|
|
(29 intermediate revisions by the same user not shown) |
Line 1: |
Line 1: |
| motif without matrices
| |
| [[Swissregulon:SRY.p1]]
| |
| [[Swissregulon:HOX(A,B,D)3.p1]]
| |
|
| |
| doubled top motif tables
| |
| CNhs10855 & CNhs11062
| |
| CNhs11245 & CNhs11183
| |
| CNhs11248 & CNhs11185
| |
| CNhs11772 & CNhs12996
| |
| CNhs11781 & CNhs12997
| |
|
| |
|
| |
| {{REVISIONTIMESTAMP}}
| |
| {{#ifexpr: {{#expr: {{REVISIONTIMESTAMP}}-20120731160000 }} > 0 | yes }}
| |
|
| |
| {{CURRENTTIMESTAMP}}
| |
|
| |
| <html>
| |
| <style type="text/css">
| |
| .rotate90 {
| |
| -webkit-transform: rotate(-90deg);
| |
| -moz-transform: rotate(-90deg);
| |
| -webkit-transform-origin: 6px 18px;
| |
| -moz-transform-origin: 6px 18px;
| |
| width:1px;
| |
| }
| |
| .highlight { background-color: yellow }
| |
| </style>
| |
| <script type="text/javascript">
| |
| $(document).ready(function() {
| |
| var oTable = $('#gene_exptable').dataTable({
| |
| "sScrollY": "300px",
| |
| "bPaginate": false,
| |
| "bScrollCollapse": true,
| |
| "iDisplayLength": -1,
| |
| "aaSorting": [[1,'desc']],
| |
| "aoColumnDefs": [ { "asSorting": [ "desc", "asc" ], "aTargets": [ "_all" ] } , { "bSortable": false, "aTargets": [ 0 ] }]
| |
| });
| |
| $('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom");
| |
|
| |
|
| |
| var data = [];
| |
| var plotdata = [];
| |
|
| |
|
| |
| // chart checkbox
| |
| for (var i2=1; i2<oTable.fnSettings().aoColumns.length; i2++){
| |
| key2 = i2-1;
| |
| $("#gene_exptable_chart_chkbox").append('<input type="checkbox" name="' + key2 +
| |
| '" checked="checked" id="id' + key2 + '"><label for="id' + key2 + '">'
| |
| + $(oTable.fnSettings().aoColumns[i2].sTitle).text() + '</label><br/>');
| |
| }
| |
|
| |
| function collectdata(){
| |
| data = [];
| |
| for (var i2=1; i2<oTable.fnSettings().aoColumns.length; i2++){
| |
| var plots = [];
| |
| for (var i1=1; i1<$('#gene_exptable tr').length; i1++) {
| |
| plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]);
| |
| }
| |
| data.push({"label": oTable.fnSettings().aoColumns[i2].sTitle.replace(/<(?:.|\n)*?>/gm, '').replace(/(^\s+)|(\s+$)/g, ""), "data": plots});
| |
| }
| |
| }
| |
|
| |
|
| |
| function drawchart(){
| |
|
| |
| plotdata = [];
| |
|
| |
| $("#gene_exptable_chart_chkbox").find("input:checked").each(function () {
| |
| var key = $(this).attr("name");
| |
| plotdata.push(data[$(this).attr("name")]);
| |
| });
| |
|
| |
| var plot1 = $.plot($("#gene_exptable_chart"), plotdata, {
| |
| yaxis : { axisLabel : 'TPM' },
| |
| lines : { show : false },
| |
| points : { show : true },
| |
| grid: { hoverable: true, clickable: true },
| |
| xaxis : { tickDecimals : 0, show: false },
| |
| legend: { show: false }
| |
| });
| |
|
| |
| //test
| |
| var data_series = plot1.getData();
| |
|
| |
| $("#gene_exptable_chart_chkbox label").css("background-color", "white");
| |
| $.each(data_series , function(){
| |
| $("#gene_exptable_chart_chkbox label:contains(" + this.label + ")").css("background-color", this.color);
| |
| });
| |
|
| |
| //test
| |
| //$('#test').text(oTable.fnSettings().aoData[1]._aData[0]);
| |
| $('#test').text(oTable.fnGetData(2, 2));
| |
| //test1 = oTable.fnSettings().oRow;
| |
|
| |
| }
| |
|
| |
| collectdata();
| |
| drawchart();
| |
|
| |
| // re-draw chart event
| |
| $(window).resize(function() { drawchart(); });
| |
| $("th").click(function() {collectdata(); drawchart(); } );
| |
| $("#gene_exptable_paginate").click(function() {collectdata(); drawchart(); } );
| |
| $('#gene_exptable').bind('filter', function() {
| |
| setTimeout(function(){
| |
| collectdata(); drawchart();}, 1000);
| |
| } );
| |
| $('#gene_exptable_length').change(function() {collectdata(); drawchart(); } );
| |
| $("#gene_exptable_chart_chkbox").find("input").click(function() { drawchart(); });
| |
|
| |
| // tooltip function start
| |
| function showTooltip(x, y, contents) {
| |
| $('<div id="tooltip">' + contents + '</div>').css( {
| |
| position: 'absolute',
| |
| display: 'none',
| |
| top: y + 5,
| |
| left: x + 5,
| |
| border: '1px solid #aaa',
| |
| padding: '2px',
| |
| 'background-color': '#fff',
| |
| opacity: 0.80
| |
| }).appendTo("body").fadeIn(200);
| |
| }
| |
|
| |
| var previousPoint = null;
| |
| $("#gene_exptable_chart").bind("plothover", function (event, pos, item) {
| |
| $("#x").text(pos.x.toFixed(2));
| |
| $("#y").text(pos.y.toFixed(2));
| |
| if (item) {
| |
| if (previousPoint != item.dataIndex) {
| |
| previousPoint = item.dataIndex;
| |
|
| |
| $("#tooltip").remove();
| |
| var x = item.datapoint[0].toFixed(0),
| |
| y = item.datapoint[1].toFixed(2);
| |
|
| |
| showTooltip(item.pageX, item.pageY,
| |
| "Gene: "+ item.series.label +"<br>TPM: "+y);
| |
| }
| |
| }
| |
| else {
| |
| $("#tooltip").remove();
| |
| previousPoint = null;
| |
| }
| |
| });
| |
| // tooltip function end
| |
|
| |
| // clicking point function
| |
| $("#gene_exptable_chart").bind("plotclick", function (event, pos, item) {
| |
| if (item){
| |
| var vdata = Math.round($('#gene_exptable').height())/item.series.data.length*item.dataIndex;
| |
| $('#gene_exptable_wrapper .dataTables_scrollBody').animate({ scrollTop: vdata-150 }, 'slow');
| |
| $("#gene_exptable_wrapper .dataTables_scrollBody tbody td").removeClass('highlight');
| |
| $('#gene_exptable_wrapper .dataTables_scrollBody tbody tr:eq(' + item.dataIndex+ ') td').addClass('highlight');
| |
| }
| |
| });
| |
| // clicking point function end
| |
|
| |
|
| |
|
| |
|
| |
|
| |
| } );
| |
| </script>
| |
| </html>
| |
|
| |
| {{#gene_exptable_hg19:ACTB|{{#ask:[[Category:FFCP]][[Short description::p1@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p1@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p2@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p2@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p3@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p3@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p4@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p4@ACTB,|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p5@ACTB]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p5@ACTB,|searchlabel=}}
| |
| }}
| |
|
| |
| <div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
| |
| <div id="gene_exptable_chart_chkbox" style="float:left;"></div>
| |
| <div style="clear:both;"></div>
| |
|
| |
| <div id="test"></div>
| |
|
| |
|
| |
| == gene mouse ==
| |
| <html> | | <html> |
| <script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script> | | <script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script> |
| <script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script> | | <script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script> |
| <script type="text/javascript" language="javascript" src="/resource_browser/rb_js/flot/jquery.flot.min.js"></script>
| |
| <style type="text/css" title="currentStyle"> | | <style type="text/css" title="currentStyle"> |
| @import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css"; | | @import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css"; |
| @import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css"; | | @import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css"; |
| </style> | | </style> |
| | <script> |
|
| |
|
| </html>
| | $(document).ready(function() { |
| | var oTable = $('.ff_sample_list').dataTable({ |
|
| |
|
| | }); |
|
| |
|
| <!--
| | }); |
| | | </script> |
| == Enrichment analysis: top 100 MCL coexpression mm9 enriched with this ontology term v019 var. ==
| | </html> |
| {{#info:TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji}}
| |
| {{#ask:[[MCL_coexpression_mm9_ontology_enrichment_uberon_id::UBERON:0002048]]
| |
| |?MCL_coexpression_mm9_ontology_enrichment_uberon_p-value|format=ttable|sort=MCL_coexpression_mm9_ontology_enrichment_uberon_p-value|order=asc|limit=100|searchlabel=}}
| |
| | |
| | |
| | |
| {{#sparql:select * where { ?x ?y ?z . } LIMIT 100 |endpoint=http://localhost:8080/sparql/}}
| |
| | |
| {{#ask:[[Category:FFCP]][[Coexpression_cluster_id::C297]]|?id|?Short_description|?Phase1_expression|format=template|template=Datatable_sampledata|sep=,|limit=20000}}
| |
| | |
| {{#jstest:
| |
| {{#ask:[[Category:FF Ontology]][[Sample_species::Mouse (Mus musculus)]]|?id|?Name|?sample_tissue|?sample_cell_line=|?sample_cell_type|?rna_sample_type|format=template|template=Datatable_sampledata|sep=,|limit=2000}}
| |
| }}
| |
| | |
| {{#sparql:
| |
| SELECT * WHERE { ?x ?y ?z FILTER regex(?z, "GO")
| |
| } LIMIT 10
| |
| |endpoint=http://go.bio2rdf.org/sparql/
| |
| |footer=NO
| |
| }}
| |
| | |
| | |
| {{#sparql:select * where { ?x ?y ?z . } LIMIT 10 |endpoint=http://localhost:8080/sparql/}}
| |
| | |
| {{#sparql:
| |
| PREFIX prop:<http://f5-webapp2/resource_browser/index.php/Special:URIResolver/Property-3A>
| |
| PREFIX page:<http://f5-webapp2/resource_browser/index.php/Special:URIResolver/>
| |
| SELECT ?x,?y WHERE {
| |
| ?x
| |
| prop:Sample_species
| |
| ?y FILTER regex(?y, "OMO", "i" )
| |
| } LIMIT 100
| |
| |endpoint=http://localhost:8080/sparql/
| |
| |headers=Page,Id
| |
| |footer=NO
| |
| }}
| |
| | |
|
| |
|
| -->
| | {{#ask:[[Concept:FF_samples_withname]]|[[Sample_species::Human (Homo sapiens)]]|mainlabel=FF ontology id|?Name|?Sample_category|?datafreeze_phase |
| | |format=ttable|class=ff_sample_list|limit=20|searchlabel=}} |