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authorDannyArends2015-10-08 10:49:23 +0200
committerDannyArends2015-10-08 10:49:23 +0200
commit6d833e9f99ff6275fd1997c6993419a66bbbe392 (patch)
tree9712c97881c54cb7e6827345f65169f9066f6f43
parent2e30a64ca583d990cd46bb9eafdad7d84b46b48d (diff)
downloadgenenetwork2-6d833e9f99ff6275fd1997c6993419a66bbbe392.tar.gz
Massive update to the templates, adding error checking and handling + the eigen genes per module
-rw-r--r--wqflask/wqflask/templates/wgcna_results.html65
-rw-r--r--wqflask/wqflask/templates/wgcna_setup.html19
2 files changed, 61 insertions, 23 deletions
diff --git a/wqflask/wqflask/templates/wgcna_results.html b/wqflask/wqflask/templates/wgcna_results.html
index 077238a5..0dc030b1 100644
--- a/wqflask/wqflask/templates/wgcna_results.html
+++ b/wqflask/wqflask/templates/wgcna_results.html
@@ -4,40 +4,73 @@
{% block content %} <!-- Start of body -->
<div class="container">
<h1>WGCNA Results</h1>
- <h4>Soft threshold table</h4>
+ Analysis found {{results['nmod']}} modules when scanning {{results['nphe']}} phenotypes, measured on {{results['nstr']}} strains.<br>
+ Additional parameters settings:
+ <ul>
+ <li>Soft thresholds checked = {{results['requestform']['SoftThresholds']}}</li>
+ <li>Power used for this analysis = {{results['Power']}}</li>
+ <li>TomType = {{results['requestform']['TOMtype']}}</li>
+ <li>Minimum module size = {{results['requestform']['MinModuleSize'] }}</li>
+ <li>mergeCutHeight = {{results['requestform']['mergeCutHeight'] }}</li>
+ </ul>
+
+ <h3>Soft threshold table</h3>
<table width="80%">
<tr><th>Power</th><th>SFT.R.sq</th><th>slope</th><th>truncated.R.sq</th><th>mean.k</th><th>median.k</th><th>max.k</th><th>Analysis</th></tr>
{% for r in range(powers[0][0]|length) %}
- <tr>
+ {% if powers[0][1][r] > 0.85 %}
+ <tr style="color: #00ff00;">
+ {% elif powers[0][1][r] > 0.75 %}
+ <tr style="color: #aaaa00;">
+ {% else %}
+ <tr style="color: #ff0000;">
+ {% endif %}
{% for c in range(powers[0]|length) %}
<td>{{powers[0][c][r]|round(3)}}</td>
{% endfor %}
- <td><input type="submit" value="Redo use power = {{powers[0][0][r]}}" /></td></tr>
+ <td style="color: #000000;">
+ {% if powers[0][1][r] > 0.75 %}
+ <input type="submit" value="Redo use power = {{powers[0][0][r]}}" /></td>
+ {% endif %}
+ </tr>
{% endfor %}
</table>
+ <h3>WGCNA module plot</h3>
+ <a href="/tmp/{{ results['imgurl'] }}">
+ <img alt="Embedded Image" src="data:image/png;base64,
+ {% for elem in results['imgdata'] -%}
+ {% print("%c"|format(elem)) %}
+ {%- endfor %}
+ " /></a>
- <h4>Phenotype / Module table</h4>
- debug: {{results['network']|length}}
- debug: {{results['network'][0]|length}}
- {{phenotypes[0][0]}}
+ <h3>Phenotype / Module table</h3>
<table width="80%">
<tr><th>Phenotype</th><th>Module</th></tr>
- {% for r in range(results['network'][0]|length) %}
+ {% for r in range(results['nphe']) %}
<tr>
- <td>{{phenotypes[r][0]}}</td>
+ <td>{{results['phenotypes'][r][0]}}</td>
<td>{{results['network'][0][r]}}</td>
</tr>
{% endfor %}
</table>
- <h2>WGCNA module plot</h2>
- <a href="/tmp/{{ results['imgurl'] }}">
- <img alt="Embedded Image" src="data:image/png;base64,
- {% for elem in results['imgdata'] -%}
- {% print("%c"|format(elem)) %}
- {%- endfor %}
- " /></a>
+ <h3>Module eigen genes</h3>
+ <table width="80%">
+ <tr><th>Phenotype</th>
+ {% for m in range(results['nmod']) %}
+ <th><input type="submit" value="Add module {{m}} to collection" /></th>
+ {% endfor %}
+ </tr>
+ {% for r in range(results['nstr']) %}
+ <tr>
+ <td>{{results['strains'][r][0]}}</td>
+ {% for m in range(results['nmod']) %}
+ <td>{{results['network'][2][m][r]}}</td>
+ {% endfor %}
+ </tr>
+ {% endfor %}
+ </table>
</div>
{% endblock %}
diff --git a/wqflask/wqflask/templates/wgcna_setup.html b/wqflask/wqflask/templates/wgcna_setup.html
index 821e4954..49181938 100644
--- a/wqflask/wqflask/templates/wgcna_setup.html
+++ b/wqflask/wqflask/templates/wgcna_setup.html
@@ -6,17 +6,22 @@
<div class="container">
<h1>WGCNA analysis parameters</h1>
- Phenotypes used as input: {{request.form}}
- <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
+ {% if request.form['trait_list'].split(",")|length <= 4 %}
+
+ <h2 style="color: #ff0000;">ERROR: Too few phenotypes as input</h2>
+ Please make sure you select enough phenotypes / genes to perform WGCNA,
+ your collection needs to contain at least 4 different phenotypes. You provided {{request.form['trait_list'].split(',')|length}} phenotypes as input
+ {% else %}
+ <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
<table>
- <tr><td>Soft threshold:</td><td><input type="text" class="form-inline" id="SoftThreshold", value="1,2,3,4,5,6,7,8,9"></td></tr>
- <tr><td>Power:</td><td><input type="text" class="form-inline" id="Power", value="6"></td></tr>
- <tr><td>Minimum module size:</td><td><input type="text" class="form-inline" id="MinModuleSize", value="30"></td></tr>
- <tr><td>TOMtype:</td><td><input type="text" class="form-inline" id="TOMtype", value="unsigned"></td></tr>
- <tr><td>mergeCutHeight:</td><td><input type="text" class="form-inline" id="mergeCutHeight", value="0.25"></td></tr>
+ <tr><td>Soft threshold:</td><td><input type="text" class="form-inline" name="SoftThresholds" id="SoftThresholds" value="1,2,3,4,5,6,7,8,9"></td></tr>
+ <tr><td>Minimum module size:</td><td><input type="text" class="form-inline" name="MinModuleSize" id="MinModuleSize" value="30"></td></tr>
+ <tr><td>TOMtype:</td><td><input type="text" class="form-inline" name="TOMtype" id="TOMtype" value="unsigned"></td></tr>
+ <tr><td>mergeCutHeight:</td><td><input type="text" class="form-inline" name="mergeCutHeight" id="mergeCutHeight" value="0.25"></td></tr>
</table>
<input type="submit" class="btn btn-primary" value="Run WGCNA using these settings" />
+ {% endif %}
</div>
</form>
{% endblock %}