path: root/gn2/wqflask/templates/show_trait_mapping_tools.html

<div class="main">
    {% if dataset.group.mapping_names|length > 0 %}
    <div class="options">
        <div class="tabbable"> <!-- Only required for left/right tabs -->

            <ul class="nav nav-pills">
                {% for mapping_method in dataset.group.mapping_names %}
                {% if mapping_method == "GEMMA" %}
                <li class="gemma-tab mapping-tab {% if dataset.group.mapping_id == '1' or dataset.group.mapping_id == '2' %}active{% endif %}">
                    <a href="#gemma" data-toggle="tab">GEMMA</a>
                </li>
                {% elif mapping_method == "R/qtl" %}
                <li class="rqtl-geno-tab mapping-tab {% if dataset.group.mapping_id == '3' %}active{% endif %}">
                    <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                </li>
                <li class="rqtl-pair-tab mapping-tab">
                    <a href="#rqtl_pair" data-toggle="tab">Pair Scan</a>
                </li>
                {% elif mapping_method == "QTLReaper" %}
                <li class="reaper-tab mapping-tab">
                    <a href="#interval_mapping" data-toggle="tab">Haley-Knott Regression</a>
                </li>
                {% endif %}
                {% endfor %}
            </ul>

            <div class="tab-content">
                {% for mapping_method in dataset.group.mapping_names %}
                {% if mapping_method == "GEMMA" %}
                <div class="tab-pane {% if dataset.group.mapping_id == '1' or dataset.group.mapping_id == '2' %}active{% endif %}" id="gemma">
                    <div class="form-horizontal section-form-div">
                        <div class="mapping_method_fields form-group">
                            <label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
                            <div class="col-xs-2 controls">
                                <select id="chr_gemma" class="form-control chr-select">
                                    {% for item in chr_list %}
                                    <option value="{{ item[1] }}">{{ item[0] }}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% if genofiles and genofiles|length>0 %}
                        <div class="mapping_method_fields form-group">
                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                            <div class="col-xs-6 controls">
                                <select id="genofile_gemma" class="form-control">
                                    {% for item in genofiles %}
                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% endif %}
                        <div class="mapping_method_fields form-group">
                            <label for="maf_gemma" class="col-xs-3 control-label">Minor Allele ≥</label>
                            <div class="col-xs-4 controls">
                                <input name="maf_gemma" value="{{ maf }}" type="text" class="form-control maf-select">
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label">Use LOCO</label>
                            <div class="col-xs-6 controls">
                                <label class="radio-inline">
                                    <input type="radio" name="use_loco" value="True" checked="">
                                    Yes
                                </label>
                                <label class="radio-inline">
                                    <input type="radio" name="use_loco" value="False">
                                    No
                               </label>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label>
                            <div class="col-xs-8 covar-options">
                              <div class="select-covar-div">
                                <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button>
                                <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
                                <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button>
                              </div>
                              <select size="2" name="selected_covariates_gemma" class="form-control selected-covariates" multiple>
                                  <option value="">No covariates selected</option>
                              </select>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                          <label class="col-xs-3 control-label"></label>
                          <div class="col-xs-6">
                            <button id="gemma_compute" type="button" class="btn submit_special btn-success" title="Compute Marker Regression" value="Compute" disabled>Loading...</button>
                          </div>
                        </div>
                    </div>
                </div>
                {% elif mapping_method == "QTLReaper" %}
                <div class="tab-pane" id="interval_mapping">
                    <div class="form-horizontal section-form-div">
                        <div class="mapping_method_fields form-group">
                            <label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
                            <div class="col-xs-2 controls">
                                    <select id="chr_reaper" class="form-control chr-select">
                                    {% for item in chr_list %}
                                    <option value="{{ item[1] }}">{{ item[0] }}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% if genofiles and genofiles|length>0 %}
                        <div class="mapping_method_fields form-group">
                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
                            <div class="col-xs-2 controls">
                                <select id="scale_reaper" class="form-control scale-select">
                                    {% for item in scales_in_geno[genofiles[0]['location']] %}
                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                            <div class="col-xs-6 controls">
                                <select id="genofile_reaper" class="form-control">
                                    {% for item in genofiles %}
                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% else %}
                        <div class="mapping_method_fields form-group">
                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
                            <div class="col-xs-2 controls">
                                <select id="scale_reaper" class="form-control scale-select">
                                    {% for item in scales_in_geno[dataset.group.name + ".geno"] %}
                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% endif %}
                        <div class="mapping_method_fields form-group">
                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                            <div class="col-xs-4 controls">
                                <input name="num_perm_reaper" value="1000" type="text" class="form-control">
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
                            <div class="col-xs-4 controls">
                                <input name="num_bootstrap" value="0" type="text" class="form-control">
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for<br>Cofactors</label>
                            <div class="col-xs-6 controls">
                                <input name="control_reaper" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
                                <br>
                                <label class="radio-inline">
                                  <input type="radio" name="do_control_reaper" value="true">
                                  Yes
                                </label>
                                <label class="radio-inline">
                                  <input type="radio" name="do_control_reaper" value="false" checked="">
                                  No
                                </label>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label">Interval Map</label>
                            <div class="col-xs-6 controls">
                                <label class="radio-inline">
                                    <input type="radio" name="manhattan_plot_reaper" value="false" checked="">
                                    Yes
                                </label>
                                <label class="radio-inline">
                                    <input type="radio" name="manhattan_plot_reaper" value="true">
                                    No
                               </label>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label"></label>
                            <div class="col-xs-6">
                              <button id="interval_mapping_compute" type="button" class="btn submit_special btn-success" title="Compute Interval Mapping" value="Compute" disabled>Loading...</button>
                            </div>
                        </div>
                    </div>
                </div>
                {% elif mapping_method == "R/qtl" %}
                <div class="tab-pane {% if dataset.group.mapping_id == '3' %}active{% endif %}" id="rqtl_geno">
                    <div class="form-horizontal section-form-div">
                        <div class="mapping_method_fields form-group">
                            <label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
                            <div class="col-xs-2 controls">
                                    <select id="chr_rqtl_geno" class="form-control chr-select">
                                    {% for item in chr_list %}
                                    <option value="{{ item[1] }}">{{ item[0] }}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% if genofiles and genofiles|length > 0 %}
                        <div class="mapping_method_fields form-group">
                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
                            <div class="col-xs-2 controls">
                                <select id="scale_rqtl_geno" class="form-control scale-select">
                                    {% for item in scales_in_geno[genofiles[0]['location']] %}
                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                            <div class="col-xs-6 controls">
                                <select id="genofile_rqtl_geno" class="form-control">
                                    {% for item in genofiles %}
                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% else %}
                        <div class="mapping_method_fields form-group">
                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
                            <div class="col-xs-2 controls">
                                <select id="scale_rqtl_geno" class="form-control scale-select">
                                    {% for item in scales_in_geno[dataset.group.name + ".geno"] %}
                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% endif %}
                        <div class="mapping_method_fields form-group">
                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                            <div class="col-xs-4 controls">
                                <input name="num_perm_rqtl_geno" value="0" type="text" class="form-control">
                            </div>
                        </div>
                        {% if sample_groups[0].attributes|length > 0 %}
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label">Stratified</label>
                            <div class="col-xs-6 controls">
                                <label class="radio-inline">
                                    <input type="radio" name="perm_strata" value="True" checked=""> 
                                    Yes
                                </label>
                                <label class="radio-inline">
                                    <input type="radio" name="perm_strata" value="False" >
                                    No
                               </label>
                            </div>
                        </div>
                        {% endif %}
                        <div class="mapping_method_fields form-group">
                            <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
                            <div class="col-xs-4 controls">
                              <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control">
                                <option value="normal">Normal</option>
                                {% if binary == "true" %}<option value="binary">Binary</option>{% endif %}
                                <!--<option value="2part">2-part</option>-->
                                <option value="np">Non-parametric</option>
                              </select>
                            </div>
                        </div>

                        <div class="mapping_method_fields form-group">
                            <label for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
                            <div class="col-xs-6 controls">
                              <select id="mapmethod_rqtl_geno" name="mapmethod_rqtl_geno" class="form-control">
                                <option value="hk" selected>Haley-Knott</option>
                                <option value="ehk">Extended Haley-Knott</option>
                                <option value="mr">Marker Regression</option>
                                <option value="em">Expectation-Maximization</option>
                                <option value="imp">Imputation</option>
                              </select>
                            </div>
                        </div>
                        <div id="missing_geno_div" class="mapping_method_fields form-group" style="display: none;">
                            <label for="missing_genotypes" class="col-xs-3 control-label"></label>
                            <div class="col-xs-6 controls">
                              <select id="missing_genotype" name="missing_genotypes" class="form-control">
                                <option value="mr">Remove Samples w/o Genotypes</option>
                                <option value="mr-imp">Single Imputation</option>
                                <option value="mr-argmax">Imputation w/ Viterbi Algorithm</option>
                              </select>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label">Manhattan<br>Plot</label>
                            <div class="col-xs-6 controls">
                                <label class="radio-inline">
                                    <input type="radio" name="manhattan_plot_rqtl" value="True">
                                    Yes
                                </label>
                                <label class="radio-inline">
                                    <input type="radio" name="manhattan_plot_rqtl" value="False" checked="">
                                    No
                               </label>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                          <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label>
                          <div class="col-xs-8 covar-options">
                            <div class="select-covar-div">
                              <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button>
                              <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
                              <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button>
                            </div>
                            <select size="2" name="selected_covariates_rqtl" class="form-control selected-covariates" multiple>
                                <option value="">No covariates selected</option>
                            </select>
                          </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label"></label>
                            <div class="col-xs-6 controls">
                              <button id="rqtl_geno_compute" type="button" class="btn submit_special btn-success" title="Compute Marker Regression" value="Compute" disabled>Loading...</button>
                            </div>
                        </div>
                    </div>
                </div>
                <div class="tab-pane" id="rqtl_pair">
                    <div class="form-horizontal section-form-div">
                        {% if genofiles and genofiles|length > 0 %}
                        <div class="mapping_method_fields form-group">
                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                            <div class="col-xs-6 controls">
                                <select id="genofile_rqtl_pair" class="form-control">
                                    {% for item in genofiles %}
                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                    {% endfor %}
                                </select>
                            </div>
                        </div>
                        {% endif %}
                        <div class="mapping_method_fields form-group">
                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
                            <div class="col-xs-6 controls">
                              <input name="control_rqtl_pair" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
                              <label class="radio-inline">
                                  <input type="radio" name="do_control_rqtl" value="true">
                                  Yes
                              </label>
                              <label class="radio-inline">
                                  <input type="radio" name="do_control_rqtl" value="false" checked="">
                                  No
                              </label>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label for="mapmodel_rqtl_pair" class="col-xs-3 control-label">Model</label>
                            <div class="col-xs-4 controls">
                              <select id="mapmodel_rqtl_pair" name="mapmodel_rqtl_pair" class="form-control">
                                <option value="normal">Normal</option>
                                {% if binary == "true" %}<option value="binary">Binary</option>{% endif %}
                                <!--<option value="2part">2-part</option>-->
                                <option value="np">Non-parametric</option>
                              </select>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label for="mapmethod_rqtl_pair" class="col-xs-3 control-label">Method</label>
                            <div class="col-xs-6 controls">
                              <select id="mapmethod_rqtl_pair" name="mapmethod_rqtl_pair" class="form-control">
                                <option value="hk" selected>Haley-Knott</option>
                                <option value="ehk">Extended Haley-Knott</option>
                                <option value="mr">Marker Regression</option>
                                <option value="em">Expectation-Maximization</option>
                                <option value="imp">Imputation</option>
                              </select>
                            </div>
                        </div>
                        <div id="missing_geno_pair_div" class="mapping_method_fields form-group" style="display: none;">
                            <label for="missing_genotypes_pair" class="col-xs-3 control-label"></label>
                            <div class="col-xs-6 controls">
                              <select id="missing_genotype_pair" name="missing_genotypes" class="form-control">
                                <option value="mr">Remove Samples w/o Genotypes</option>
                                <option value="mr-imp">Single Imputation</option>
                                <option value="mr-argmax">Imputation w/ Viterbi Algorithm</option>
                              </select>
                            </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                          <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label>
                          <div class="col-xs-8 covar-options">
                            <div class="select-covar-div">
                              <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
                              <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
                            </div>
                            <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
                          </div>
                        </div>
                        <div class="mapping_method_fields form-group">
                            <label class="col-xs-3 control-label"></label>
                            <div class="col-xs-6 controls">
                              <button id="rqtl_pair_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Pair Scan" value="Compute" disabled>Loading...</button>
                            </div>
                        </div>
                    </div>
                </div>
                {% endif %}
                {% endfor %}
            </div>
        </div>
    </div>
    <div class="descriptions">
        <div class="section-form-div">
            <dl>
                {% for mapping_method in dataset.group.mapping_names %}
                {% if mapping_method == "GEMMA" %}
                <dt>GEMMA</dt>
                <dd>GEMMA maps with correction for kinship using a linear mixed model and can include covariates such as sex and age. Defaults include a minor allele frequency of 0.05  and the leave-one-chromosome-out method (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>).</dd>
                {% elif mapping_method == "R/qtl" %}
                <dt class="map-method-text">R/qtl (version 1.44.9)</dt>
                <dd><a href="https://www.ncbi.nlm.nih.gov/pubmed/12724300">R/qtl</a> maps using several models and uniquely support 4-way intercrosses such as the "Aging Mouse Lifespan Studies" (NIA UM-HET3). We will add support for R/qtl2 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>) in 2023—a version that handles complex populations with admixture and many haplotypes.</dd>
                <dt class="map-method-text">Pair Scan (R/qtl v 1.44.9)</dt>
                <dd>The Pair Scan mapping tool performs a search for joint effects of two separate loci that may influence a trait. This search typically requires large sample sizes. Pair Scans can included covariates such as age and sex. For more on this function by K. Broman and colleagues see www.rdocumentation.org/packages/qtl/versions/1.60/topics/scantwo</dd>
                {% elif mapping_method == "QTLReaper" %}
                <dt class="map-method-text">Haley-Knott Regression</dt>
                <dd>HK regression (QTL Reaper) is a fast mapping method with permutation that works well with F2 intercrosses and backcrosses (<a href="https://www.ncbi.nlm.nih.gov/pubmed/16718932">PMID 16718932</a>), but is not recommended for admixed populations, advanced intercrosses, or strain families such as the BXDs (<a href="https://github.com/pjotrp/QTLReaper">QTL Reaper code</a>).</dd>
                {% endif %}
                {% endfor %}
            </dl>
            <div class="rqtl-description">
            More information on R/qtl mapping models and methods can be found <a href="http://www.rqtl.org/tutorials/rqtltour.pdf">here</a>.
            </div>
        </div>
    </div>
    <div id="mapping_result_holder_wrapper" style="display:none;">
        <div id="mapping_result_holder"></div>
    </div>
    {% else %}
    Mapping options are disabled for data not matched with genotypes.
    {% endif %}
</div>