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Diffstat (limited to 'gn2/wqflask/templates/partial_correlations')
5 files changed, 627 insertions, 0 deletions
diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_error.html b/gn2/wqflask/templates/partial_correlations/pcorrs_error.html new file mode 100644 index 00000000..8d6c4bbe --- /dev/null +++ b/gn2/wqflask/templates/partial_correlations/pcorrs_error.html @@ -0,0 +1,65 @@ +{% extends "base.html" %} +{% block title %}Error: {{message}}{% endblock %} +{% block content %} +<!-- Start of body --> + +<div class="container"> + <div class="col-md-8"> + <div class="form-group has-error"> + <div class="control-label" for="inputError1"> + + <img src="/static/gif/error/{{ error_image }}"> + + <h1>ERROR</h1> + + <p> + This error is not what we wanted to see. Unfortunately errors + are part of all software systems and we need to resolve this + together. + </p> + <p> + <b>It is important to report this ERROR so we can fix it for everyone</b>. + </p> + + <p> + Report to the GeneNetwork team by recording the steps you take + to reproduce this ERROR. Next to those steps, copy-paste below + stack trace, either as + a <a href="https://github.com/genenetwork/genenetwork2/issues/new">new + issue</a> or E-mail this full page to one of the developers + directly. + </p> + </div> + + <p> + GeneNetwork error:<br /> + {{message}} + </p> + + {%if command_id %} + <p> + Please provide the following information to help with + troubleshooting:<br /> + <strong>Command ID</strong>: <em>{{command_id}}</em> + </p> + {%endif%} + + <p> + To check if this already a known issue, search the + <a href="https://github.com/genenetwork/genenetwork2/issues">issue + tracker</a>. + </p> + + <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a> + <div id="Stack" class="collapse"> + <pre> + GeneNetwork {{ version }} {% for line in stack %} {{ line }} + {% endfor %} + </pre> + </div> + </div> + </div> +</div> + + +{% endblock %} diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_poll_results.html b/gn2/wqflask/templates/partial_correlations/pcorrs_poll_results.html new file mode 100644 index 00000000..38577c32 --- /dev/null +++ b/gn2/wqflask/templates/partial_correlations/pcorrs_poll_results.html @@ -0,0 +1,19 @@ +{%extends "base.html"%} + +{%block title%}Partial Correlations:{%endblock%} + +{%block css%} +<meta http-equiv="refresh" + content="5;URL=/partial_correlations/{{command_id}}"> +{%endblock%} + +{%block content%} + +<div class="container"> + <center> + <h1>Computing partial correlations...</h1> + <img src="/static/gif/waitAnima2.gif" + alt="Image indicating computation of partial correlations is ongoing" /> + </center> +</div> +{%endblock%} diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_results_presentation.html b/gn2/wqflask/templates/partial_correlations/pcorrs_results_presentation.html new file mode 100644 index 00000000..dac02397 --- /dev/null +++ b/gn2/wqflask/templates/partial_correlations/pcorrs_results_presentation.html @@ -0,0 +1,261 @@ +{%extends "base.html"%} + +{%block title%}Partial Correlations:{%endblock%} + +{%block css%} +<link rel="stylesheet" type="text/css" href="/static/new/css/partial_correlations.css" /> +<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> +{%endblock%} + +{%block content%} +<div class="container"> + <p> + <strong>Primary Trait</strong><br /><br /> + <a href="{{url_for( + 'show_trait_page', + trait_id=primary['trait_name'], + dataset=primary['dataset_name'])}}" + title="Link to trait data for trait {{primary['trait_name']}}"> + {{primary["dataset_type"]}}/{{primary["trait_name"]}} + [{{primary["symbol"] }} on Chr {{primary["chr"]}} @ {{primary["mb"]}}]: + {{primary["description"]}} + </a> --- FROM: {{primary["dataset_name"]}} + </p> + <p><strong>Control Traits</strong><br /><br /> + {%for trait in controls:%} + <a href="{{url_for( + 'show_trait_page', + trait_id=trait['trait_name'], + dataset=trait['dataset_name'])}}" + title="Link to trait data for trait {{trait['trait_name']}}"> + {{trait["dataset_type"]}}/{{trait["trait_name"]}} + [{{trait["symbol"] }} on Chr {{trait["chr"]}} @ {{trait["mb"]}}]: + {{trait["description"]}} + </a> --- FROM: {{trait["dataset_name"]}}<br /> + {%endfor%} + </p> + + <div id="partial-correlation-results"> + {%if dataset_type == "Publish":%} + <table id="part-corr-results-publish" + class="table-hover table-striped cell-border dataTable" + style="float: left;"> + <thead> + <tr> + <th> + </th> + <th>Index</th> + <th>Record</th> + <th>Phenotype</th> + <th>Authors</th> + <th>Year</th> + <th>N</th> + <th>Partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>p(partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th> + <th>{%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th> + <th>delta {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + </tr> + </thead> + + <tbody> + {%for idx, trait in enumerate(correlations, start=1):%} + <tr class="results-row"> + <td> + <input type="checkbox" name="chk_{{trait['trait_name']}}" + value="{{trait['trait_fullname']}}" /> + </td> + <td data-column-heading="Index">{{idx}}</td> + <td data-column-heading="Record"> + <a href="{{url_for( + 'show_trait_page', + trait_id=trait['trait_name'], + dataset=trait['dataset_name'])}}" + title="Link to trait data for trait {{trait['trait_name']}}"> + {{trait["trait_name"]}} + </a> + </td> + <td data-column-heading="Phenotype"> + {{trait["post_publication_description"]}}</td> + <td data-column-heading="Authors">{{trait["authors"]}}</td> + <td data-column-heading="Year">{{trait["year"]}}</td> + <td data-column-heading="N">{{trait["noverlap"]}}</td> + <td data-column-heading="Partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("partial_corr"))}} + </td> + <td data-column-heading="p(partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})"> + {{format_number(trait.get("partial_corr_p_value"))}} + </td> + <td data-column-heading="{%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("corr"))}} + </td> + <td data-column-heading="p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})"> + {{format_number(trait.get("corr_p_value"))}} + </td> + <td data-column-heading="delta {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("delta"))}} + </td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} + + {%if dataset_type == "Geno":%} + <table id="part-corr-results-geno" + class="table-hover table-striped cell-border dataTable" + style="float: left;"> + <thead> + <tr> + <th></th> + <th>Index</th> + <th>Locus</th> + <th>Chr</th> + <th>Megabase</th> + <th>N</th> + <th>Partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>p(partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th> + <th>{%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th> + <th>delta {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + </tr> + </thead> + + <tbody> + {%for idx, trait in enumerate(correlations, start=1):%} + <tr class="results-row"> + <td> + <input type="checkbox" name="chk_{{trait['trait_name']}}" + value="{{trait['trait_fullname']}}" /> + </td> + <td data-column-heading="Index">{{idx}}</td> + <td data-column-heading="Locus"> + <a href="{{url_for( + 'show_trait_page', + trait_id=trait['trait_name'], + dataset=trait['dataset_name'])}}" + title="Link to trait data for trait {{trait['trait_name']}}"> + {{trait["trait_name"]}} + </a> + </td> + <td data-column-heading="Chr">{{trait["chr"]}}</td> + <td data-column-heading="Megabase">{{trait["mb"]}}</td> + <td data-column-heading="N">{{trait["noverlap"]}}</td> + <td data-column-heading="Partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("partial_corr"))}} + </td> + <td data-column-heading="p(partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})"> + {{format_number(trait.get("partial_corr_p_value"))}} + </td> + <td data-column-heading="{%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("corr"))}} + </td> + <td data-column-heading="p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})"> + {{format_number(trait.get("corr_p_value"))}} + </td> + <td data-column-heading="delta {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("delta"))}} + </td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} + + {%if dataset_type == "ProbeSet":%} + <table id="part-corr-results-probeset" + class="table-hover table-striped cell-border dataTable" + style="float: left;"> + <thead> + <tr> + <th></th> + <th>Index</th> + <th>Record</th> + <th>Gene ID</th> + <th>Homologene ID</th> + <th>Symbol</th> + <th>Description</th> + <th>Chr</th> + <th>Megabase</th> + <th>Mean Expr</th> + <th>N</th> + <th>Sample Partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>Sample p(partial {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th> + <th>Sample {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>Sample p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th> + <th>delta {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>Lit Corr</th> + <th>Tissue {%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%}</th> + <th>Tissue p({%if "spearman" in (method | lower):%}rho{%else:%}r{%endif%})</th> + </tr> + </thead> + + <tbody> + {%for idx, trait in enumerate(correlations, start=1):%} + <tr class="results-row"> + <td> + <input type="checkbox" name="chk_{{trait['trait_name']}}" + value="{{trait['trait_fullname']}}" /> + </td> + <td data-column-heading="Index">{{idx}}</td> + <td data-column-heading="Record"> + <a href="{{url_for( + 'show_trait_page', + trait_id=trait['trait_name'], + dataset=trait['dataset_name'])}}" + title="Link to trait data for trait {{trait['trait_name']}}"> + {{trait["trait_name"]}} + </a> + </td> + <td data-column-heading="Gene ID">{{trait["geneid"]}}</td> + <td data-column-heading="Homologene ID">{{trait["homologeneid"]}}</td> + <td data-column-heading="Symbol">{{trait["symbol"]}}</td> + <td data-column-heading="Description">{{trait["description"]}}</td> + <td data-column-heading="Chr">{{trait["chr"]}}</td> + <td data-column-heading="Megabase">{{trait["mb"]}}</td> + <td data-column-heading="Mean Expr">{{trait["mean_expr"]}}</td> + <td data-column-heading="N">{{trait["noverlap"]}}</td> + <td data-column-heading="Sample Partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("partial_corr"))}} + </td> + <td data-column-heading="Sample p(partial {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})"> + {{format_number(trait.get("partial_corr_p_value"))}} + </td> + <td data-column-heading="Sample {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("corr"))}} + </td> + <td data-column-heading="Sample p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})"> + {{format_number(trait.get("corr_p_value"))}} + </td> + <td data-column-heading="delta {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("delta"))}} + </td> + <td data-column-heading="Lit Corr"> + {{format_number(trait.get("l_corr"))}} + </td> + <td data-column-heading="Tissue {%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%}"> + {{format_number(trait.get("tissue_corr"))}} + </td> + <td data-column-heading="Tissue p({%if 'spearman' in (method | lower):%}rho{%else:%}r{%endif%})"> + {{format_number(trait.get("tissue_p_value"))}} + </td> + </tr> + {%endfor%} + </tbody> + </table> + {%endif%} + + </div> +</div> +{%endblock%} + +{%block js%} +{%if step == "select-corr-method":%} +<script type="text/javascript" + src="/static/new/javascript/partial_correlations.js"></script> +<script language="javascript" type="text/javascript" + src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> +{%endif%} +{%endblock%} diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html b/gn2/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html new file mode 100644 index 00000000..c1ef6001 --- /dev/null +++ b/gn2/wqflask/templates/partial_correlations/pcorrs_results_with_target_traits.html @@ -0,0 +1,115 @@ +{%extends "base.html"%} + +{%block title%}Partial Correlations:{%endblock%} + +{%block css%} +<link rel="stylesheet" type="text/css" + href="{{url_for('css', filename='DataTables/css/jquery.dataTables.css')}}" /> +<link rel="stylesheet" type="text/css" + href="{{url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css')}}"> +<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" /> +<link rel="stylesheet" type="text/css" + href="/static/new/css/partial_correlations.css" /> +{%endblock%} + +{%block content%} +<div class="container"> + <p> + <strong>Primary Trait</strong><br /><br /> + <a href="{{url_for( + 'show_trait_page', + trait_id=primary['trait_name'], + dataset=primary['dataset_name'])}}" + title="Link to trait data for trait {{primary['trait_name']}}"> + {{primary["dataset_type"]}}/{{primary["trait_name"]}} + [{{primary["symbol"] }} on Chr {{primary["chr"]}} @ {{primary["mb"]}}]: + {{primary["description"]}} + </a> --- FROM: {{primary["dataset_name"]}} + </p> + <p><strong>Control Traits</strong><br /><br /> + {%for trait in controls:%} + <a href="{{url_for( + 'show_trait_page', + trait_id=trait['trait_name'], + dataset=trait['dataset_name'])}}" + title="Link to trait data for trait {{trait['trait_name']}}"> + {{trait["dataset_type"]}}/{{trait["trait_name"]}} + [{{trait["symbol"] }} on Chr {{trait["chr"]}} @ {{trait["mb"]}}]: + {{trait["description"]}} + </a> --- FROM: {{trait["dataset_name"]}}<br /> + {%endfor%} + </p> + + <table id="part-corr-results-publish" + class="table-hover table-striped cell-border dataTable"> + <thead> + <tr> + <th>_</th> + <th>Index</th> + <th>Database</th> + <th>Record</th> + <th>Symbol</th> + <th>Description</th> + <th>N</th> + {%if method == "spearmans":%} + <th>Partial rho</th> + <th>p(partial rho)</th> + <th>rho</th> + <th>p(rho)</th> + <th>delta rho</th> + {%else:%} + <th>Partial r</th> + <th>p(partial r)</th> + <th>r</th> + <th>p(r)</th> + <th>delta r</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for idx, trait in enumerate(pcorrs, start=1):%} + <tr> + <td> + <input type="checkbox" name="chk_{{trait['trait_name']}}" + value="{{trait['trait_fullname']}}"> + </td> + <td>{{idx}}</td> + <td>{{trait["dataset_name"]}}</td> + <td> + <a href="{{url_for( + 'show_trait_page', + trait_id=trait['trait_name'], + dataset=trait['dataset_name'])}}"> + {{trait["trait_name"]}} + </a> + </td> + <td>{{trait["symbol"]}}</td> + <td>{{trait["description"]}}</td> + <td>{{trait["noverlap"]}}</td> + <td>{{format_number(trait["partial_corr"])}}</td> + <td>{{format_number(trait["partial_corr_p_value"])}}</td> + <td>{{format_number(trait["corr"])}}</td> + <td>{{format_number(trait["corr_p_value"])}}</td> + <td>{{format_number(trait["delta"])}}</td> + </tr> + {%else:%} + <tr> + <td colspan="12"> + No correlations were computed + </td> + </tr> + {%endfor%} + </tbody> + </table> + +</div> +{%endblock%} + +{%block js%} +<!-- + <script type="text/javascript" + src="/static/new/javascript/partial_correlations.js"></script> +--> +{%endblock%} diff --git a/gn2/wqflask/templates/partial_correlations/pcorrs_select_operations.html b/gn2/wqflask/templates/partial_correlations/pcorrs_select_operations.html new file mode 100644 index 00000000..fe7f8cd4 --- /dev/null +++ b/gn2/wqflask/templates/partial_correlations/pcorrs_select_operations.html @@ -0,0 +1,167 @@ +{%extends "base.html"%} + +{%block title%}Partial Correlations:{%endblock%} + +{%block css%} +<link rel="stylesheet" type="text/css" + href="{{url_for('css', filename='DataTables/css/jquery.dataTables.css')}}" /> +<link rel="stylesheet" type="text/css" + href="{{url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css')}}"> +<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" /> +<link rel="stylesheet" type="text/css" + href="/static/new/css/partial_correlations.css" /> +{%endblock%} + +{%block content%} +<div class="container"> + <form id="pcorrs-form" + method="POST" + action="{{url_for('partial_correlations')}}"> + {%with messages = get_flashed_messages(with_categories=true)%} + {%if messages:%} + <ul class=flashes> + {%for category, message in messages:%} + <li class="{{category}}">{{message}}</li> + {%endfor%} + </ul> + {%endif%} + {%endwith%} + + <input type="hidden" value="{{trait_list_str}}" name="trait_list"> + <h1>Partial Correlation</h1> + <div>Please select one primary trait, one to three control traits, and at least one target trait.</div> + <br /> + <table id="pcorrs_traits_table" + class="table-hover table-striped cell-border dataTable" + role="grid"> + <thead> + <tr> + <th>Primary (X)</th> + <th>Controls (Z)</th> + <th>Targets (Y)</th> + <th>Ignored</th> + <th>Dataset</th> + <th>Trait ID</th> + <th>Symbol</th> + <th>Description</th> + <th>Location</th> + <th>Mean</th> + <th>Max LRS</th> + <th>Max LRS Location Chr and Mb</th> + </tr> + </thead> + + <tbody> + {%for trait in traits:%} + <tr> + <td> + <input type="radio" name="trait_{{trait['trait_name']}}" + id="trait_{{trait['trait_name']}}" + value="primary_{{trait['trait_name']}}" /> + </td> + <td> + <input type="radio" name="trait_{{trait['trait_name']}}" + id="trait_{{trait['trait_name']}}" + value="controls_{{trait['trait_name']}}" /> + </td> + <td> + <input type="radio" name="trait_{{trait['trait_name']}}" + id="trait_{{trait['trait_name']}}" + value="targets_{{trait['trait_name']}}" checked="checked" /> + </td> + <td> + <input type="radio" name="trait_{{trait['trait_name']}}" + id="trait_{{trait['trait_name']}}" + value="ignored_{{trait['trait_name']}}" /> + </td> + <td>{{trait.get("dataset", "_")}} + <td>{{trait.get("trait_name", "_")}}</td> + <td>{{trait.get("symbol", "_")}}</td> + <td>{{trait.get("description", "_")}}</td> + <td>{{trait.get("location", "_")}}</td> + <td>{{trait.get("mean", "_")}}</td> + <td>{{trait.get("lrs", "_")}}</td> + <td>{{trait.get("lrs_location", "_")}}</td> + </tr> + {%endfor%} + </tbody> + </table> + + <br /> + <p>Compute partial correlations for target selected above:</p> + <button type="submit" class="btn btn-primary" name="submit" + value="with_target_pearsons"> + Pearson's r + </button> + <button type="submit" class="btn btn-primary" name="submit" + value="with_target_spearmans"> + Spearman's rho + </button> + + <hr /> + + <p style="color: red; font-weight: bold;">OR</p> + <p>Compute partial correlation for each trait in the database below:</p> + + <div class="form-group"> + <label for="corr-method-input" class="form-label">Compute</label> + <select id="corr-method-input" required="required" name="method" + class="form-control"> + <option value="Pearson's r">Pearson's r</option> + <option value="Spearman's rho">Spearman's rho</option> + </select> + </div> + + <div class="form-group"> + <label for="target-db-input" class="form-label">Choose Database</label> + <select id="target-db-input" required="required" name="target_db" + class="form-control"> + {%if target_dbs:%} + {%for item in target_dbs:%} + {%if "description" in item.keys():%} + <option value="{{item['value']}}">{{item['description']}}</option> + {%else:%} + {%for group, opts in item.items()%} + {%if opts | length > 0:%} + <optgroup label="{{group}} ------"> + {%for item2 in opts:%} + <option value="{{item2['value']}}">{{item2['description']}}</option> + {%endfor%} + </optgroup> + {%endif%} + {%endfor%} + {%endif%} + {%endfor%} + {%endif%} + </select> + </div> + + <div class="form-group"> + <label for="criteria-input" class="form-label">Return</label> + <select id="criteria-input" required="required" name="criteria" size="1" + class="form-control"> + <option value="100">top 100</option> + <option value="200">top 200</option> + <option value="500" selected="selected">top 500</option> + <option value="1000">top 1000</option> + <option value="2000">top 2000</option> + <option value="5000">top 5000</option> + <option value="10000">top 10000</option> + <option value="15000">top 15000</option> + <option value="20000">top 20000</option> + </select> + </div> + + <button type="submit" class="btn btn-primary" name="submit" + value="Run Partial Correlations"> + Run Partial Correlations + </button> + </form> +</div> +{%endblock%} + +{%block js%} +<script type="text/javascript" + src="/static/new/javascript/partial_correlations.js"></script> +{%endblock%} |