diff options
| -rw-r--r-- | wqflask/wqflask/templates/ctl_setup.html | 131 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gn3_ctl_results.html | 133 |
2 files changed, 99 insertions, 165 deletions
diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html index b9fe1656..caaf6300 100644 --- a/wqflask/wqflask/templates/ctl_setup.html +++ b/wqflask/wqflask/templates/ctl_setup.html @@ -1,86 +1,69 @@ {% extends "base.html" %} {% block title %}CTL analysis{% endblock %} - -{% block content %} <!-- Start of body --> +{% block content %} +<!-- Start of body --> <div class="container"> - {% if request.form['trait_list'].split(",")|length < 2 %} - <div class="alert alert-danger" role="alert"> - <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span> - <span class="sr-only">Error:</span> - <h2>Too few traits as input</h2> - Please make sure you select enough traits to perform CTL. Your collection needs to contain at least 2 different traits. You provided {{request.form['trait_list'].split(',')|length}} traits as input. - </div> - {% else %} - <h1>CTL analysis</h1> - CTL analysis is published as open source software, if you are using this method in your publications, please cite:<br><br> - Arends D, Li Y, Brockmann GA, Jansen RC, Williams RW, Prins P<br> - Correlation trait locus (CTL) mapping: Phenotype network inference subject to genotype.<br> - The Journal of Open Source Software (2016)<br> - Published in <a href="http://joss.theoj.org/papers/10.21105/joss.00087"><img src="http://joss.theoj.org/papers/10.21105/joss.00087/status.svg"></a> - <br><br> - - <form class="col-md-8" action="/ctl_results" method="post" class="form-horizontal" id="ctl_form"> - - - <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}"> - - <div class="form-group row"> - <label for="Strategy" class="col-md-3 col-form-label col-form-label-sm">Strategy</label> - <div class="col-md-9"> - <select class="form-control col-md-9" name="strategy" id="strategy"> - <option value="Exact">Exact</option> - <option value="Full">Full</option> - <option value="Pairwise">Pairwise</option> - </select> - </div> + {% if request.form['trait_list'].split(",")|length < 2 %} <div class="alert alert-danger" role="alert"> + <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span> + <span class="sr-only">Error:</span> + <h2>Too few traits as input</h2> + Please make sure you select enough traits to perform CTL. Your collection needs to contain at least 2 different traits. You provided {{request.form['trait_list'].split(',')|length}} traits as input. +</div> +{% else %} +<h1>CTL analysis</h1> +CTL analysis is published as open source software, if you are using this method in your publications, please cite:<br><br> +Arends D, Li Y, Brockmann GA, Jansen RC, Williams RW, Prins P<br> +Correlation trait locus (CTL) mapping: Phenotype network inference subject to genotype.<br> +The Journal of Open Source Software (2016)<br> +Published in <a href="http://joss.theoj.org/papers/10.21105/joss.00087"><img src="http://joss.theoj.org/papers/10.21105/joss.00087/status.svg"></a> +<br><br> +<form class="col-md-8" action="/ctl_results" method="post" class="form-horizontal" id="ctl_form"> + <input type="hidden" name="trait_list" id="trait_list" value="{{request.form['trait_list']}}"> + <div class="form-group row"> + <label for="Strategy" class="col-md-3 col-form-label col-form-label-sm">Strategy</label> + <div class="col-md-9"> + <select class="form-control col-md-9" name="strategy" id="strategy"> + <option value="Exact">Exact</option> + <option value="Full">Full</option> + <option value="Pairwise">Pairwise</option> + </select> + </div> </div> - - - <div class="form-group row"> - <label for="corType" class="col-md-3 col-form-label col-form-label-sm">Types of correlation coefficients:</label> - <div class="col-md-9"> + <div class="form-group row"> + <label for="corType" class="col-md-3 col-form-label col-form-label-sm">Types of correlation coefficients:</label> + <div class="col-md-9"> <select class="form-control col-md-9" name="parametric" id="parametric"> - <option value="False">spearman</option> - <option value="True">pearson</option> - </select> - </div> - + <option value="False">spearman</option> + <option value="True">pearson</option> + </select> </div> - - - <div class="form-group row"> - <label for="Permutations" class="col-md-3 col-form-label col-form-label-sm">Number of permutation <span style="color:red;">(Used when strategy is Full or Pairwise)</span></label> - <div class="col-md-9"> - <select class="form-control" name="nperm" id="nperm"> - <option value="100">100</option> - <option value="1000" selected="selected">1000</option> - <option value="10000">10000</option> - </select> - </div> </div> - - <div class="form-group row"> - <label for="Significance" class="col-md-3 col-form-label col-form-label-sm"> Significance level</label> - <div class="col-md-9"> - <select class="form-control" name="significance" id="significance"> - <option value="0.1">0.1</option> - <option value="0.05" selected="selected">0.05</option> - <option value="0.001">0.001</option> - </select> - </div> - + <label for="Permutations" class="col-md-3 col-form-label col-form-label-sm">Number of permutation <span style="color:red;">(Used when strategy is Full or Pairwise)</span></label> + <div class="col-md-9"> + <select class="form-control" name="nperm" id="nperm"> + <option value="100">100</option> + <option value="1000" selected="selected">1000</option> + <option value="10000">10000</option> + </select> + </div> </div> - - <div class="form-group"> - <div class="text-center"> - <input type="submit" class="btn btn-primary" value="Run CTL using these settings" /> - </div> + <div class="form-group row"> + <label for="Significance" class="col-md-3 col-form-label col-form-label-sm"> Significance level</label> + <div class="col-md-9"> + <select class="form-control" name="significance" id="significance"> + <option value="0.1">0.1</option> + <option value="0.05" selected="selected">0.05</option> + <option value="0.001">0.001</option> + </select> + </div> + </div> + <div class="form-group"> + <div class="text-center"> + <input type="submit" class="btn btn-primary" value="Run CTL using these settings" /> </div> - - - - </form> + </div> +</form> {% endif %} </div> -{% endblock %} +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/gn3_ctl_results.html b/wqflask/wqflask/templates/gn3_ctl_results.html index 08944b0f..ca45fe76 100644 --- a/wqflask/wqflask/templates/gn3_ctl_results.html +++ b/wqflask/wqflask/templates/gn3_ctl_results.html @@ -1,119 +1,72 @@ {% extends "base.html" %} {% block title %}Ctl results{% endblock %} {% block content %} - <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous"> - <link REL="stylesheet" TYPE="text/css" href="{{ url_for('css', filename='bootstrap/css/bootstrap.css') }}" /> <link rel="stylesheet" href="https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css"> - <style type="text/css"> - - .carousel-control-next, -.carousel-control-prev /*, .carousel-indicators */ { +.carousel-control-prev + +/*, .carousel-indicators */ + { filter: invert(100%); } - - </style> <div style="margin-top:10px"> <div> - <div style="text-align: center;"> - <h3>CTL/QTL Plots for Individual Traits</h3> - <h4> {{ctl_plots|length}} phenotypes as input</h4> - + <h3>CTL/QTL Plots for Individual Traits</h3> + <h4> {{ctl_plots|length}} phenotypes as input</h4> + </div> + <div id="carouselExampleControls" class="carousel slide" data-interval="false"> + <div class="carousel-inner"> + {% for ctl_plot in ctl_plots %} + <div class="item{% if loop.index == 1 %} active{% endif %}"> + <img style="width:1000px;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ ctl_plot | safe }}" alt="First slide"> + </div> + {% endfor %} + <a class="carousel-control-prev" href="#carouselExampleControls" role="button" data-slide="prev"> + <span class="carousel-control-prev-icon" aria-hidden="true"></span> + <span class="sr-only">Previous</span> + </a> + <a class="carousel-control-next" href="#carouselExampleControls" role="button" data-slide="next"> + <span class="carousel-control-next-icon" aria-hidden="true"></span> + <span class="sr-only">Next</span> + </a> + </div> </div> - - - <div id="carouselExampleControls" class="carousel slide" data-interval="false"> - <div class="carousel-inner"> - - {% for ctl_plot in ctl_plots %} - - - <div class="item{% if loop.index == 1 %} active{% endif %}"> - <img style="width:1000px;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ ctl_plot | safe }}" alt="First slide"> - </div> - - {% endfor %} - - <a class="carousel-control-prev" href="#carouselExampleControls" role="button" data-slide="prev"> - <span class="carousel-control-prev-icon" aria-hidden="true"></span> - <span class="sr-only">Previous</span> - </a> - <a class="carousel-control-next" href="#carouselExampleControls" role="button" data-slide="next"> - <span class="carousel-control-next-icon" aria-hidden="true"></span> - <span class="sr-only">Next</span> - </a> - - </div> - -</div> - - </div> - - <div > - + <div> <div style="text-align:center;"> - <h2 >Ctl line plot</h2> - <h4>Plot the CTL for genome-wide CTL on all traits (the output of CTLscan).</h4> - + <h2>Ctl line plot</h2> + <h4>Plot the CTL for genome-wide CTL on all traits (the output of CTLscan).</h4> </div> - - <div class="row"> - <div class="col-8"> - - - <img style="width:100%;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ image_data | safe }}"> - - - </div> - - - - <div class= "col-4"> - - <ol style="height: 100%;display:flex;flex-direction: column;align-items: center;justify-content: center;"> - - {% for trait in phenotypes %} - - - {% set trait_data = trait.split(':') %} - - - <li><a href="/show_trait?trait_id={{trait_data[0]}}&dataset={{trait_data[1]}}">{{trait_data[0]}}</a></li> - - - {% endfor %} - </ol> - </div> - + <div class="row"> + <div class="col-8"> + <img style="width:100%;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ image_data | safe }}"> + </div> + <div class="col-4"> + <ol style="height: 100%;display:flex;flex-direction: column;align-items: center;justify-content: center;"> + {% for trait in phenotypes %} + {% set trait_data = trait.split(':') %} + <li><a href="/show_trait?trait_id={{trait_data[0]}}&dataset={{trait_data[1]}}">{{trait_data[0]}}</a></li> + {% endfor %} + </ol> + </div> </div> - </div> <h2 style="text-align:center">Significant CTL </h2> <table id="significance" width="80vw"></table> - <div style="text-align: center;margin-top: 20px;"> <h3 style="text-align:center;">Network figure</h3> - - <div style="margin-top: 20px;"> - -<p>Use tools like cytoscape to visualize the network</p> - -<a href="/ctl_network_files/{{network_file_name}}/sif" class="btn btn-secondary btn-lg mx-2">Download Sif file</a> - -<a href="/ctl_network_files/{{network_file_name}}/nodes" class="btn btn-secondary btn-lg mx-2">Download Node file</a> + <div style="margin-top: 20px;"> + <p>Use tools like cytoscape to visualize the network</p> + <a href="/ctl_network_files/{{network_file_name}}/sif" class="btn btn-secondary btn-lg mx-2">Download Sif file</a> + <a href="/ctl_network_files/{{network_file_name}}/nodes" class="btn btn-secondary btn-lg mx-2">Download Node file</a> </div> </div> - - - </div> - <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script> @@ -121,8 +74,6 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> <script type="text/javascript"> - - let { data_set_rows, col_names } = {{ significance_data | safe }} |