integration of oligotype distribution per sample in pie chart form vi…

…suals and various little corrections
merenlab · Apr 4, 2012 · fddb3fb · fddb3fb
1 parent 1409860
commit fddb3fb
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Showing 3 changed files with 40 additions and 23 deletions.
diff --git a/utils/html/generate.py b/utils/html/generate.py
@@ -46,14 +46,26 @@ def get_list_item(l, index):
         return l[index]
     return ''
 
+@register.filter(name='mod') 
+def mod(value, arg):
+    return value % arg 
+
 @register.filter(name='multiply') 
 def multiply(value, arg):
     return int(value) * int(arg) 
 
+@register.filter(name='var') 
+def multiply(arg):
+    return 'x_' + arg.replace(' ', '_').replace('-', '_').replace('+', '_') 
+
 @register.filter(name='cleangaps') 
 def celangaps(arg):
     return arg.replace('-', '')
 
+@register.filter(name='sumvals') 
+def sumvals(arg):
+    return pretty_print(sum(arg.values()))
+
 @register.filter(name='mklist') 
 def celangaps(arg):
     return range(0, int(arg))
@@ -77,6 +89,9 @@ def generate_html_output(run_info_dict, html_output_directory = None, entropy_fi
     shutil.copy2(os.path.join(absolute, 'static/header.png'), os.path.join(html_output_directory, 'header.png'))
     shutil.copy2(os.path.join(absolute, 'scripts/jquery-1.7.1.js'), os.path.join(html_output_directory, 'jquery-1.7.1.js'))
     shutil.copy2(os.path.join(absolute, 'scripts/popup.js'), os.path.join(html_output_directory, 'popup.js'))
+    shutil.copy2(os.path.join(absolute, 'scripts/g.pie.js'), os.path.join(html_output_directory, 'g.pie.js'))
+    shutil.copy2(os.path.join(absolute, 'scripts/g.raphael.js'), os.path.join(html_output_directory, 'g.raphael.js'))
+    shutil.copy2(os.path.join(absolute, 'scripts/raphael.js'), os.path.join(html_output_directory, 'raphael.js'))
 
     def copy_as(source, dest_name):
         dest = os.path.join(html_output_directory, dest_name)
@@ -120,18 +135,11 @@ def copy_as(source, dest_name):
         html_dict['oligo_reps_dict'] = get_oligo_reps_dict(html_dict, html_output_directory)
         html_dict['component_reference'] = ''.join(['<a onmouseover="popup(\'\#%d\', 50)" href="">|</a>' % i for i in range(0, html_dict['alignment_length'])])
 
-    # get datasets dict
-    if html_dict.has_key('output_directory_for_datasets'):
-        dataset_network_figures = {}
-        for dataset in html_dict['datasets']:
-            src = os.path.join(run_info_dict['output_directory_for_datasets'], dataset + '.png')
-            dest = dataset + '.png'
-            if os.path.exists(src):
-                dataset_network_figures[dataset] = copy_as(src, dest)
-            else:
-                dataset_network_figures[dataset] = None
-        html_dict['dataset_network_figures'] = dataset_network_figures
-
+    # get javascript code for dataset pie-charts
+    html_dict['pie_charts_js'] = render_to_string('pie_charts_js.tmpl', html_dict)
+
+    # FIXME: code below is very inefficient and causes a huge
+    # memory issue. fix it by not using deepcopy.
     # generate individual oligotype pages
     if html_dict.has_key('output_directory_for_reps'):
         for oligo in html_dict['oligos']:

diff --git a/utils/html/templates/index.tmpl b/utils/html/templates/index.tmpl
@@ -8,6 +8,12 @@
 
     <script type="text/javascript" src="jquery-1.7.1.js"></script>
     <script type="text/javascript" src="popup.js"></script>
+    <script type="text/javascript" src="raphael.js"></script>
+    <script type="text/javascript" src="g.raphael.js"></script>
+    <script type="text/javascript" src="g.pie.js"></script>
+
+{{ pie_charts_js }}
+
 </head>
 
 <body >
@@ -45,6 +51,7 @@
 </table>
 </div>
 
+
 <div class="smallhead">Download</div>
 <p class="smallheadtitle">» Files to analyze results further via third partry applications
 <div class="info_table">
@@ -67,22 +74,13 @@
 <p class="smallheadtitle">» Oligotype Profiles Among Datasets
 <p align="center"><a href="{{ stackbar_figure }}"><img src="{{ stackbar_figure }}" style="max-width:1200px" border="0"></a>
 
-<div class="smallhead">Datasets</div>
-<p class="smallheadtitle">» Overview of datasets.
-
-<div class="wrap_regular"><p style="line-height: 2em;">
-    {% for dataset in datasets %}
-        <span style="padding: 5px; margin-right: 5px; background-color: #EEE;" onmouseover="popup('<img src={{dataset_network_figures|lookup:dataset}} style=max-width:790px;>', 800); style.backgroundColor='#AAA';" onmouseout="style.backgroundColor='#EEE';">{{dataset}}&nbsp;</span>
-    {% endfor %}
-</div>
-
 
 <div class="smallhead">Oligotypes</div><p class="smallheadtitle">» Abundan oligotypes with their frequencies within the dataset are shown below along with the most frequent sequence within the group of oligotype. {% if blast_results_found %}<span class="check">✓</span> indicates that the most frequent sequence which was represented by the given oligotype hit something duing the BLAST search with 100% identity. In contrary, <span class="cross">✗</span> sign means that there was no perfect hit during the BLAST search. <br /><br /> Here are the oligotypes with a perfect hit: {% for oligo in oligos %} {% if oligo_reps_dict.blast_results|lookup:oligo|lookup:0|lookup:"identity" == 100.0 %} {{oligo}}, {% endif %}{% endfor %}{% else %}BLAST results are missing for this analysis.{% endif %}
 
 {% if output_directory_for_reps %}
     <div class="wrap">
         <div id='sequences' style="height: auto;"> 
-            <div style="width: {{alignment_length|multiply:10}}px; position: relative;">
+            <div style="width: {% if alignment_length|multiply:8 > 800 %}{{alignment_length|multiply:8}}{% else %}800{%endif%}px; position: relative;">
                      <p>
                         <span class="check">&nbsp;</span>
                         <span class="frequency">&nbsp;</span>
@@ -121,6 +119,17 @@
 
 </div>
 </div>
+
+<div class="smallhead">Datasets</div>
+<p class="smallheadtitle">» Overview of datasets.
+{% for dataset in datasets %}
+{% if forloop.counter0|mod:3 == 0 %}
+    <div id="p_container_{{forloop.counter0}}"></div>
+{% endif %}
+{% endfor %}
+
+
+
 <div class="footer"><p>For questions and comments: meren / mbl.edu</div>
 </body>
 </html>

diff --git a/utils/html/templates/oligo.tmpl b/utils/html/templates/oligo.tmpl
@@ -53,7 +53,7 @@
 <p class="smallheadtitle">» First 20 Unique sequences
     <div class="wrap">
         <div id='sequences' style="height: auto;"> 
-            <div style="width: {{alignment_length|multiply:10}}px; position: relative;">
+            <div style="width: {% if alignment_length|multiply:8 > 800 %}{{alignment_length|multiply:8}}{% else %}800{%endif%}px; position: relative;">
                      <p><span class="frequency">&nbsp;</span><span style="background-color:{{white}}; border: 1px solid white;">&nbsp;&nbsp;</span> <span style="color: white;"> b <strong>{{oligos.0}}</strong> {{ oligo_reps_dict.component_references|lookup:oligo|safe }} </span>
                 {% for i in oligo_reps_dict.fancy_seqs|lookup:oligo|length|mklist %}
                     <p><span class="frequency">{{ oligo_reps_dict.frequency|lookup:oligo|get_list_item:i }}</span><span style="background-color:{{color_dict|lookup:oligo}}; border: 1px solid black;">&nbsp;&nbsp;</span> <span style="border-bottom:1px solid {{ color_dict|lookup:oligo }}"> <strong>{{oligo}}</strong> <em><a title="BLAST search this sequence in NCBI" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome&DATABASE=nr&QUERY=>{{ oligo }}_{{i}}%0d{{ oligo_reps_dict.clear_seqs|lookup:oligo|get_list_item:i|cleangaps }}">b</a></em> {{ oligo_reps_dict.fancy_seqs|lookup:oligo|get_list_item:i|safe }}</span>