d56bc09614b5ad60ec9defcd02af1eabed9fabe3 kate Sat Oct 29 23:05:02 2011 -0700 1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others diff --git src/hg/js/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js index 396198e..e9207f1 100644 --- src/hg/js/encodeChipMatrix.js +++ src/hg/js/encodeChipMatrix.js @@ -1,212 +1,232 @@ // encodeChipMatrix.js - pull experiment table and metadata from server // and display ChIP antibodies vs. cell types in a matrix // Formatted: jsbeautify.py -j // Syntax checked: jslint indent:4, plusplus: true, continue: true, unparam: true, sloppy: true, browser: true */ /*global $, encodeProject */ $(function () { var dataType, server, requests = [ - // Requests to server API + // requests to server API encodeProject.serverRequests.experiment, encodeProject.serverRequests.cellType, encodeProject.serverRequests.antibody]; - function tableOut(matrix, cellTiers, cellTypeHash, antibodyGroups, antibodyHash, targetHash) { - // Create table where rows = cell types and columns are datatypes - // create table and first row 2 rows (column title and column headers) + var cellTypeHash = {}, antibodyHash = {}, targetHash = {}; + var cellType, antibody, target; + var organism, assembly, server, header; + var karyotype; + var spinner; + + function tableOut(matrix, cellTiers, antibodyGroups) { + // Create table with rows for each cell type and columns for each antibody target var table, tableHeader, row, td; - var antibodyHeaderLabel = "Antibody Targets"; - var cellHeaderLabel = "Cell Types"; - table = $('<table id="matrixTable"><thead><tr id="headerLabelRow"><td></td><td id="antibodyHeaderLabel" class="axisType" colspan=6 title="Click to view information about all element types">' + antibodyHeaderLabel + '</td></tr>' + '<tr id="columnHeaders"><td id="cellHeaderLabel" class="axisType" title="Click to view information about all cell types"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&type=Cell+Line&organism=' + organism + '">' + cellHeaderLabel + '</td></tr></thead><tbody>'); - tableHeader = $('#columnHeaders', table); + // fill in column headers from antibody targets returned by server + tableHeader = $('#columnHeaders'); $.each(antibodyGroups, function (i, group) { - tableHeader.append('<th class="groupType"><div class="verticalText">' + group.label + '</div></th>'); + tableHeader.append('<th class="groupType"><div class="verticalText">' + + group.label + '</div></th>'); $.each(group.targets, function (i, target) { if (targetHash[target] === undefined) { return true; } // prune out targets with no experiments if (targetHash[target].count !== undefined) { - tableHeader.append('<th class="elementType"><div class="verticalText">' + target + '</div></th>'); + tableHeader.append('<th class="elementType"><div class="verticalText">' + + target + '</div></th>'); } }); }); - // add rows with cell type labels and matrix elements for indicating if - // there's an experiment + // fill in matrix: + // add rows with cell type labels (column 1) and cells for experiments + table = $('#matrixTable'); + + // add sections for each Tier of cells $.each(cellTiers, function (i, tier) { //skip bogus 4th tier (not my property ?) if (tier === undefined) { return true; } - // td or th here ? - table.append($('<tr class="matrix"><th class="groupType">' + "Tier " + tier.term + '</th></td></tr>')); - + table.append($('<tr class="matrix"><th class="groupType">' + "Tier " + + tier.term + '</th></td></tr>')); $.each(tier.cellTypes, function (i, cellType) { if (!cellType) { return true; } if (!matrix[cellType]) { return true; } - row = $('<tr><th class="elementType">' + cellType + '</th>'); + karyotype = cellTypeHash[cellType].karyotype; + if (karyotype !== 'cancer' && karyotype !== 'normal') { + karyotype = 'unknown'; + } + row = $('<tr><th class="elementType" title="' + + cellTypeHash[cellType].description + + '"><a href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=' + cellType + + '">' + cellType + '</a><span title="karyotype: ' + karyotype + + '" class="' + karyotype + '">•</span></th>'); $.each(antibodyGroups, function (i, group) { // skip group header row.append('<td></td>'); $.each(group.targets, function (i, target) { - // TODO: change this class to matrixElementType - //$(".cellType").click(matrixClickHandler); - //"searchWindow"); // prune out targets with no experiments if (targetHash[target] === undefined) { return true; } if (targetHash[target].count === undefined) { return true; } td = $('<td></td>'); td.addClass('matrixCell'); if (matrix[cellType][target]) { td.addClass('experiment'); - } - td += '">'; - if (matrix[cellType][target]) { - td += '<a target="searchWindow" href="http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&hgt_mdbVar1=cell&hgt_mdbVar2=target&hgt_mdbVar3=view&hgt_mdbVal2=Any&hgt_mdbVal1='; - td += cellType; - td += '&hgt_mdbVal2='; - // TODO: needs to be join of all antibodies for this target - td += target; - //td += '"><font color=#00994D>'; - td += '"><font>'; - td += matrix[cellType][target]; - //td += "....."; - td += '</font></a>'; - td += '</td>'; + td.text(matrix[cellType][target]); + td.data({ + 'target' : target, + 'cellType' : cellType + }); + td.mouseover(function() { + $(this).attr('title', 'Click to select: ' + + $(this).data().target + ' ' + ' in ' + + $(this).data().cellType +' cells'); + }); + td.click(function() { + // TODO: base on preview ? + var url = encodeProject.getSearchUrl(assembly); + + // TODO: encapsulate var names + // TODO: search on antibody + url += + ('&hgt_mdbVar1=dataType&hgt_mdbVal1=' + 'ChipSeq' + + '&hgt_mdbVar2=cell&hgt_mdbVal2=' + cellType + + // TODO: all antibodies for target + '&hgt_mdbVar3=target&hgt_mdbVal3=' + target + + '&hgt_mdbVar4=view&hgt_mdbVal4=Any'); + // TODO: open search window + //window.open(url, "searchWindow"); + window.location = url; + }); } row.append(td); }); table.append(row); }); table.append(row); }); }); - table.append('</tbody>'); $("body").append(table); // use floating-table-header plugin table.floatHeader({ cbFadeIn: function (header) { // hide axis labels -- a bit tricky to do so // as special handling needed for X axis label $(".floatHeader #headerLabelRow").remove(); + $(".floatHeader #searchTypePanel").remove(); $(".floatHeader #cellHeaderLabel").html(''); // Note: user-defined callback requires // default actions from floatHeader plugin // implementation (stop+fadeIn) header.stop(true, true); header.fadeIn(100); - //header.fadeIn(100); - - }/*, - cbFadeOut: function (header) { - // show elements with class axisType - header.stop(true, true) - header.fadeOut(100); - $("#cellHeaderLabel").html(cellHeaderLabel); - $("#antibodyHeaderLabel").html(antibodyHeaderLabel); } - */ }); } function handleServerData(responses) { - // Main actions, called when loading data from server is complete - var experiments = responses[0], - cellTypes = responses[1], - antibodies = responses[2], - antibodyGroups, antibodyHash = {}, - targetHash = {}, - cellTypeHash = {}, - antibody, target, cellTiers, cellType, matrix = {}, - organism, assembly, header; + // main actions, called when loading data from server is complete + var experiments = responses[0], cellTypes = responses[1], antibodies = responses[2]; + var antibodyGroups, cellTiers; + var matrix = {}; + + hideLoadingImage(spinner); + $('#matrixTable').show(); // variables passed in hidden fields organism = encodeChipMatrix_organism; assembly = encodeChipMatrix_assembly; header = encodeChipMatrix_pageHeader; $("#pageHeader").text(header); document.title = 'ENCODE ' + header; // set up structures for antibodies and their groups $.each(antibodies, function (i, item) { antibodyHash[item.term] = item; }); antibodyGroups = encodeProject.getAntibodyGroups(antibodies); // set up structures for cell types and their tiers $.each(cellTypes, function (i, item) { cellTypeHash[item.term] = item; }); cellTiers = encodeProject.getCellTiers(cellTypes); // gather experiments into matrix $.each(experiments, function (i, exp) { // todo: filter out with arg to hgApi if (exp.organism !== organism) { return true; } // exclude ref genome annotations if (exp.cellType === 'None') { return true; } // todo: filter out with arg to hgApi ? if (exp.dataType !== 'ChipSeq') { return true; } // count experiments per target so we can prune those having none // (the matrix[cellType] indicates this for cell types // so don't need hash for those antibody = encodeProject.antibodyFromExp(exp); target = encodeProject.targetFromAntibody(antibody, antibodyHash); if (!targetHash[target]) { targetHash[target] = { count: 0, antibodies: {} }; } if (!targetHash[target].antibodies[antibody]) { targetHash[target].antibodies[antibody] = antibody; } targetHash[target].count++; cellType = exp.cellType; if (!matrix[cellType]) { matrix[cellType] = {}; } if (!matrix[cellType][target]) { matrix[cellType][target] = 0; } matrix[cellType][target]++; }); // fill in table - tableOut(matrix, cellTiers, cellTypeHash, antibodyGroups, antibodyHash, targetHash); + tableOut(matrix, cellTiers, antibodyGroups); } // get server from calling web page (intended for genome-preview) if ('encodeDataMatrix_server' in window) { server = encodeDataMatrix_server; } else { server = document.location.hostname; } // initialize encodeProject.setup({ server: server }); + + // show only spinner until data is retrieved + $('#matrixTable').hide(); + spinner = showLoadingImage("spinner"); + + // add radio buttons for search type to specified div on page + encodeProject.addSearchPanel('#searchTypePanel'); + encodeProject.loadAllFromServer(requests, handleServerData); });