5532506f80e32d334d9898c6e7d23a054c7df5b1
kate
  Wed Jun 27 21:12:18 2012 -0700
Add special-casing to separate out Small RNA as a separate data type
diff --git src/hg/js/encodeChipMatrix.js src/hg/js/encodeChipMatrix.js
index da7cbea..6deab13 100644
--- src/hg/js/encodeChipMatrix.js
+++ src/hg/js/encodeChipMatrix.js
@@ -1,199 +1,204 @@
 /* encodeChipMatrix.js - ENCODE web app to display ChIP-seq data 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
         ];
 
     var $matrixTable = $('#matrixTable');
 
     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 antibodyTarget, cellType;
         var matrix, antibodyTargetExps = {};
 
         // hide spinner and show table
         encodeMatrix.show($matrixTable);
 
         // set up structures for antibody targets and groups
         antibodyGroups = encodeProject.getAntibodyGroups(antibodies);
 
         // set up structures for cell types and their tiers
         cellTiers = encodeProject.getCellTiers(cellTypes, encodeMatrix_organism);
 
         // gather experiments into matrix
         matrix = makeExperimentMatrix(experiments, antibodyTargetExps);
 
        // fill in table using matrix
         encodeMatrix.tableOut($matrixTable, matrix, cellTiers, antibodyGroups, antibodyTargetExps, 
                 encodeProject.pruneAntibodyGroupsToExps, tableHeaderOut, rowAddCells);
     }
 
     function makeExperimentMatrix(experiments, antibodyTargetExps) {
         // Populate antibodyTarget vs. cellType array with counts of experiments
 
-        var antibody, target, cellType;
+        var antibody, target, cellType, exp;
         var matrix = {};
 
-        $.each(experiments, function (i, exp) {
+        $.each(experiments, function (i, experiment) {
+
+            // adjust experiment as needed for display purposes
+            exp = encodeProject.adjustExperiment(experiment);
+
             // 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);
             if (antibody === undefined) {
                 return true;
             }
             target = encodeProject.targetFromAntibody(antibody);
             if (target === undefined) {
                 return true;
             }
             if (antibodyTargetExps[target] === undefined) {
                 antibodyTargetExps[target] = 0;
             }
             antibodyTargetExps[target]++;
 
             cellType = exp.cellType;
             if (!matrix[cellType]) {
                 matrix[cellType] = {};
             }
             if (!matrix[cellType][target]) {
                 matrix[cellType][target] = 0;
             }
             matrix[cellType][target]++;
         });
     return matrix;
     }
 
     function tableHeaderOut($table, antibodyGroups) {
         // Generate table header and add to document
 
         var $tableHeaders, $thead, $th;
         var maxLen;  // for resizing header cells to accomodate label lengths
         var antibodyTarget;
 
         // fill in column headers from antibody targets returned by server
         $tableHeaders = $('#columnHeaders');
         $thead = $('thead');
 
         // 1st column is row headers
         // colgroups are needed to support cross-hair hover effect
         $thead.before('<colgroup></colgroup>');
 
         $.each(antibodyGroups, function (i, group) {
             $tableHeaders.append('<th class="groupType"><div class="verticalText">' + 
                                 group.label + '</div></th>');
             maxLen = Math.max(maxLen, group.label.length);
             $thead.before('<colgroup></colgroup>');
 
             $.each(group.targets, function (i, target) {
                 antibodyTarget = encodeProject.getAntibodyTarget(target);
                 $th = $('<th class="elementType">' + '<div class="verticalText">'+
                     '<a target="cvWindow" href="/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&target=' + 
                     encodeURIComponent(target) + '">' + target + '</a></div></th>');
                 if (!encodeProject.isIE8()) {
                     // Suppress mouseover under IE8 as QA noted flashing effect
                     $th.attr('title', antibodyTarget.description);
                 }
                 $tableHeaders.append($th);
                 // add colgroup element to support cross-hair hover effect
                 $thead.before('<colgroup class="experimentCol"></colgroup>');
                 maxLen = Math.max(maxLen, target.length);
             });
         });
         // adjust size of headers based on longest label length
         // empirically len/2 em's is right
         $('#columnHeaders th').css('height', (String((maxLen/2 + 2)).concat('em')));
         $('#columnHeaders th').css('width', '1em');
 
         //also need to set additional width for non-IE
         if (!$.browser.msie) {
             $('.verticalText').css('width', '1em');
         }
     }
 
     function rowAddCells($row, antibodyGroups, matrix, cellType) {
         // populate a row in the matrix with cells for antibody target groups and the targets
         // null cellType indicates this is a row for a cell group (tier)
 
         var $td;
 
         $.each(antibodyGroups, function (i, group) {
             // skip group header
             $td = $('<td></td>');
             $td.addClass('matrixCell');
             $row.append($td);
 
             $.each(group.targets, function (i, target) {
                 $td = $('<td></td>');
                 $td.addClass('matrixCell');
                 $row.append($td);
 
                 if (cellType === null) {
                     return true;
                 }
                 if (!matrix[cellType][target]) {
                     $td.addClass('todoExperiment');
                     return true;
                 }
                 // this cell represents experiments that
                 // fill in count, mouseover and selection by click
                 $td.addClass('experiment');
                 $td.text(matrix[cellType][target]);
                 $td.data({
                     'target' : target,
                     'cellType' : cellType
                 });
 
                 $td.attr('title', 'Click to select: ' +  target +
                         ' in ' + cellType +' cells');
 
                 // add highlight when moused over
                 encodeMatrix.hoverExperiment($td);
 
                 $td.click(function() {
                     var url, antibodyTarget;
                     var antibodies = []; 
 
                     // get list of antibodies for this protein target
                     antibodyTarget = encodeProject.getAntibodyTarget($(this).data().target);
                     $.each(antibodyTarget.antibodies, function (i, antibody) {
                         antibodies.push(antibody);
                     });
                     url = encodeMatrix.getSearchUrl(
                             {'mdbVar': 'dataType', 'mdbVal': 'ChipSeq'},
                             {'mdbVar': 'cell', 'mdbVal': $(this).data().cellType},
                             {'mdbVar': 'antibody', 'mdbVal': antibodies});
                     window.open(url, "searchWindow");
                 });
             });
         });
     }
 
     // initialize
     encodeMatrix.start($matrixTable);
 
     // load data from server and set up callback
     encodeProject.loadAllFromServer(requests, handleServerData);
 });