] ] $('#clstr-ratio-affi').highcharts( pie_param("OTUs affiliation", pie_series, 'OTUs') ); var pie_series = [ ["With affiliation", global_results["nb_seq_with_affi"]], ["Without affiliation", (global_results["nb_seq"] - global_results["nb_seq_with_affi"])] ] $('#seq-ratio-affi').highcharts( pie_param("Sequences affiliation", pie_series, 'sequences') ); Highcharts.getOptions().colors = std_color ; var histogram_series = [ { 'name': 'OTUs', 'data': global_results["nb_clstr_ambiguous"].map(function(num) { var prct = (num/global_results["nb_clstr"])*10000/100 ; return( parseFloat(numberDisplay(prct)) ); }) }, { 'name': 'Sequences', 'data': global_results["nb_seq_ambiguous"].map(function(num) { var prct = (num/global_results["nb_seq"])*10000/100 ; return( parseFloat(numberDisplay(prct)) ); }) } ]; $('#clstr-multi-affi').highcharts( histogram_param('Multi-affiliation by taxonomic rank', '% of multi-affiliated', taxonomy_ranks, histogram_series, '%') ); // Display data by sample var table_categories = [ 'Sample', 'Nb OTUs', '% OTUs affiliated by blast', 'Nb seq', '% seq affiliated by blast' ]; var table_series = new Array(); for( var sample_name in sample_results ){ table_series.push([ sample_name, sample_results[sample_name]['nb_clstr'], Math.round(((sample_results[sample_name]['nb_clstr_with_affi']/sample_results[sample_name]['nb_clstr'])*10000)/100), sample_results[sample_name]['nb_seq'], Math.round(((sample_results[sample_name]['nb_seq_with_affi']/sample_results[sample_name]['nb_seq'])*10000)/100) ]); }; $('#samples-details').append( table("Blast affiliation by sample", table_categories, table_series) ); $('#samples-details table').prop( 'id', 'details-table' ); $('#samples-details table').DataTable({ //"sDom": '<"top"<"#details-csv-export"><"clear">lf>rt<"bottom"ip><"clear">' dom: "<'#details-csv-export'><'row'<'col-sm-5'l><'col-sm-7'f>>" + "<'row'<'col-sm-12'tr>>" + "<'row'<'col-sm-5'i><'col-sm-7'p>>", "pagingType": "simple" }); $('#details-csv-export').html( '<button class="btn btn-primary" ><span class="fa fa-download" aria-hidden="true"> CSV</span></button>' ); $('#details-csv-export').addClass( 'dataTables_filter' ); $('#details-csv-export').datatableExport({ 'table_id': "details-table" }); }); </script> </head> <body> <p id="js-alert" class="alert alert-warning"> javascript is needed to display data.<br /> If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view. </p> <div id="content" class="hidden"> <div id="global-summary"> <h2 class="pb-2-first mt-4 mb-2 border-bottom" style="margin-top: 1rem">Blast affiliation summary</h2> <div class="row"> <div class="col-md-1"></div> <div id="clstr-ratio-affi" class="col-md-5"></div> <div id="seq-ratio-affi" class="col-md-5"></div> <div class="col-md-1"></div> </div> <h2 class="pb-2 mt-4 mb-2 border-bottom">Blast multi-affiliation summary</h2> <div class="row"> <div class="col-md-1"></div> <div id="clstr-multi-affi" class="col-md-10"></div> <div class="col-md-1"></div> </div> </div> <div id="samples-details"> <h2 class="pb-2 mt-4 mb-2 border-bottom">Blast affiliation by sample</h2> </div> </div> </body> </html>