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-rwxr-xr-xwqflask/wqflask/correlation_matrix/.show_corr_matrix.py.swnbin16384 -> 0 bytes
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py7
-rwxr-xr-xwqflask/wqflask/show_trait/SampleList.py11
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py1
-rw-r--r--wqflask/wqflask/static/new/css/panelutil.css4
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css3
-rw-r--r--wqflask/wqflask/static/new/javascript/create_interval_map.coffee26
-rw-r--r--wqflask/wqflask/static/new/javascript/create_interval_map.js14
-rw-r--r--wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee21
-rw-r--r--wqflask/wqflask/static/new/javascript/create_manhattan_plot.js14
-rwxr-xr-xwqflask/wqflask/static/new/javascript/dataset_select_menu.js137
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_probability_plot.coffee37
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.coffee12
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.js12
-rw-r--r--wqflask/wqflask/static/new/javascript/manhattan_plot.coffee97
-rw-r--r--wqflask/wqflask/static/new/javascript/manhattan_plot.js10
-rw-r--r--wqflask/wqflask/static/new/javascript/probability_plot.coffee424
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.coffee4
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.js4
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee194
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js127
-rwxr-xr-xwqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css2
-rwxr-xr-xwqflask/wqflask/templates/corr_scatter_plot_old.html63
-rwxr-xr-xwqflask/wqflask/templates/interval_mapping.html7
-rwxr-xr-xwqflask/wqflask/templates/marker_regression.html7
-rw-r--r--wqflask/wqflask/templates/marker_regression_old.html106
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html3
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html1
-rwxr-xr-xwqflask/wqflask/views.py12
29 files changed, 900 insertions, 460 deletions
diff --git a/wqflask/wqflask/correlation_matrix/.show_corr_matrix.py.swn b/wqflask/wqflask/correlation_matrix/.show_corr_matrix.py.swn
deleted file mode 100755
index fd928439..00000000
--- a/wqflask/wqflask/correlation_matrix/.show_corr_matrix.py.swn
+++ /dev/null
Binary files differ
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 30c6453c..0bee5994 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -65,6 +65,8 @@ class MarkerRegression(object):
self.dataset.group.get_markers()
if self.mapping_method == "gemma":
qtl_results = self.run_gemma()
+ elif self.mapping_method == "rqtl":
+ qtl_results = self.run_rqtl()
elif self.mapping_method == "plink":
qtl_results = self.run_plink()
#print("qtl_results:", pf(qtl_results))
@@ -184,6 +186,11 @@ class MarkerRegression(object):
#
#
+ #def run_rqtl(self):
+ # os.chdir("/home/zas1024/plink")
+ #
+
+
def run_plink(self):
os.chdir("/home/zas1024/plink")
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 9cd7d895..6be6ddcd 100755
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -6,6 +6,8 @@ from base import webqtlCaseData
from utility import webqtlUtil, Plot, Bunch
from base.trait import GeneralTrait
+import numpy as np
+from scipy import stats
from pprint import pformat as pf
class SampleList(object):
@@ -71,6 +73,15 @@ class SampleList(object):
def __repr__(self):
return "<SampleList> --> %s" % (pf(self.__dict__))
+ def get_z_scores(self):
+ values = [sample.value for sample in self.sample_list if sample.value != None]
+ numpy_array = np.array(values)
+ z_scores = stats.zscore(numpy_array)
+
+ for i, sample in enumerate(self.sample_list):
+ if sample.value:
+ sample.z_score = z_scores[i]
+
def do_outliers(self):
values = [sample.value for sample in self.sample_list if sample.value != None]
upper_bound, lower_bound = Plot.find_outliers(values)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 670a1188..a7dd59d5 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -97,6 +97,7 @@ class ShowTrait(object):
hddn['trait_id'] = self.trait_id
hddn['dataset'] = self.dataset.name
+ hddn['use_outliers'] = False
hddn['method'] = "pylmm"
hddn['mapping_display_all'] = True
hddn['suggestive'] = 0
diff --git a/wqflask/wqflask/static/new/css/panelutil.css b/wqflask/wqflask/static/new/css/panelutil.css
index 35e40db7..ff363e49 100644
--- a/wqflask/wqflask/static/new/css/panelutil.css
+++ b/wqflask/wqflask/static/new/css/panelutil.css
@@ -30,7 +30,7 @@ div.qtlcharts .x.axis text.title {
fill: slateblue;
}
-div.qtlcharts line.axis.grid {
+/*div.qtlcharts line.axis.grid {
fill: none;
stroke-width: 1;
pointer-events: none;
@@ -48,7 +48,7 @@ div.qtlcharts line.y.axis.grid {
div.qtlcharts .extent {
fill: #cac;
opacity: 0.3;
-}
+}*/
div.qtlcharts circle.selected {
fill: hotpink;
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
new file mode 100644
index 00000000..9dcbfce9
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -0,0 +1,3 @@
+tr .outlier {
+ background-color: #ffff99;
+} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
index cacba03e..2b4b20c8 100644
--- a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
@@ -1,4 +1,4 @@
-create_interval_map = ->
+create_interval_map = () ->
h = 500
w = 1200
margin = {left:60, top:40, right:40, bottom: 40, inner:5}
@@ -39,6 +39,7 @@ create_interval_map = ->
create_interval_map()
$("#export").click =>
+
#Get d3 SVG element
svg = $("#topchart").find("svg")[0]
@@ -54,6 +55,29 @@ $("#export").click =>
form.find("#data").val(svg_xml)
form.find("#filename").val(filename)
form.submit()
+
+
+$("#export_pdf").click =>
+
+ #$('#topchart').remove()
+ #$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')
+ #create_interval_map()
+
+ #Get d3 SVG element
+ svg = $("#topchart").find("svg")[0]
+
+ #Extract SVG text string
+ svg_xml = (new XMLSerializer).serializeToString(svg)
+ console.log("svg_xml:", svg_xml)
+
+ #Set filename
+ filename = "interval_map_pdf"
+
+ #Make a form with the SVG data
+ form = $("#exportpdfform")
+ form.find("#data").val(svg_xml)
+ form.find("#filename").val(filename)
+ form.submit()
# two LOD charts within one SVG
#d3.json "data.json", (data) ->
diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.js b/wqflask/wqflask/static/new/javascript/create_interval_map.js
index 5041cfea..341e92c0 100644
--- a/wqflask/wqflask/static/new/javascript/create_interval_map.js
+++ b/wqflask/wqflask/static/new/javascript/create_interval_map.js
@@ -51,3 +51,17 @@ $("#export").click((function(_this) {
return form.submit();
};
})(this));
+
+$("#export_pdf").click((function(_this) {
+ return function() {
+ var filename, form, svg, svg_xml;
+ svg = $("#topchart").find("svg")[0];
+ svg_xml = (new XMLSerializer).serializeToString(svg);
+ console.log("svg_xml:", svg_xml);
+ filename = "interval_map_pdf";
+ form = $("#exportpdfform");
+ form.find("#data").val(svg_xml);
+ form.find("#filename").val(filename);
+ return form.submit();
+ };
+})(this));
diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
index 258d5c01..05ad5419 100644
--- a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
@@ -55,3 +55,24 @@ $("#export").click =>
form.find("#filename").val(filename)
form.submit()
+$("#export_pdf").click =>
+
+ #$('#topchart').remove()
+ #$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')
+ #create_interval_map()
+
+ #Get d3 SVG element
+ svg = $("#topchart").find("svg")[0]
+
+ #Extract SVG text string
+ svg_xml = (new XMLSerializer).serializeToString(svg)
+ console.log("svg_xml:", svg_xml)
+
+ #Set filename
+ filename = "manhattan_plot_" + js_data.this_trait
+
+ #Make a form with the SVG data
+ form = $("#exportpdfform")
+ form.find("#data").val(svg_xml)
+ form.find("#filename").val(filename)
+ form.submit()
diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
index 7daaa921..62584fb2 100644
--- a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
@@ -51,3 +51,17 @@ $("#export").click((function(_this) {
return form.submit();
};
})(this));
+
+$("#export_pdf").click((function(_this) {
+ return function() {
+ var filename, form, svg, svg_xml;
+ svg = $("#topchart").find("svg")[0];
+ svg_xml = (new XMLSerializer).serializeToString(svg);
+ console.log("svg_xml:", svg_xml);
+ filename = "manhattan_plot_" + js_data.this_trait;
+ form = $("#exportpdfform");
+ form.find("#data").val(svg_xml);
+ form.find("#filename").val(filename);
+ return form.submit();
+ };
+})(this));
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
deleted file mode 100755
index f4ca2c37..00000000
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ /dev/null
@@ -1,137 +0,0 @@
-// Generated by CoffeeScript 1.7.1
-$(function() {
- var apply_default, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown;
- process_json = function(data) {
- window.jdata = data;
- populate_species();
- return apply_default();
- };
- $.ajax('/static/new/javascript/dataset_menu_structure.json', {
- dataType: 'json',
- success: process_json
- });
- populate_species = function() {
- var species_list;
- species_list = this.jdata.species;
- redo_dropdown($('#species'), species_list);
- return populate_group();
- };
- window.populate_species = populate_species;
- populate_group = function() {
- var group_list, species;
- console.log("in populate group");
- species = $('#species').val();
- group_list = this.jdata.groups[species];
- redo_dropdown($('#group'), group_list);
- return populate_type();
- };
- window.populate_group = populate_group;
- populate_type = function() {
- var group, species, type_list;
- species = $('#species').val();
- group = $('#group').val();
- type_list = this.jdata.types[species][group];
- redo_dropdown($('#type'), type_list);
- return populate_dataset();
- };
- window.populate_type = populate_type;
- populate_dataset = function() {
- var dataset_list, group, species, type;
- species = $('#species').val();
- group = $('#group').val();
- type = $('#type').val();
- console.log("sgt:", species, group, type);
- dataset_list = this.jdata.datasets[species][group][type];
- console.log("pop_dataset:", dataset_list);
- return redo_dropdown($('#dataset'), dataset_list);
- };
- window.populate_dataset = populate_dataset;
- redo_dropdown = function(dropdown, items) {
- var item, _i, _len, _results;
- console.log("in redo:", dropdown, items);
- dropdown.empty();
- _results = [];
- for (_i = 0, _len = items.length; _i < _len; _i++) {
- item = items[_i];
- _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
- }
- return _results;
- };
- $('#species').change((function(_this) {
- return function() {
- return populate_group();
- };
- })(this));
- $('#group').change((function(_this) {
- return function() {
- return populate_type();
- };
- })(this));
- $('#type').change((function(_this) {
- return function() {
- return populate_dataset();
- };
- })(this));
- open_window = function(url, name) {
- var options;
- options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900";
- return open(url, name, options).focus();
- };
- group_info = function() {
- var group, species, url;
- species = $('#species').val();
- group = $('#group').val();
- url = "/" + species + "Cross.html#" + group;
- return open_window(url, "Group Info");
- };
- $('#group_info').click(group_info);
- dataset_info = function() {
- var dataset, url;
- dataset = $('#dataset').val();
- url = "/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset;
- return open_window(url, "Dataset Info");
- };
- $('#dataset_info').click(dataset_info);
- make_default = function() {
- var holder, item, jholder, _i, _len, _ref;
- holder = {};
- _ref = ['species', 'group', 'type', 'dataset'];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- item = _ref[_i];
- holder[item] = $("#" + item).val();
- }
- jholder = JSON.stringify(holder);
- return $.cookie('search_defaults', jholder, {
- expires: 365
- });
- };
- apply_default = function() {
- var defaults, item, populate_function, _i, _len, _ref, _results;
- defaults = $.cookie('search_defaults');
- if (defaults) {
- defaults = $.parseJSON(defaults);
- } else {
- defaults = {
- species: "mouse",
- group: "BXD",
- type: "Hippocampus mRNA",
- dataset: "HC_M2_0606_P"
- };
- }
- _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]];
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- item = _ref[_i];
- $("#" + item[0]).val(defaults[item[0]]);
- if (item[1]) {
- populate_function = "populate_" + item[1];
- console.log("Calling:", populate_function);
- _results.push(window[populate_function]());
- } else {
- _results.push(void 0);
- }
- }
- return _results;
- };
- return $("#make_default").click(make_default);
-});
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.coffee b/wqflask/wqflask/static/new/javascript/draw_probability_plot.coffee
new file mode 100644
index 00000000..90db990a
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.coffee
@@ -0,0 +1,37 @@
+# illustration of use of the scatterplot function
+
+h = 400
+w = 500
+margin = {left:60, top:40, right:40, bottom: 40, inner:5}
+halfh = (h+margin.top+margin.bottom)
+totalh = halfh*2
+halfw = (w+margin.left+margin.right)
+totalw = halfw*2
+
+# Example 1: simplest use
+#d3.json "data.json", (data) ->
+mychart = scatterplot().xvar(0)
+ .yvar(1)
+ .xlab(js_data.trait_1)
+ .ylab(js_data.trait_2)
+ .height(h)
+ .width(w)
+ .margin(margin)
+
+data = js_data.data
+indID = js_data.indIDs
+slope = js_data.slope
+intercept = js_data.intercept
+
+console.log("THE DATA IS:", data)
+
+d3.select("div#chart1")
+ .datum({data:data, indID:indID, slope:slope, intercept:intercept})
+ .call(mychart)
+
+# animate points
+mychart.pointsSelect()
+ .on "mouseover", (d) ->
+ d3.select(this).attr("r", mychart.pointsize()*3)
+ .on "mouseout", (d) ->
+ d3.select(this).attr("r", mychart.pointsize())
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index 777aac2a..8794625a 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -123,6 +123,8 @@ lodchart = () ->
.text((d) -> d[0])
.attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2)
.attr("y", margin.top+height+axispos.xlabel)
+ .attr("dominant-baseline", "hanging")
+ .attr("text-anchor", "middle")
.attr("cursor", "pointer")
.on("click", (d) ->
redraw_plot(d)
@@ -131,6 +133,7 @@ lodchart = () ->
xaxis.append("text").attr("class", "title")
.attr("y", margin.top+height+axispos.xtitle)
.attr("x", margin.left+width/2)
+ .attr("fill", "slateblue")
.text(xlab)
@@ -164,6 +167,8 @@ lodchart = () ->
.attr("y", (d) -> yscale(d))
.attr("x", margin.left-axispos.ylabel)
.attr("fill", "blue")
+ .attr("dominant-baseline", "middle")
+ .attr("text-anchor", "end")
.text((d) -> formatAxis(yticks)(d))
yaxis.append("text").attr("class", "title")
@@ -171,6 +176,8 @@ lodchart = () ->
.attr("x", margin.left-axispos.ytitle)
.text(ylab)
.attr("transform", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "")
+ .attr("text-anchor", "middle")
+ .attr("fill", "slateblue")
if data['additive'].length > 0
rotate_additive_ylab = rotate_additive_ylab ? (additive_ylab.length > 1)
@@ -195,6 +202,8 @@ lodchart = () ->
.attr("y", (d) -> additive_yscale(d))
.attr("x", (d) -> margin.left + width + axispos.ylabel + 20)
.attr("fill", "green")
+ .attr("dominant-baseline", "middle")
+ .attr("text-anchor", "end")
.text((d) -> formatAxis(additive_yticks)(d))
additive_yaxis.append("text").attr("class", "title")
@@ -202,7 +211,8 @@ lodchart = () ->
.attr("x", margin.left + width + axispos.ytitle)
.text(additive_ylab)
.attr("transform", if rotate_additive_ylab then "rotate(270,#{margin.left + width + axispos.ytitle}, #{margin.top+height*1.5})" else "")
-
+ .attr("text-anchor", "middle")
+ .attr("fill", "green")
suggestive_bar = g.append("g").attr("class", "suggestive")
suggestive_bar.selectAll("empty")
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index c974c9d2..75adc792 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -120,10 +120,10 @@ lodchart = function() {
return d[0];
}).attr("x", function(d, i) {
return (data.chrStart[i] + data.chrEnd[i]) / 2;
- }).attr("y", margin.top + height + axispos.xlabel).attr("cursor", "pointer").on("click", function(d) {
+ }).attr("y", margin.top + height + axispos.xlabel).attr("dominant-baseline", "hanging").attr("text-anchor", "middle").attr("cursor", "pointer").on("click", function(d) {
return redraw_plot(d);
});
- xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).text(xlab);
+ xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).attr("fill", "slateblue").text(xlab);
redraw_plot = function(chr_ob) {
var chr_plot;
console.log("chr_name is:", chr_ob[0]);
@@ -141,10 +141,10 @@ lodchart = function() {
}).attr("x1", margin.left).attr("x2", margin.left + 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) {
return yscale(d);
- }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").text(function(d) {
+ }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").attr("dominant-baseline", "middle").attr("text-anchor", "end").text(function(d) {
return formatAxis(yticks)(d);
});
- yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "");
+ yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue");
if (data['additive'].length > 0) {
rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1;
additive_yaxis = g.append("g").attr("class", "y axis");
@@ -157,10 +157,10 @@ lodchart = function() {
return additive_yscale(d);
}).attr("x", function(d) {
return margin.left + width + axispos.ylabel + 20;
- }).attr("fill", "green").text(function(d) {
+ }).attr("fill", "green").attr("dominant-baseline", "middle").attr("text-anchor", "end").text(function(d) {
return formatAxis(additive_yticks)(d);
});
- additive_yaxis.append("text").attr("class", "title").attr("y", margin.top + 1.5 * height).attr("x", margin.left + width + axispos.ytitle).text(additive_ylab).attr("transform", rotate_additive_ylab ? "rotate(270," + (margin.left + width + axispos.ytitle) + ", " + (margin.top + height * 1.5) + ")" : "");
+ additive_yaxis.append("text").attr("class", "title").attr("y", margin.top + 1.5 * height).attr("x", margin.left + width + axispos.ytitle).text(additive_ylab).attr("transform", rotate_additive_ylab ? "rotate(270," + (margin.left + width + axispos.ytitle) + ", " + (margin.top + height * 1.5) + ")" : "").attr("text-anchor", "middle").attr("fill", "green");
}
suggestive_bar = g.append("g").attr("class", "suggestive");
suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) {
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
index 492c2f3f..37226b8a 100644
--- a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
@@ -105,10 +105,11 @@ lodchart = () ->
.data(data.chrnames)
.enter()
.append("text")
- .attr("class", "chr_label")
.text((d) -> d[0])
.attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2)
.attr("y", margin.top+height+axispos.xlabel)
+ .attr("dominant-baseline", "hanging")
+ .attr("text-anchor", "middle")
.attr("cursor", "pointer")
.on("click", (d) ->
redraw_plot(d)
@@ -117,16 +118,18 @@ lodchart = () ->
xaxis.append("text").attr("class", "title")
.attr("y", margin.top+height+axispos.xtitle)
.attr("x", margin.left+width/2)
+ .attr("fill", "slateblue")
.text(xlab)
-
+
+
redraw_plot = (chr_ob) ->
console.log("chr_name is:", chr_ob[0])
console.log("chr_length is:", chr_ob[1])
$('#topchart').remove()
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')
chr_plot = new Chr_Manhattan_Plot(600, 1200, chr_ob)
-
-
+
+
# y-axis
rotate_ylab = rotate_ylab ? (ylab.length > 1)
yaxis = g.append("g").attr("class", "y axis")
@@ -150,6 +153,8 @@ lodchart = () ->
.attr("y", (d) -> yscale(d))
.attr("x", margin.left-axispos.ylabel)
.attr("fill", "blue")
+ .attr("dominant-baseline", "middle")
+ .attr("text-anchor", "end")
.text((d) -> formatAxis(yticks)(d))
yaxis.append("text").attr("class", "title")
@@ -157,86 +162,10 @@ lodchart = () ->
.attr("x", margin.left-axispos.ytitle)
.text(ylab)
.attr("transform", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "")
-
- # lod curves by chr
- #lodcurve = (chr, lodcolumn) ->
- # d3.svg.line()
- # .x((d) -> xscale[chr](d))
- # .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn]))
-
- #add_plot_points: () ->
- # @plot_point = @svg.selectAll("circle")
- # .data(@plot_coordinates)
- # .enter()
- # .append("circle")
- # .attr("cx", (d) =>
- # return @x_scale(d[0])
- # )
- # .attr("cy", (d) =>
- # return @y_scale(d[1])
- # )
- # .attr("r", (d) =>
- # #if d[1] > 3
- # # return 3
- # #else
- # return 2
- # )
- # .attr("fill", (d) =>
- # #if d[1] > 3
- # # return "white"
- # #else
- # return "black"
- # )
- # .attr("stroke", "black")
- # .attr("stroke-width", "1")
- # .attr("id", (d) =>
- # return "point_" + String(d[2])
- # )
- # .classed("circle", true)
- # .on("mouseover", (d) =>
- # console.log("d3.event is:", d3.event)
- # console.log("d is:", d)
- # this_id = "point_" + String(d[2])
- # d3.select("#" + this_id).classed("d3_highlight", true)
- # .attr("r", 5)
- # .attr("stroke", "none")
- # .attr("fill", "blue")
- # .call(@show_marker_in_table(d))
- # )
- # .on("mouseout", (d) =>
- # this_id = "point_" + String(d[2])
- # d3.select("#" + this_id).classed("d3_highlight", false)
- # .attr("r", (d) =>
- # #if d[1] > 2
- # # return 3
- # #else
- # return 2
- # )
- # .attr("fill", (d) =>
- # #if d[1] > 2
- # # return "white"
- # #else
- # return "black"
- # )
- # .attr("stroke", "black")
- # .attr("stroke-width", "1")
- # )
- # .append("svg:title")
- # .text((d) =>
- # return d[2]
- # )
-
- #curves = g.append("g").attr("id", "curves")
-
- #for chr in data.chrnames
- # curves.append("path")
- # .datum(data.posByChr[chr])
- # .attr("d", lodcurve(chr, lodvarnum))
- # .attr("stroke", lodlinecolor)
- # .attr("fill", "none")
- # .attr("stroke-width", linewidth)
- # .style("pointer-events", "none")
-
+ .attr("text-anchor", "middle")
+ .attr("fill", "slateblue")
+
+
# points at markers
if pointsize > 0
markerpoints = g.append("g").attr("id", "markerpoints_visible")
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.js b/wqflask/wqflask/static/new/javascript/manhattan_plot.js
index 546cf9a9..203f3a1b 100644
--- a/wqflask/wqflask/static/new/javascript/manhattan_plot.js
+++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.js
@@ -91,14 +91,14 @@ lodchart = function() {
return redraw_plot(d);
});
xaxis = g.append("g").attr("class", "x axis");
- xaxis.selectAll("empty").data(data.chrnames).enter().append("text").attr("class", "chr_label").text(function(d) {
+ xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) {
return d[0];
}).attr("x", function(d, i) {
return (data.chrStart[i] + data.chrEnd[i]) / 2;
- }).attr("y", margin.top + height + axispos.xlabel).attr("cursor", "pointer").on("click", function(d) {
+ }).attr("y", margin.top + height + axispos.xlabel).attr("dominant-baseline", "hanging").attr("text-anchor", "middle").attr("cursor", "pointer").on("click", function(d) {
return redraw_plot(d);
});
- xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).text(xlab);
+ xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).attr("fill", "slateblue").text(xlab);
redraw_plot = function(chr_ob) {
var chr_plot;
console.log("chr_name is:", chr_ob[0]);
@@ -116,10 +116,10 @@ lodchart = function() {
}).attr("x1", margin.left).attr("x2", margin.left + 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) {
return yscale(d);
- }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").text(function(d) {
+ }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").attr("dominant-baseline", "middle").attr("text-anchor", "end").text(function(d) {
return formatAxis(yticks)(d);
});
- yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "");
+ yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue");
if (pointsize > 0) {
markerpoints = g.append("g").attr("id", "markerpoints_visible");
markerpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
diff --git a/wqflask/wqflask/static/new/javascript/probability_plot.coffee b/wqflask/wqflask/static/new/javascript/probability_plot.coffee
new file mode 100644
index 00000000..c1f26941
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/probability_plot.coffee
@@ -0,0 +1,424 @@
+probability_plot = () ->
+ width = 800
+ height = 600
+ margin = {left:60, top:40, right:40, bottom: 40, inner:5}
+ axispos = {xtitle:25, ytitle:45, xlabel:5, ylabel:5}
+ titlepos = 20
+ xNA = {handle:true, force:false, width:15, gap:10}
+ yNA = {handle:true, force:false, width:15, gap:10}
+ xlim = null
+ ylim = null
+ nxticks = 5
+ xticks = null
+ nyticks = 5
+ yticks = null
+ rectcolor = d3.rgb(230, 230, 230)
+ pointcolor = null
+ pointstroke = "black"
+ pointsize = 3 # default = no visible points at markers
+ title = "Correlation Scatterplot"
+ xlab = "X"
+ ylab = "Y"
+ rotate_ylab = null
+ yscale = d3.scale.linear()
+ xscale = d3.scale.linear()
+ xvar = 0
+ yvar = 1
+ pointsSelect = null
+ dataByInd = false
+
+ ## the main function
+ chart = (selection) ->
+ selection.each (data) ->
+
+ if dataByInd
+ x = data.data.map (d) -> d[xvar]
+ y = data.data.map (d) -> d[yvar]
+ else # reorganize data
+ x = data.data[xvar]
+ y = data.data[yvar]
+
+ console.log("x:", x)
+ console.log("y:", y)
+
+ # grab indID if it's there
+ # if no indID, create a vector of them
+ indID = data?.indID ? null
+ indID = indID ? [1..x.length]
+
+ console.log("indID:", indID)
+
+ # groups of colors
+ group = data?.group ? (1 for i in x)
+ ngroup = d3.max(group)
+ group = (g-1 for g in group) # changed from (1,2,3,...) to (0,1,2,...)
+
+ # colors of the points in the different groups
+ pointcolor = pointcolor ? selectGroupColors(ngroup, "dark")
+ pointcolor = expand2vector(pointcolor, ngroup)
+
+ # if all (x,y) not null
+ xNA.handle = false if x.every (v) -> (v?) and !xNA.force
+ yNA.handle = false if y.every (v) -> (v?) and !yNA.force
+ if xNA.handle
+ paneloffset = xNA.width + xNA.gap
+ panelwidth = width - paneloffset
+ else
+ paneloffset = 0
+ panelwidth = width
+ if yNA.handle
+ panelheight = height - (yNA.width + yNA.gap)
+ else
+ panelheight = height
+
+ xlim = xlim ? d3.extent(x)
+ ylim = ylim ? d3.extent(y)
+
+ # I'll replace missing values something smaller than what's observed
+ na_value = d3.min(x.concat y) - 100
+
+ # Select the svg element, if it exists.
+ svg = d3.select(this).selectAll("svg").data([data])
+
+ # Otherwise, create the skeletal chart.
+ gEnter = svg.enter().append("svg").append("g")
+
+ # Update the outer dimensions.
+ svg.attr("width", width+margin.left+margin.right)
+ .attr("height", height+margin.top+margin.bottom)
+
+ g = svg.select("g")
+
+ # box
+ g.append("rect")
+ .attr("x", paneloffset+margin.left)
+ .attr("y", margin.top)
+ .attr("height", panelheight)
+ .attr("width", panelwidth)
+ .attr("fill", rectcolor)
+ .attr("stroke", "none")
+ if xNA.handle
+ g.append("rect")
+ .attr("x", margin.left)
+ .attr("y", margin.top)
+ .attr("height", panelheight)
+ .attr("width", xNA.width)
+ .attr("fill", rectcolor)
+ .attr("stroke", "none")
+ if xNA.handle and yNA.handle
+ g.append("rect")
+ .attr("x", margin.left)
+ .attr("y", margin.top+height - yNA.width)
+ .attr("height", yNA.width)
+ .attr("width", xNA.width)
+ .attr("fill", rectcolor)
+ .attr("stroke", "none")
+ if yNA.handle
+ g.append("rect")
+ .attr("x", margin.left+paneloffset)
+ .attr("y", margin.top+height-yNA.width)
+ .attr("height", yNA.width)
+ .attr("width", panelwidth)
+ .attr("fill", rectcolor)
+ .attr("stroke", "none")
+
+ # simple scales (ignore NA business)
+ xrange = [margin.left+paneloffset+margin.inner, margin.left+paneloffset+panelwidth-margin.inner]
+ yrange = [margin.top+panelheight-margin.inner, margin.top+margin.inner]
+ xscale.domain(xlim).range(xrange)
+ yscale.domain(ylim).range(yrange)
+ xs = d3.scale.linear().domain(xlim).range(xrange)
+ ys = d3.scale.linear().domain(ylim).range(yrange)
+
+ # "polylinear" scales to handle missing values
+ if xNA.handle
+ xscale.domain([na_value].concat xlim)
+ .range([margin.left + xNA.width/2].concat xrange)
+ x = x.map (e) -> if e? then e else na_value
+ if yNA.handle
+ yscale.domain([na_value].concat ylim)
+ .range([height+margin.top-yNA.width/2].concat yrange)
+ y = y.map (e) -> if e? then e else na_value
+
+ # if yticks not provided, use nyticks to choose pretty ones
+ yticks = yticks ? ys.ticks(nyticks)
+ xticks = xticks ? xs.ticks(nxticks)
+
+ # title
+ titlegrp = g.append("g").attr("class", "title")
+ .append("text")
+ .attr("x", margin.left + width/2)
+ .attr("y", margin.top - titlepos)
+ .text(title)
+
+ # x-axis
+ xaxis = g.append("g").attr("class", "x axis")
+ xaxis.selectAll("empty")
+ .data(xticks)
+ .enter()
+ .append("line")
+ .attr("x1", (d) -> xscale(d))
+ .attr("x2", (d) -> xscale(d))
+ .attr("y1", margin.top)
+ .attr("y2", margin.top+height)
+ .attr("fill", "none")
+ .attr("stroke", "white")
+ .attr("stroke-width", 1)
+ .style("pointer-events", "none")
+ xaxis.selectAll("empty")
+ .data(xticks)
+ .enter()
+ .append("text")
+ .attr("x", (d) -> xscale(d))
+ .attr("y", margin.top+height+axispos.xlabel)
+ .text((d) -> formatAxis(xticks)(d))
+ xaxis.append("text").attr("class", "title")
+ .attr("x", margin.left+width/2)
+ .attr("y", margin.top+height+axispos.xtitle)
+ .text(xlab)
+ if xNA.handle
+ xaxis.append("text")
+ .attr("x", margin.left+xNA.width/2)
+ .attr("y", margin.top+height+axispos.xlabel)
+ .text("N/A")
+
+ # y-axis
+ rotate_ylab = rotate_ylab ? (ylab.length > 1)
+ yaxis = g.append("g").attr("class", "y axis")
+ yaxis.selectAll("empty")
+ .data(yticks)
+ .enter()
+ .append("line")
+ .attr("y1", (d) -> yscale(d))
+ .attr("y2", (d) -> yscale(d))
+ .attr("x1", margin.left)
+ .attr("x2", margin.left+width)
+ .attr("fill", "none")
+ .attr("stroke", "white")
+ .attr("stroke-width", 1)
+ .style("pointer-events", "none")
+ yaxis.selectAll("empty")
+ .data(yticks)
+ .enter()
+ .append("text")
+ .attr("y", (d) -> yscale(d))
+ .attr("x", margin.left-axispos.ylabel)
+ .text((d) -> formatAxis(yticks)(d))
+ yaxis.append("text").attr("class", "title")
+ .attr("y", margin.top+height/2)
+ .attr("x", margin.left-axispos.ytitle)
+ .text(ylab)
+ .attr("transform", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "")
+ if yNA.handle
+ yaxis.append("text")
+ .attr("x", margin.left-axispos.ylabel)
+ .attr("y", margin.top+height-yNA.width/2)
+ .text("N/A")
+
+ indtip = d3.tip()
+ .attr('class', 'd3-tip')
+ .html((d,i) -> indID[i])
+ .direction('e')
+ .offset([0,10])
+ svg.call(indtip)
+
+ #g.append("line")
+ # .attr("x1")
+ #
+ #g.append("line")
+ # .attr("x1", xscale(minx))
+ # .attr("x2", xscale(maxx*0.995))
+ # .attr("y2", yscale(slope*maxx*0.995+intercept))
+ # .style("stroke", "black")
+ # .style("stroke-width", 2);
+
+ points = g.append("g").attr("id", "points")
+ pointsSelect =
+ points.selectAll("empty")
+ .data(d3.range(x.length))
+ .enter()
+ .append("circle")
+ .attr("cx", (d,i) -> xscale(x[i]))
+ .attr("cy", (d,i) -> yscale(y[i]))
+ .attr("class", (d,i) -> "pt#{i}")
+ .attr("r", pointsize)
+ .attr("fill", (d,i) -> pointcolor[group[i]])
+ .attr("stroke", pointstroke)
+ .attr("stroke-width", "1")
+ .attr("opacity", (d,i) ->
+ return 1 if (x[i]? or xNA.handle) and (y[i]? or yNA.handle)
+ return 0)
+ .on("mouseover.paneltip", indtip.show)
+ .on("mouseout.paneltip", indtip.hide)
+
+ # box
+ g.append("rect")
+ .attr("x", margin.left+paneloffset)
+ .attr("y", margin.top)
+ .attr("height", panelheight)
+ .attr("width", panelwidth)
+ .attr("fill", "none")
+ .attr("stroke", "black")
+ .attr("stroke-width", "none")
+ if xNA.handle
+ g.append("rect")
+ .attr("x", margin.left)
+ .attr("y", margin.top)
+ .attr("height", panelheight)
+ .attr("width", xNA.width)
+ .attr("fill", "none")
+ .attr("stroke", "black")
+ .attr("stroke-width", "none")
+ if xNA.handle and yNA.handle
+ g.append("rect")
+ .attr("x", margin.left)
+ .attr("y", margin.top+height - yNA.width)
+ .attr("height", yNA.width)
+ .attr("width", xNA.width)
+ .attr("fill", "none")
+ .attr("stroke", "black")
+ .attr("stroke-width", "none")
+ if yNA.handle
+ g.append("rect")
+ .attr("x", margin.left+paneloffset)
+ .attr("y", margin.top+height-yNA.width)
+ .attr("height", yNA.width)
+ .attr("width", panelwidth)
+ .attr("fill", "none")
+ .attr("stroke", "black")
+ .attr("stroke-width", "none")
+
+ ## configuration parameters
+ chart.width = (value) ->
+ return width if !arguments.length
+ width = value
+ chart
+
+ chart.height = (value) ->
+ return height if !arguments.length
+ height = value
+ chart
+
+ chart.margin = (value) ->
+ return margin if !arguments.length
+ margin = value
+ chart
+
+ chart.axispos = (value) ->
+ return axispos if !arguments.length
+ axispos = value
+ chart
+
+ chart.titlepos = (value) ->
+ return titlepos if !arguments.length
+ titlepos
+ chart
+
+ chart.xlim = (value) ->
+ return xlim if !arguments.length
+ xlim = value
+ chart
+
+ chart.nxticks = (value) ->
+ return nxticks if !arguments.length
+ nxticks = value
+ chart
+
+ chart.xticks = (value) ->
+ return xticks if !arguments.length
+ xticks = value
+ chart
+
+ chart.ylim = (value) ->
+ return ylim if !arguments.length
+ ylim = value
+ chart
+
+ chart.nyticks = (value) ->
+ return nyticks if !arguments.length
+ nyticks = value
+ chart
+
+ chart.yticks = (value) ->
+ return yticks if !arguments.length
+ yticks = value
+ chart
+
+ chart.rectcolor = (value) ->
+ return rectcolor if !arguments.length
+ rectcolor = value
+ chart
+
+ chart.pointcolor = (value) ->
+ return pointcolor if !arguments.length
+ pointcolor = value
+ chart
+
+ chart.pointsize = (value) ->
+ return pointsize if !arguments.length
+ pointsize = value
+ chart
+
+ chart.pointstroke = (value) ->
+ return pointstroke if !arguments.length
+ pointstroke = value
+ chart
+
+ chart.dataByInd = (value) ->
+ return dataByInd if !arguments.length
+ dataByInd = value
+ chart
+
+ chart.title = (value) ->
+ return title if !arguments.length
+ title = value
+ chart
+
+ chart.xlab = (value) ->
+ return xlab if !arguments.length
+ xlab = value
+ chart
+
+ chart.ylab = (value) ->
+ return ylab if !arguments.length
+ ylab = value
+ chart
+
+ chart.rotate_ylab = (value) ->
+ return rotate_ylab if !arguments.length
+ rotate_ylab = value
+ chart
+
+ chart.xvar = (value) ->
+ return xvar if !arguments.length
+ xvar = value
+ chart
+
+ chart.yvar = (value) ->
+ return yvar if !arguments.length
+ yvar = value
+ chart
+
+ chart.xNA = (value) ->
+ return xNA if !arguments.length
+ xNA = value
+ chart
+
+ chart.yNA = (value) ->
+ return yNA if !arguments.length
+ yNA = value
+ chart
+
+ chart.yscale = () ->
+ return yscale
+
+ chart.xscale = () ->
+ return xscale
+
+ chart.pointsSelect = () ->
+ return pointsSelect
+
+ # return the chart function
+ chart
+
+probability_plot() \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 1a7f6a0b..2cdad5ee 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -1,7 +1,7 @@
-root = exports ? this
-
console.log("start_b")
+#root = exports ? this
+
# this is our isNumber, do not confuse with the underscore.js one
is_number = (o) ->
return ! isNaN (o-0) && o != null
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 5f452f32..71c23272 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1,10 +1,8 @@
// Generated by CoffeeScript 1.7.1
-var Stat_Table_Rows, is_number, root,
+var Stat_Table_Rows, is_number,
__hasProp = {}.hasOwnProperty,
__slice = [].slice;
-root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
console.log("start_b");
is_number = function(o) {
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 b37cfe09..27bf80d5 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -1,7 +1,8 @@
# http://stackoverflow.com/a/4215132/1175849
-root = exports ? this
+#root = exports ? this
$ ->
+
submit_special = ->
# Add submit_special class plus a data-url field to any button
# And it will submit to that url
@@ -52,15 +53,12 @@ $ ->
)
return false
- $("#interval_mapping_compute").click(() =>
- 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)
+ ##Block Outliers Code
+ block_outliers = ->
+ $('.outlier').each (_index, element) =>
+ $(element).find('.trait_value_input').val('x')
+
+ do_ajax_post = (url, form_data) ->
$.ajax(
type: "POST"
url: url
@@ -77,9 +75,57 @@ $ ->
$("body").html(data)
)
console.log("settingInterval")
-
+
this.my_timer = setInterval(get_progress, 1000)
return false
+
+ showalert = (message,alerttype) ->
+ $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">×</a><span>'+message+'</span></div>')
+
+
+ $("#interval_mapping_compute").click(() =>
+ showalert("One or more outliers exist in this data set. Please review values before mapping. \
+ Including outliers when mapping may lead to misleading results. \
+ We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \
+ or simply deleting them.", "alert-success")
+ 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 = $('#trait_data_form').serialize()
+ console.log("form_data is:", form_data)
+
+ do_ajax_post(url, form_data)
+
+ #remove_outliers = confirm("Remove outliers?")
+ #if use_outliers == true
+ # block_outliers()
+ # do_ajax_post(url, form_data)
+ #else
+ # do_ajax_post(url, form_data)
+ #$.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
)
$('#suggestive').hide()
@@ -98,25 +144,31 @@ $ ->
$('input[name=method]').val("pylmm")
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')
- $("body").html(data)
- )
- console.log("settingInterval")
-
- this.my_timer = setInterval(get_progress, 1000)
- return false
+
+ #remove_outliers = confirm("Remove outliers?")
+ #if use_outliers == true
+ # block_outliers()
+ do_ajax_post(url, form_data)
+
+ #$.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
)
$("#plink_compute").click(() =>
@@ -128,25 +180,28 @@ $ ->
$('input[name=maf]').val($('input[name=maf_plink]').val())
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)
- $('#static_progress_bar_container').modal('hide')
- $("body").html("We got an error.")
- success: (data) =>
- clearInterval(this.my_timer)
- $('#static_progress_bar_container').modal('hide')
- $("body").html(data)
- )
- console.log("settingInterval")
-
- this.my_timer = setInterval(get_progress, 1000)
- return false
+
+ do_ajax_post(url, form_data)
+
+ #$.ajax(
+ # type: "POST"
+ # url: url
+ # data: form_data
+ # error: (xhr, ajaxOptions, thrownError) =>
+ # alert("Sorry, an error occurred")
+ # console.log(xhr)
+ # clearInterval(this.my_timer)
+ # $('#static_progress_bar_container').modal('hide')
+ # $("body").html("We got an error.")
+ # success: (data) =>
+ # clearInterval(this.my_timer)
+ # $('#static_progress_bar_container').modal('hide')
+ # $("body").html(data)
+ #)
+ #console.log("settingInterval")
+ #
+ #this.my_timer = setInterval(get_progress, 1000)
+ #return false
)
$("#gemma_compute").click(() =>
@@ -158,25 +213,28 @@ $ ->
$('input[name=maf]').val($('input[name=maf_gemma]').val())
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)
- $('#static_progress_bar_container').modal('hide')
- $("body").html("We got an error.")
- success: (data) =>
- clearInterval(this.my_timer)
- $('#static_progress_bar_container').modal('hide')
- $("body").html(data)
- )
- console.log("settingInterval")
-
- this.my_timer = setInterval(get_progress, 1000)
- return false
+
+ do_ajax_post(url, form_data)
+
+ #$.ajax(
+ # type: "POST"
+ # url: url
+ # data: form_data
+ # error: (xhr, ajaxOptions, thrownError) =>
+ # alert("Sorry, an error occurred")
+ # console.log(xhr)
+ # clearInterval(this.my_timer)
+ # $('#static_progress_bar_container').modal('hide')
+ # $("body").html("We got an error.")
+ # success: (data) =>
+ # clearInterval(this.my_timer)
+ # $('#static_progress_bar_container').modal('hide')
+ # $("body").html(data)
+ #)
+ #console.log("settingInterval")
+ #
+ #this.my_timer = setInterval(get_progress, 1000)
+ #return false
)
#$(".submit_special").click(submit_special)
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 1a2ad637..d02bca4b 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,10 +1,6 @@
// Generated by CoffeeScript 1.7.1
-var root;
-
-root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
$(function() {
- var composite_mapping_fields, get_progress, mapping_method_fields, submit_special, toggle_enable_disable, update_time_remaining;
+ var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, showalert, submit_special, toggle_enable_disable, update_time_remaining;
submit_special = function() {
var url;
console.log("In submit_special");
@@ -61,9 +57,46 @@ $(function() {
});
return false;
};
+ block_outliers = function() {
+ return $('.outlier').each((function(_this) {
+ return function(_index, element) {
+ return $(element).find('.trait_value_input').val('x');
+ };
+ })(this));
+ };
+ do_ajax_post = function(url, form_data) {
+ $.ajax({
+ type: "POST",
+ url: url,
+ data: form_data,
+ error: (function(_this) {
+ return 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.");
+ };
+ })(this),
+ success: (function(_this) {
+ return function(data) {
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return $("body").html(data);
+ };
+ })(this)
+ });
+ console.log("settingInterval");
+ this.my_timer = setInterval(get_progress, 1000);
+ return false;
+ };
+ showalert = function(message, alerttype) {
+ return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
+ };
$("#interval_mapping_compute").click((function(_this) {
return function() {
var form_data, url;
+ showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success");
console.log("In interval mapping");
$("#progress_bar_container").modal();
url = "/interval_mapping";
@@ -72,26 +105,7 @@ $(function() {
$('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
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;
+ return do_ajax_post(url, form_data);
};
})(this));
$('#suggestive').hide();
@@ -113,26 +127,7 @@ $(function() {
$('input[name=method]').val("pylmm");
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;
+ return do_ajax_post(url, form_data);
};
})(this));
$("#plink_compute").click((function(_this) {
@@ -146,26 +141,7 @@ $(function() {
$('input[name=maf]').val($('input[name=maf_plink]').val());
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);
- $('#static_progress_bar_container').modal('hide');
- return $("body").html("We got an error.");
- },
- success: function(data) {
- clearInterval(_this.my_timer);
- $('#static_progress_bar_container').modal('hide');
- return $("body").html(data);
- }
- });
- console.log("settingInterval");
- _this.my_timer = setInterval(get_progress, 1000);
- return false;
+ return do_ajax_post(url, form_data);
};
})(this));
$("#gemma_compute").click((function(_this) {
@@ -179,26 +155,7 @@ $(function() {
$('input[name=maf]').val($('input[name=maf_gemma]').val());
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);
- $('#static_progress_bar_container').modal('hide');
- return $("body").html("We got an error.");
- },
- success: function(data) {
- clearInterval(_this.my_timer);
- $('#static_progress_bar_container').modal('hide');
- return $("body").html(data);
- }
- });
- console.log("settingInterval");
- _this.my_timer = setInterval(get_progress, 1000);
- return false;
+ return do_ajax_post(url, form_data);
};
})(this));
composite_mapping_fields = function() {
diff --git a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
index 7da7faec..68d5e4fa 100755
--- a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
+++ b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
@@ -41,6 +41,8 @@ table.dataTable tr.even td.sorting_1 { background-color: #EAEBFF; }
table.dataTable tr.even td.sorting_2 { background-color: #F2F3FF; }
table.dataTable tr.even td.sorting_3 { background-color: #F9F9FF; }
+table.dataTable tr.outlier td{ background-color: #FFFF00; }
+
/*
* Table wrapper
diff --git a/wqflask/wqflask/templates/corr_scatter_plot_old.html b/wqflask/wqflask/templates/corr_scatter_plot_old.html
deleted file mode 100755
index 79c63ada..00000000
--- a/wqflask/wqflask/templates/corr_scatter_plot_old.html
+++ /dev/null
@@ -1,63 +0,0 @@
-{% extends "base.html" %}
-
-{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/corr_scatter_plot.css" />
-{% endblock %}
-
-{% block content %}
-<form action="" method="get">
-<input type="hidden" name="dataset_1" value="{{data_set_1.name}}">
-<input type="hidden" name="dataset_2" value="{{data_set_2.name}}">
-<input type="hidden" name="trait_1" value="{{trait_1.name}}">
-<input type="hidden" name="trait_2" value="{{trait_2.name}}">
-<table class="table" style="width: auto;">
- <tr>
- <td>Canvas Width</td>
- <td>Canvas Height</td>
- <td>Circle Color</td>
- <td>Circle Radius</td>
- <td>Line Color</td>
- <td>Line Width</td>
- <td rowspan="2" style="vertical-align:middle;"><button type="submit" class="btn btn-primary"><i class="icon-refresh"></i>Redraw</button></td>
- </tr>
- <tr>
- <td><input type="text" name="width" value="{{width}}" style="width: 100px;"></td>
- <td><input type="text" name="height" value="{{height}}" style="width: 100px;"></td>
- <td>
- <select name="circle_color" style="width: 100px;">
- <option value="red">Red</option>
- <option value="green">Green</option>
- <option value="blue">Blue</option>
- </select>
- </td>
- <td><input type="text" name="circle_radius" value="{{circle_radius}}" style="width: 100px;"></td>
- <td>
- <select name="line_color" style="width: 100px;">
- <option value="red">Red</option>
- <option value="green">Green</option>
- <option value="blue">Blue</option>
- </select>
- </td>
- <td><input type="text" name="line_width" value="{{line_width}}" style="width: 100px;"></td>
- </tr>
-</table>
-</form>
-<div id='scatter_plot'></div>
-{% endblock %}
-
-{% block js %}
- <script>
- js_data = {{ js_data | safe }}
- </script>
- <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/corr_scatter_plot.js"></script>
-{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
index 25ee22ac..4fe5d0f8 100755
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -19,11 +19,16 @@
<h2>
Whole Genome Mapping
</h2>
- <form id="exportform" action="export" method="post">
+ <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post">
<input type="hidden" id="data" name="data" value="">
<input type="hidden" id="filename" name="filename" value="">
<input type="submit" id="export" value="Download SVG">
</form>
+ <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post">
+ <input type="hidden" id="data" name="data" value="">
+ <input type="hidden" id="filename" name="filename" value="">
+ <input type="submit" id="export_pdf" value="Download PDF">
+ </form>
</div>
<div id="chart_container">
<div class="qtlcharts" id="topchart">
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 3dce5266..451b3754 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -18,11 +18,16 @@
<h2>
Whole Genome Mapping
</h2>
- <form id="exportform" action="export" method="post">
+ <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post">
<input type="hidden" id="data" name="data" value="">
<input type="hidden" id="filename" name="filename" value="">
<input type="submit" id="export" value="Download SVG">
</form>
+ <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post">
+ <input type="hidden" id="data" name="data" value="">
+ <input type="hidden" id="filename" name="filename" value="">
+ <input type="submit" id="export_pdf" value="Download PDF">
+ </form>
<!-- <button id="export_pdf" class="btn">Export PDF</button>-->
</div>
<div id="chart_container">
diff --git a/wqflask/wqflask/templates/marker_regression_old.html b/wqflask/wqflask/templates/marker_regression_old.html
new file mode 100644
index 00000000..defcd929
--- /dev/null
+++ b/wqflask/wqflask/templates/marker_regression_old.html
@@ -0,0 +1,106 @@
+{% extends "base.html" %}
+{% block title %}Marker Regression{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+{% endblock %}
+{% block content %} <!-- Start of body -->
+
+ {{ header("Marker Regression",
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
+ <div class="container">
+ <div>
+ <h2>
+ Manhattan Plot
+ </h2>
+ </div>
+ <div id="manhattan_plot_container" class="manhattan_plot_container">
+ <div id="manhattan_plot" class="manhattan_plots">
+
+ </div>
+ </div>
+ <div>
+ <h2>
+ Genome Association Results
+ </h2>
+ </div>
+
+ <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <td>Index</td>
+ <td>LOD Score</td>
+ <td>Chr</td>
+ <td>Mb</td>
+ <td>Locus</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in filtered_markers %}
+ {% if marker.lod_score > lod_cutoff %}
+ <tr>
+ <td>{{loop.index}}</td>
+ <td>{{marker.lod_score}}</td>
+ <td>{{marker.chr}}</td>
+ <td>{{marker.Mb}}</td>
+ <td>{{marker.name}}</td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+
+ <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script>
+ js_data = {{ js_data | safe }}
+ </script>
+
+ <!--[if lt IE 9]>
+<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
+ <![endif]-->
+ <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.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 language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_manhattan_plot.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/marker_regression.js"></script>
+
+
+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ console.time("Creating table");
+ $('#qtl_results').dataTable( {
+ //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+ "sDom": "lTftipr",
+ "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"
+ },
+ "iDisplayLength": 50,
+ "bLengthChange": true,
+ "bDeferRender": true,
+ "bSortClasses": false
+ } );
+ console.timeEnd("Creating table");
+ });
+ </script>
+{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index f20d66ed..d2b748ca 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -2,6 +2,7 @@
{% block title %}Trait Data and Analysis{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
@@ -107,7 +108,7 @@
console.time("Creating table");
{% if sample_groups[0].se_exists() %}
- $('#samples_primary, #samples_other').dataTable( {
+ $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'yellow').dataTable( {
//"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
"aoColumns": [
{ "sType": "natural" },
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index f8542c78..705eda88 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -127,6 +127,7 @@
</button>
</div>
</div>
+ <div id="alert_placeholder"></div>
</div>
<div class="tab-pane" id="pylmm">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 6315260d..47a18149 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -269,6 +269,18 @@ def export():
response.headers["Content-Disposition"] = "attchment; filename=%s"%filename
return response
+@app.route("/export_pdf", methods = ('POST',))
+def export_pdf():
+ import cairosvg
+ print("request.form:", request.form)
+ svg_xml = request.form.get("data", "Invalid data")
+ print("svg_xml:", svg_xml)
+ filename = request.form.get("filename", "interval_map_pdf")
+ filepath = "/home/zas1024/gene/wqflask/output/"+filename
+ pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
+ response = Response(pdf_file, mimetype="application/pdf")
+ response.headers["Content-Disposition"] = "attchment; filename=%s"%filename
+ return response
@app.route("/interval_mapping", methods=('POST',))
def interval_mapping_page():