0713a8a2c7e4622e18d58b9028756d955a3bccd4 kate Tue Sep 6 21:47:53 2011 -0700 ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters). diff --git src/hg/js/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js new file mode 100644 index 0000000..2c75a6e --- /dev/null +++ src/hg/js/encodeChipMatrix.js @@ -0,0 +1,175 @@ +// 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 requests = [ + // Requests to server API + encodeProject.serverRequests.experiment, encodeProject.serverRequests.cellType, encodeProject.serverRequests.antibody], + dataType; + + 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 table, tableHeader, row, td; + + table = $('<table>' + '<tr><td><td class="axisType" colspan=6>Antibody Targets</td></tr>' + '<tr id="columnHeaders"><td class="axisType">Cell Types</td></tr>'); + tableHeader = $('#columnHeaders', table); + $.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>'); + } + }); + }); + // add rows with cell type labels and matrix elements for indicating if + // there's an experiment + $.each(cellTiers, function (i, tier) { + //skip bogus 4th tier (not my property ?) + if (tier === undefined) { + return true; + } + // td or th here ? + table.append($('<tr class="matrix"><th class="groupType">' + "Tier " + tier.term + '</th></td></tr>')); + $.each(tier.cellTypes, function (i, cellType) { + if (!cellType) { + return true; + } + if (!matrix[cellType]) { + return true; + } + row = $('<tr><th class="elementType">' + cellType + '</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 class="cellType'; + if (matrix[cellType][target]) { + td += ' experiment'; + } + td += '">'; + if (matrix[cellType][target]) { + td += '<a target=_blank 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_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>'; + } + row.append(td); + }); + table.append(row); + }); + table.append(row); + }); + }); + $("body").append(table); + } + + 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; + + // variables passed in hidden fields + organism = $("#var_organism").val(); + assembly = $("#var_assembly").val(); + header = $("#var_pageHeader").val(); + + $("#pageHeader").text(header); + $("title").text('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); + } + + // initialize + encodeProject.setup({ + // todo: add hidden page variable for server + server: "hgwdev-kate.cse.ucsc.edu" + //server: "genome-preview.ucsc.edu" + }); + encodeProject.loadAllFromServer(requests, handleServerData); +});