diff options
Diffstat (limited to 'wqflask')
10 files changed, 270 insertions, 62 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 54cc9006..c220d2c9 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -58,6 +58,8 @@ class MarkerRegression(object): if self.mapping_method == "gemma": qtl_results = self.run_gemma() + elif self.mapping_method == "plink": + qtl_results = self.run_plink() elif self.mapping_method == "pylmm": #self.qtl_results = self.gen_data(tempdata) qtl_results = self.gen_data(str(temp_uuid)) @@ -151,6 +153,10 @@ class MarkerRegression(object): # # + def run_plink(self): + + os.chdir("/home/zas1024/plink") + #def gen_data(self, tempdata): def gen_data(self, temp_uuid): """Generates p-values for each marker""" diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index db8d4f1a..6f0ff44b 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -98,7 +98,10 @@ class ShowTrait(object): hddn['trait_id'] = self.trait_id hddn['dataset'] = self.dataset.name hddn['method'] = "pylmm" - + hddn['mapping_display_all'] = True + hddn['suggestive'] = 0 + hddn['maf'] = 0.01 + # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.hddn = hddn diff --git a/wqflask/wqflask/static/new/css/bar_chart.css b/wqflask/wqflask/static/new/css/bar_chart.css index c8e081f9..3e6e7bd6 100755 --- a/wqflask/wqflask/static/new/css/bar_chart.css +++ b/wqflask/wqflask/static/new/css/bar_chart.css @@ -9,7 +9,7 @@ fill: steelblue;
shape-rendering: crispEdges;
}
-
+/*
.x.axis path {
display: none;
-}
\ No newline at end of file +}*/
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee index 6c1e65e9..98f89ac6 100755 --- a/wqflask/wqflask/static/new/javascript/histogram.coffee +++ b/wqflask/wqflask/static/new/javascript/histogram.coffee @@ -41,13 +41,15 @@ class Histogram create_x_scale: () ->
console.log("min/max:", d3.min(@sample_vals) + "," + d3.max(@sample_vals))
- if (d3.min(@sample_vals) < 0)
- min_domain = d3.min(@sample_vals)
- else
- min_domain = 0
+ x0 = Math.max(-d3.min(@sample_vals), d3.max(@sample_vals))
+ #if (d3.min(@sample_vals) < 0)
+ # min_domain = d3.min(@sample_vals)
+ #else
+ # min_domain = 0
@x_scale = d3.scale.linear()
- .domain([min_domain, parseFloat(d3.max(@sample_vals))])
- .range([0, @plot_width])
+ .domain([d3.min(@sample_vals), d3.max(@sample_vals)])
+ .range([0, @plot_width])
+ .nice()
get_histogram_data: () ->
console.log("sample_vals:", @sample_vals)
@@ -62,6 +64,7 @@ class Histogram create_graph: () ->
@add_x_axis()
+ @add_y_axis()
@add_bars()
add_x_axis: () ->
@@ -74,11 +77,32 @@ class Histogram .attr("transform", "translate(0," + @plot_height + ")")
.call(x_axis)
+ #add_y_axis: () ->
+ # y_axis = d3.svg.axis()
+ # .scale(@y_scale)
+ # .orient("left")
+ # .ticks(5)
+ #
+ # @svg.append("g")
+ # .attr("class", "y axis")
+ # #.attr("transform", "translate(0," + @plot_width + ")")
+ # .call(y_axis)
+
+
add_y_axis: () ->
- y_axis = d3.svg.axis()
+ yAxis = d3.svg.axis()
.scale(@y_scale)
.orient("left")
.ticks(5)
+
+ @svg.append("g")
+ .attr("class", "y axis")
+ .call(yAxis)
+ .append("text")
+ .attr("transform", "rotate(-90)")
+ .attr("y", 6)
+ .attr("dy", ".71em")
+ .style("text-anchor", "end")
add_bars: () ->
console.log("bar_width:", @x_scale(@histogram_data[0].dx))
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js index 1603cb77..d8067ced 100755 --- a/wqflask/wqflask/static/new/javascript/histogram.js +++ b/wqflask/wqflask/static/new/javascript/histogram.js @@ -55,14 +55,10 @@ }; Histogram.prototype.create_x_scale = function() { - var min_domain; + var x0; console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals)); - if (d3.min(this.sample_vals) < 0) { - min_domain = d3.min(this.sample_vals); - } else { - min_domain = 0; - } - return this.x_scale = d3.scale.linear().domain([min_domain, parseFloat(d3.max(this.sample_vals))]).range([0, this.plot_width]); + x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals)); + return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice(); }; Histogram.prototype.get_histogram_data = function() { @@ -82,6 +78,7 @@ Histogram.prototype.create_graph = function() { this.add_x_axis(); + this.add_y_axis(); return this.add_bars(); }; @@ -92,8 +89,9 @@ }; Histogram.prototype.add_y_axis = function() { - var y_axis; - return y_axis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + var yAxis; + yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end"); }; Histogram.prototype.add_bars = function() { diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 84e465e8..a410baf3 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -204,6 +204,7 @@ $ -> name = $.trim(name) real_value = $(row).find('.edit_sample_value').val() console.log("real_value:", real_value) + checkbox = $(row).find(".edit_sample_checkbox") checked = $(checkbox).attr('checked') diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee index f1024cd1..1d375686 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -56,6 +56,9 @@ $ -> console.log("In interval mapping") $("#progress_bar_container").modal() url = "/interval_mapping" + $('input[name=method]').val("reaper") + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')) + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')) form_data = $('#trait_data_form').serialize() console.log("form_data is:", form_data) $.ajax( @@ -116,9 +119,41 @@ $ -> return false ) + $("#plink_compute").click(() => + url = "/marker_regression" + $('input[name=method]').val("plink") + $('input[name=mapping_display_all]').val($('input[name=display_all_plink]')) + $('input[name=suggestive]').val($('input[name=suggestive_plink]')) + $('input[name=maf]').val($('input[name=maf_plink]')) + form_data = $('#trait_data_form').serialize() + console.log("form_data is:", form_data) + $.ajax( + type: "POST" + url: url + data: form_data + error: (xhr, ajaxOptions, thrownError) => + alert("Sorry, an error occurred") + console.log(xhr) + clearInterval(this.my_timer) + $('#progress_bar_container').modal('hide') + $("body").html("We got an error.") + success: (data) => + clearInterval(this.my_timer) + $('#progress_bar_container').modal('hide') + $("body").html(data) + ) + console.log("settingInterval") + + this.my_timer = setInterval(get_progress, 1000) + return false + ) + $("#gemma_compute").click(() => url = "/marker_regression" $('input[name=method]').val("gemma") + $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]')) + $('input[name=suggestive]').val($('input[name=suggestive_gemma]')) + $('input[name=maf]').val($('input[name=maf_gemma]')) form_data = $('#trait_data_form').serialize() console.log("form_data is:", form_data) $.ajax( diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index a5a49ace..dbc26e3b 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -67,6 +67,9 @@ console.log("In interval mapping"); $("#progress_bar_container").modal(); url = "/interval_mapping"; + $('input[name=method]').val("reaper"); + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); form_data = $('#trait_data_form').serialize(); console.log("form_data is:", form_data); $.ajax({ @@ -127,10 +130,43 @@ _this.my_timer = setInterval(get_progress, 1000); return false; }); + $("#plink_compute").click(function() { + var form_data, url; + url = "/marker_regression"; + $('input[name=method]').val("plink"); + $('input[name=mapping_display_all]').val($('input[name=display_all_plink]')); + $('input[name=suggestive]').val($('input[name=suggestive_plink]')); + $('input[name=maf]').val($('input[name=maf_plink]')); + form_data = $('#trait_data_form').serialize(); + console.log("form_data is:", form_data); + $.ajax({ + type: "POST", + url: url, + data: form_data, + error: function(xhr, ajaxOptions, thrownError) { + alert("Sorry, an error occurred"); + console.log(xhr); + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + return $("body").html("We got an error."); + }, + success: function(data) { + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + return $("body").html(data); + } + }); + console.log("settingInterval"); + _this.my_timer = setInterval(get_progress, 1000); + return false; + }); $("#gemma_compute").click(function() { var form_data, url; url = "/marker_regression"; $('input[name=method]').val("gemma"); + $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]')); + $('input[name=suggestive]').val($('input[name=suggestive_gemma]')); + $('input[name=maf]').val($('input[name=maf_gemma]')); form_data = $('#trait_data_form').serialize(); console.log("form_data is:", form_data); $.ajax({ diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index e15d043b..ff05e859 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -69,38 +69,98 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> + <script type="text/javascript" charset="utf-8"> + + function getValue(x) { + if (x.indexOf('input') >= 0) { + if ($(x).val() == 'x') { + return 0 + } + else { + return parseFloat($(x).val()); + } + } + return parseFloat(x); + } + + jQuery.fn.dataTableExt.oSort['cust-txt-asc'] = function (a, b) { + var x = getValue(a); + var y = getValue(b); + return ((x < y) ? -1 : ((x > y) ? 1 : 0)); + }; + + jQuery.fn.dataTableExt.oSort['cust-txt-desc'] = function (a, b) { + var x = getValue(a); + var y = getValue(b); + return ((x < y) ? 1 : ((x > y) ? -1 : 0)); + }; + + $(document).ready( function () { + console.time("Creating table"); + + {% if sample_groups[0].se_exists() %} + $('#samples_primary, #samples_other').dataTable( { + //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>", + "aoColumns": [ + { "sType": "natural" }, + null, + { "sType": "cust-txt" }, + { "bSortable": false }, + { "sType": "cust-txt" } + ], + "sDom": "ftr", + "oTableTools": { + "aButtons": [ + "copy", + "print", + { + "sExtends": "collection", + "sButtonText": 'Save <span class="caret" />', + "aButtons": [ "csv", "xls", "pdf" ] + } + ], + "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf" + }, + "bPaginate": false, + "bLengthChange": true, + "bDeferRender": true, + "bSortClasses": false + } ); + console.timeEnd("Creating table"); + + {% else %} + + + console.time("Creating table"); + + $('#samples_primary, #samples_other').dataTable( { + //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>", + "aoColumns": [ + { "sType": "natural" }, + null, + { "sType": "cust-txt" } + ], + "sDom": "ftr", + "oTableTools": { + "aButtons": [ + "copy", + "print", + { + "sExtends": "collection", + "sButtonText": 'Save <span class="caret" />', + "aButtons": [ "csv", "xls", "pdf" ] + } + ], + "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf" + }, + "bPaginate": false, + "bLengthChange": true, + "bDeferRender": true, + "bSortClasses": false + } ); + console.timeEnd("Creating table"); + {% endif %} + }); + </script> - <script type="text/javascript" charset="utf-8"> - $(document).ready( function () { - console.time("Creating table"); - $('#samples_primary, #samples_other').dataTable( { - //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>", - "aoColumns": [ - { "sType": "natural" }, - null, - null, - { "bSortable": false }, - null - ], - "sDom": "ftr", - "oTableTools": { - "aButtons": [ - "copy", - "print", - { - "sExtends": "collection", - "sButtonText": 'Save <span class="caret" />', - "aButtons": [ "csv", "xls", "pdf" ] - } - ], - "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf" - }, - "bPaginate": false, - "bLengthChange": true, - "bDeferRender": true, - "bSortClasses": false - } ); - console.timeEnd("Creating table"); - }); - </script> {% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index cc995f2f..f380988e 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -10,6 +10,9 @@ <a href="#marker_regression" data-toggle="tab">Marker Regression</a> </li> <li> + <a href="#plink" data-toggle="tab">PLINK</a> + </li> + <li> <a href="#gemma" data-toggle="tab">GEMMA</a> </li> <!--<li> @@ -114,20 +117,20 @@ <label class="control-label">Display all</label> <div class="controls"> <label class="radio inline"> - <input type="radio" name="display_all" value="True" checked> + <input type="radio" name="display_all_reaper" value="True" checked> Yes </label> <label class="radio inline"> - <input type="radio" name="display_all" value="False"> + <input type="radio" name="display_all_reaper" value="False"> No </label> </div> </div> <div class="control-group" id="suggestive" > - <label for="suggestive" class="control-label" + <label for="suggestive_reaper" class="control-label" title="Control Locus">LOD score greater than: </label> <div class="controls"> - <input name="suggestive" type="text" value="0"/> + <input name="suggestive_reaper" type="text" value="0"/> </div> </div> @@ -151,32 +154,74 @@ </div> + <div class="tab-pane" id="plink"> + <div class="control-group" id="display_all_div"> + <label class="control-label">Display all</label> + <div class="controls"> + <label class="radio inline"> + <input type="radio" name="display_all_plink" value="True" checked> + Yes + </label> + <label class="radio inline"> + <input type="radio" name="display_all_plink" value="False"> + No + </label> + </div> + </div> + <div class="control-group" id="suggestive" > + <label for="suggestive_plink" class="control-label" + title="Control Locus">LOD score greater than: </label> + <div class="controls"> + <input name="suggestive_plink" type="text" value="0"/> + </div> + </div> + <div class="control-group" id="suggestive" > + <label for="maf_plink" class="control-label" + title="Control Locus">Minor allele threshold: </label> + <div class="controls"> + <input name="maf_plink" type="text" value="0.01"/> + </div> + </div> + + <div class="control-group"> + <div class="controls"> + <button id="plink_compute" + class="btn btn-inverse submit_special" + data-url="/marker_regression" + title="Compute using PLINK"> + <i class="icon-ok-circle icon-white"></i> Compute + </button> + </div> + </div> + + </div> + <div class="tab-pane" id="gemma"> <div class="control-group" id="display_all_div"> <label class="control-label">Display all</label> <div class="controls"> <label class="radio inline"> - <input type="radio" name="display_all" value="True" checked> + <input type="radio" name="display_all_gemma" value="True" checked> Yes </label> <label class="radio inline"> - <input type="radio" name="display_all" value="False"> + <input type="radio" name="display_all_gemma" value="False"> No </label> </div> </div> <div class="control-group" id="suggestive" > - <label for="suggestive" class="control-label" + <label for="suggestive_gemma" class="control-label" title="Control Locus">LOD score greater than: </label> <div class="controls"> - <input name="suggestive" type="text" value="0"/> + <input name="suggestive_gemma" type="text" value="0"/> </div> </div> <div class="control-group" id="suggestive" > - <label for="maf" class="control-label" + <label for="maf_gemma" class="control-label" title="Control Locus">Minor allele threshold: </label> <div class="controls"> - <input name="maf" type="text" value="0.01"/> + <input name="maf_gemma" type="text" value="0.01"/> </div> </div> |