MARQ 0.0.1

data/merb/public/javascripts/marq.js

@@ -0,0 +1,51 @@
+function json(text){
+  var data;
+  eval("data = " + text);
+  return(data);
+}
+
+function tag(name){
+  return($('<' + name + '></' + name + '>'));
+}
+
+function random_name(){
+  return(Math.floor(Math.random() * 10000000));
+}
+
+function percent(e, elem){
+  var top = $(elem).offset().top;
+  var mtop = e.pageY;
+  var vsize = $(elem).height();
+  var percent = (mtop - top) / vsize;
+
+  return(percent);
+}
+
+
+function findPos(obj){
+  var curleft = curtop = 0;
+  if (obj.offsetParent) {
+    do {
+      curleft += obj.offsetLeft;
+      curtop += obj.offsetTop;
+    } while (obj = obj.offsetParent);
+  }
+  return [curleft,curtop];
+}
+
+function fit_window(elem,margin){
+   var height;
+   height = $(window).height() - findPos(elem[0])[1] - margin;
+   elem[0].style.height = height.toString() + "px";
+}
+
+function clear_textareas(){
+  $('textarea').after('<a class="clear textarea_link" href="#">[clear]</a>');
+  $('a.clear').click(
+    function(){
+      $(this).prev().attr('value','')
+      return(false);
+    })
+}  
+
+

data/merb/public/javascripts/marq_pages.js

@@ -0,0 +1,504 @@
+/* RESULTS MAIN */
+var hits  = [];
+var up    = 0;
+var down  = 0;
+var inprocess = false;
+
+
+function reset_checkboxes(){
+   $('input:checkbox').each( function() {
+       this.checked = false;
+   });
+}
+
+function has_term(terms, annotation){
+  for(term in terms)
+    if (annotation == terms[term]) return true
+  return false
+}
+
+function mark(type, annotation){
+  set_status("Marking " + type + ": " + annotation + '...')
+  var experiments = $('table#table_results > tbody > tr');
+  var total = experiments.length;
+  hits = [];
+
+  var i = 0;
+  experiments.each(function(){
+    var e = $(this);
+    var terms = annotations[type][e.attr('id')];      
+
+    if (has_term(terms, annotation)){
+      hits.push(i/total);
+      e.addClass('marked');
+    }else{
+      e.removeClass('marked');
+    }
+    i = i + 1;
+  })
+  hide_status()
+}
+
+function update_hits_main(){
+  $("#canvas").hitarea('hits', hits, {up: up, down: down, vertical: true});
+}
+
+
+function fit_size_main(){
+  var scroller = $('#table .table_scroller');
+
+  fit_window(scroller, 45)
+
+ 
+  $('#canvas').css('margin-top', scroller[0].offsetTop - 3);
+  $('#canvas').height(parseInt(scroller.css('height')));
+}
+
+
+function up_down(){
+  var experiments = $('table#table_results > tbody > tr');
+  var total = experiments.length;
+
+  up   = 0;
+  down = 0;
+  experiments.each(function(){
+    var e = $(this);
+    var pvalue = parseFloat(e.find('td.pvalue').html());
+    var score =  parseFloat(e.find('td.score').html());
+    if (pvalue < 0.05){
+      if (score > 0){
+        up = up + 1;
+      }else{
+        down = down + 1;
+      }
+    }
+  })
+
+  up = up/total;
+  down = down/total;
+}
+
+
+function update_annotations(cell){
+  cell = $(cell);
+  var list       = cell.find('ul.annotation_types');
+  var experiment = cell.parents('tr').attr('id');
+  var positive   = parseFloat(cell.parents('tr').find('td.score').html()) > 0;
+
+  list.children().remove();
+
+  for (var type in annotations) {
+    
+    if (type != "Words"){
+      if (type == selected_annotation_type){
+        var name = type;
+
+        if (positive){
+          name = name.replace(/_direct/," terms enriched in <span class=bold>up</span> genes").replace(/_inverse/, " terms enriched in <span class=bold>down</span> genes")
+        }else{
+          name = name.replace(/_inverse/," terms enriched in <span class=bold>up</span> genes").replace(/_direct/, " terms enriched in <span class=bold>down</span> genes")
+        }
+       
+
+        var title = tag('h5').html(name).addClass('title');
+        var ul = tag('ul').attr('id', type).addClass('annotations');
+
+        var terms = annotations[type][experiment];      
+        for (var i in terms) {
+          var term = terms[i];
+          var li = tag('li');
+          li.html(term)
+
+          li.click(click_term);
+
+          ul.append(li);
+        }
+
+        var type_list = tag('li');
+        type_list.append(title).append(ul);
+        list.append(type_list);
+      }
+    }
+    // Words are treated different, put triggers in the actual text
+    else{
+      var terms = annotations[type][experiment];      
+      cell.find('span.word').each(function(){
+        var span = $(this);
+        if (jQuery.inArray($(span).attr('data-stem'),terms) >= 0){
+          span.click(click_word).addClass('click');
+        }
+      })
+    }
+  }      
+}
+
+function click_term(){
+  if (inprocess){
+    return false;
+  }
+  inprocess = true;
+  var type = $(this).parents('ul.annotations').attr('id');
+  var annotation = $(this).html();
+
+  mark(type,annotation); 
+  update_hits_main();
+  inprocess = false;
+}
+
+function click_word(){
+  if (inprocess){
+    return false;
+  }
+  inprocess = true;
+  var annotation = $(this).attr('data-stem');
+
+  mark('Words',annotation); 
+  update_hits_main();
+  inprocess = false;
+}
+
+function cell_togle(cell){
+  var cell = $(this).parents('td');
+
+  var link = $(this);
+  if (cell.find('.info').length > 0){
+    cell.find('.info').toggle();
+  }else{
+    var experiment = $(cell).parents('tr').attr('id');
+    link.hide();
+    $.ajax({
+      url: "/experiment_info?job=" + job + "&experiment=" + encodeURIComponent(experiment),
+      success: function(html){
+        var info = $('<div class="info"></div>');
+        info.append($(html));
+        cell.append(info);
+        update_annotations(cell);
+        link.html('[-]');
+        link.show();
+      }
+    })
+  }
+
+  if (cell.find('.info').is(':visible'))
+    link.html('[-]');
+  else
+    link.html('[+]');
+
+  return(false);
+}
+
+function scroll_to_main(e){
+  var p = percent(e, this);
+
+  var table = $('table#table_results')
+  var rows = table.find('tbody > tr')
+  var num_rows = rows.length;
+
+  var position = Math.round(num_rows * p)
+  position = Math.max(0, position);
+  
+
+  for (var offset = 0; offset < num_rows * 0.01; offset++){
+    if ($(rows[position + offset]).hasClass('marked') || position + offset == num_rows - 1){
+      position = position + offset;
+      break;
+    }
+    if ($(rows[position - offset]).hasClass('marked') || position - offset == 0){
+      position = position - offset;
+      break;
+    }
+  }
+
+  if (position == 0){ position = 1;}
+
+  var selected = rows[position - 1];
+
+  $('#table .table_scroller').scrollTo($(selected),1000);
+}
+
+function load_annotations(type){
+  $.ajax({
+    url: '/annotations?job=' + job +'&type=' + type, 
+    beforeSend: function(){set_status("Loading annotations: " + type + "...")},
+    complete: function(){hide_status()},
+    success: function(data){ 
+    set_status("Preparing annotations: " + type + "...")
+      annotations[type] =  json(data)['annotations']; 
+      enrichment[type] =  json(data)['terms']; 
+      $('td.experiment > .info').each(function(){ update_annotations($(this).parents('td.experiment')) })
+    }
+  })
+}
+
+function prepare_selects(){
+    $('.compare_select:checked, .compare_invert:checked').each(function(){
+      $(this).attr('checked', false)
+    })
+
+    $('.compare_select').click(function(){
+      $('.compare_invert[id=' + $(this).attr('id').replace(/up/,"down") +']').attr('checked',false)
+    })
+    
+    $('.compare_invert').click(function(){ 
+       $('.compare_select[id=' + $(this).attr('id').replace(/down/,"up") +']').attr('checked',false)
+    })
+
+    $('#compare_link').click(function(){
+      var experiments = ""
+      var invert = ""
+      $('.compare_select:checked').each(function(){
+        experiments += encodeURI($(this).attr('name')) + "|";
+      })
+      $('.compare_invert:checked').each(function(){
+        experiments += encodeURI($(this).attr('name')) + "|";
+        invert += encodeURI($(this).attr('name')) + "|";
+      })
+      window.open('/compare?job=' + job + '&experiments=' + experiments + '&invert=' + invert)
+      return false;
+    })
+} 
+
+
+
+function start_results_main(){
+  load_annotations("Words")
+  prepare_selects()
+  $('a.toggle').click(cell_togle);
+  
+  $('#canvas').hitarea({
+    color:      '#618bc7', //'#183152',
+    up_color:   '#ecf169', // '#e8ec83', //'#E1E6FA',
+    down_color: '#ecf169', //'#e8ec83', //'#E1E6FA',
+    hit_color:  '#7f2153'  //'#ef72a7', //'#d293a9', //'#009200'
+  });
+  $('#canvas').dblclick(scroll_to_main);
+
+  $('#table').width($('#table_results_headers').width() + 20);
+  up_down();
+
+  fit_size_main();
+  $('#canvas').show();
+
+  update_hits_main();
+
+  $(window).resize(function(){
+    set_status("Resizing Table...")
+    fit_size_main()   
+    update_hits_main();
+    hide_status();
+  });
+
+  $(window).unbind('unload')
+  $(window).bind('unload',function(){
+    $('table#table_results > tbody > tr > td.experiment > a.toggle').unbind('click');
+    $('table#table_results > tbody > tr > td.experiment > div.info > dl.annotation_types > dd > span ').unbind('click');
+  })
+} 
+
+/*  RESULTS HITS */
+
+
+  var genes = [];
+
+  function update_hits_hits(){
+    var hits = $('table#table_genes > tbody > tr > td.hit').map(function(){ return($(this).html() / total_genes) });
+    $("#canvas").hitarea('hits', hits, {up: 0, down: 0, vertical: true});
+  }
+
+  function fit_size_hits(){
+    var scroller = $('.table_scroller');
+
+    fit_window(scroller, 43);
+    var height = scroller.css('height');
+
+    $('#canvas').height(parseInt(height));
+    $('#canvas').css('margin-top', scroller[0].offsetTop - 3);
+  }
+
+  function scroll_to_hits(e){
+    var p = percent(e, this);
+    var position = p * total_genes;
+
+    position = Math.max(0, position - 4);
+
+    var table = $('table#table_genes')
+    var rows = table.find('tbody > tr')
+
+    var selected = null
+    rows.each(function(){
+      selected = $(this);
+      if (parseInt($(this).find('td.hit').html()) > position){
+        return false
+      }
+    })
+
+    $('.table_scroller').scrollTo($(selected),1000);
+  }
+
+  function unselect(element){
+    element.removeClass('marked');
+  }
+
+  function select(element){
+    element.addClass('marked');
+
+    var name = element.attr('id');
+    genes.push(name);
+  }
+
+  function selected(event, area){
+    genes = [];
+    var first = null;
+    $('table#table_genes > tbody > tr').each(function(){ 
+      unselect($(this));
+      var position = parseInt($(this).find('td.hit').html()) / total_genes;
+      if (position <= area.top && position >= area.bottom){
+        if (first == null){
+          first = this;
+        }
+        select($(this));
+      }
+    });
+    $('.table_scroller').scrollTo($(first),1000);
+  }
+
+  function start_results_hits(){
+    $('#canvas').hitarea({
+      color:      '#618bc7', //'#183152',
+      up_color:   '#ecf169', //'#E1E6FA',
+      down_color: '#ecf169', //'#E1E6FA',
+      hit_color:  '#7f2153', //'#e8ec83', //'#ABC8E2',
+      lasso: true,
+      selected: selected
+    });
+    $('#canvas').bind('dblclick', scroll_to_hits);
+
+    $('#genes_hits').width($('#table_genes_headers').width() + 20);
+
+    fit_size_hits();   
+    $('#canvas').show();
+    update_hits_hits();
+
+    $(window).resize(function(){
+      fit_size_hits()   
+      update_hits_hits();
+    });
+
+    $('a.selected_genes').click(function(){
+      window.location = '/genes?genes=' + genes.join('|');
+      return(false);
+    })
+
+    $(window).unbind('unload')
+    $(window).bind('unload',function(){
+      $('a.selected_genes').unbind('click');
+    })
+  }
+  
+
+/* Annotations */
+
+var selected_annotation_type = "Words";
+
+function insert_in_table(tbody, term, value, support){
+  var done = false;
+
+  var trs = tbody.find('tr');
+  if(trs.length > 0){
+    trs.each(function(){
+      var row_value = parseFloat($(this).attr('data-value'));
+      if (row_value > value ||
+          row_value == value && 
+            support > parseFloat($(this).attr('data-support'))
+         ){
+
+        var tr = tag('tr');
+        tr.append(tag('td').addClass('term').html(term));
+        if (value == 0){
+          tr.append(tag('td').addClass('value').html('< 0.001'));
+        }else{
+          tr.append(tag('td').addClass('value').html(parseInt(value * 10000) / 10000));
+        }
+        tr.attr('data-support', support);
+        tr.attr('data-value', value);
+        $(this).before(tr);
+
+        done = true;
+        return false;
+      }
+    })
+  }
+  if (!done){
+    var tr = tag('tr');
+    tr.append(tag('td').addClass('term').html(term));
+    if (value == 0){
+      tr.append(tag('td').addClass('value').html('< 0.001'));
+    }else{
+      tr.append(tag('td').addClass('value').html(parseInt(value * 10000) / 10000));
+    }
+ 
+    tr.attr('data-support', support);
+    tr.attr('data-value', value);
+    tbody.append(tr);
+  }
+}
+
+function update_annotations_table(){
+  
+  $('#enrichment_table_div').show();
+  var type = $('#annotations_select').val();
+  terms = enrichment[type];
+
+  selected_annotation_type = type;
+  if (terms === undefined && type != ''){
+    if (!working){
+      status_callback= function(){
+        status_callback = null;
+        $('#enrichment_table > tbody').show();
+        $('#annotations_select').show();
+        $('#enrichment_waiting').remove();
+        update_annotations_table();
+      }
+      $('#annotations_select').hide();
+      $('#enrichment_table > tbody').hide().after(tag('span').attr('id','enrichment_waiting').html("Loading, please wait..."));
+      $('#enrichment_waiting').show();
+      load_annotations(type);
+    }else{
+      $('#annotations_select').val('');
+    }
+  }else{
+    $('td.experiment > .info').each(function(){ update_annotations($(this).parents('td.experiment')) })
+    $('#enrichment_table').attr('data-type',type);
+    var tbody = $('#enrichment_table > tbody')
+    tbody.children().remove();
+    for (term in terms){
+      var value = terms[term]['pvalue'];
+      var hits = terms[term]['hits'];
+
+      // This will invert the order of words, sparse words seem better
+      if (type == "Words"){
+        hits = -hits;
+      }
+
+      if (value < 0.1){
+        insert_in_table(tbody, term, value, hits)
+      }
+    }
+
+    if ($('#enrichment_table').height() > 300){
+      $('#enrichment_table_div').height(300);
+    }else{
+      $('#enrichment_table_div').height('');
+    }
+
+    tbody.find('td.term').click(click_annot_term)
+  }
+}
+
+function click_annot_term(){
+  var type = $('#enrichment_table').attr('data-type');
+  var term = $(this).html();
+  mark(type, term);
+  update_hits_main();
+}
+