f20f28b07df4e9738560a839a7636a7708d64969 kate Mon Oct 31 20:23:33 2011 -0700 Add filtering by assembly diff --git src/hg/js/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js index e9207f1..2f9a811 100644 --- src/hg/js/encodeChipMatrix.js +++ src/hg/js/encodeChipMatrix.js @@ -1,232 +1,243 @@ // 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 encodeProject.serverRequests.experiment, encodeProject.serverRequests.cellType, - encodeProject.serverRequests.antibody]; + encodeProject.serverRequests.antibody, + encodeProject.serverRequests.expId + ]; 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; // 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>'); $.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>'); } }); }); // fill in matrix: // add rows with cell type labels (column 1) and cells for experiments table = $('#matrixTable'); // add sections for each Tier of cells $.each(cellTiers, function (i, tier) { //skip bogus 4th tier (not my property ?) if (tier === undefined) { return true; } table.append($('<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; } 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) { // 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.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); }); }); $("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); } }); } function handleServerData(responses) { // main actions, called when loading data from server is complete - var experiments = responses[0], cellTypes = responses[1], antibodies = responses[2]; - var antibodyGroups, cellTiers; + var experiments = responses[0], cellTypes = responses[1], + antibodies = responses[2], expIds = responses[3]; + var antibodyGroups, cellTiers, expIdHash; 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); + // use to filter out experiments not in this assembly + expIdHash = encodeProject.getExpIdHash(expIds); + // 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; } + if (expIdHash[exp.ix] === undefined) { + 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, antibodyGroups); } + // initialize + // get server from calling web page (intended for genome-preview) if ('encodeDataMatrix_server' in window) { server = encodeDataMatrix_server; } else { server = document.location.hostname; } - // initialize + // variables passed from calling page + organism = encodeChipMatrix_organism; + assembly = encodeChipMatrix_assembly; + $("#assemblyLabel").text(assembly); + header = encodeChipMatrix_pageHeader; + $("#pageHeader").text(header); + document.title = 'ENCODE ' + header; + encodeProject.setup({ - server: server + server: server, + assembly: assembly }); // 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); });