diff options
| -rw-r--r-- | wqflask/wqflask/templates/wgcna_results.html | 65 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/wgcna_setup.html | 19 |
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 %} |