diff options
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/init_genome_browser.js | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_mapping_tools.html | 26 |
3 files changed, 18 insertions, 16 deletions
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js index a544f3cb..6a19fe08 100644 --- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js +++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js @@ -17,7 +17,7 @@ var legendWidth = 140.0; if ('significant' in js_data) { var significant_score = parseFloat(js_data.significant) } else { - var significant_score = 4 + var significant_score = js_data.max_score * 0.75 } var score = { min: 0.0, max: js_data.max_score, sig: significant_score }; var gwasPadding = { top: 35.0, diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index bdf51bf8..3b008d83 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -150,14 +150,14 @@ <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li> - <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li> + <li><b>LRS=(15 1000)</b> finds all traits with peak LRS scores between lower and upper limits.</li> <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li> - <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits, + <li><b>cisLRS=(15 1000 5)</b> finds all cis eQTLs with peak LRS scores between lower and upper limits, with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li> - <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits, + <li><b>transLRS=(15 1000 5)</b> finds all trans eQTLs with peak LRS scores between lower and upper limits, with an <b>exclusion</b> zone of 5 Mb around the parent gene.</li> <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 369bbe43..04480e69 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,6 +1,6 @@ <div> {% if dataset.group.mapping_names|length > 0 %} - <div class="col-xs-5"> + <div class="col-xs-4" style="min-width: 560px;"> <div class="tabbable"> <!-- Only required for left/right tabs --> <ul class="nav nav-pills"> @@ -9,7 +9,7 @@ <a href="#gemma" data-toggle="tab">GEMMA</a> </li> <li class="mapping_tab"> - <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> + <a href="#interval_mapping" data-toggle="tab">Haley-Knott Regression</a> </li> <li class="mapping_tab rqtl"> <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> @@ -162,10 +162,12 @@ <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control for</label> <div style="margin-left:20px;" class="col-xs-6 controls"> {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" /> + <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px; display: inline-block;" class="form-control" /> {% else %} - <input name="control_reaper" value="" type="text" class="form-control" /> + <input name="control_reaper" value="" type="text" style="display: inline-block; padding-right: 10px;" class="form-control" /> {% endif %} + <input type="radio" name="do_control_reaper" value="true"> Yes <input type="radio" name="do_control_reaper" value="false" checked=""> No</span> + <!-- <label class="radio-inline"> <input type="radio" name="do_control_reaper" value="true"> Yes @@ -174,6 +176,7 @@ <input type="radio" name="do_control_reaper" value="false" checked=""> No </label> + --> </div> </div> @@ -202,14 +205,14 @@ </div> --> <div class="mapping_method_fields form-group"> - <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label> + <label style="text-align: right;" class="col-xs-3 control-label">Interval<br>Mapping</label> <div style="margin-left:20px;" class="col-xs-6 controls"> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_reaper" value="True"> + <input type="radio" name="manhattan_plot_reaper" value="False"> Yes </label> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_reaper" value="False" checked=""> + <input type="radio" name="manhattan_plot_reaper" value="True" checked=""> No </label> </div> @@ -351,15 +354,14 @@ </div> </div> </div> - <div class="col-xs-5"> + <div class="col-xs-6"> <dl> <dt>GEMMA</dt> <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd> {% if dataset.group.mapping_id == "1" %} - <dt style="margin-top: 20px;">Interval Mapping</dt> - <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.<br><br> - The default option is a version of qtlrearper rewritten in RUST that should fix some of the issues the original had. You can still use the original with the Version option.<br> - <i>Please let us know if you encounter any issues while using the new version.</i></dd> + <dt style="margin-top: 20px;">Haley-Knott Regression</dt> + <dd>This method is implementing using the tool QTLReaper. Interval mapping (the last option) is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.<br><br> + The default option is a version of QTLReaper rewritten in RUST that should fix some of the issues the original had. You can still use the original with the Version option.</dd> <dt style="margin-top: 20px;">R/qtl</dt> <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd> {% endif %} |