diff options
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 Binary files differdeleted file mode 100755 index fd928439..00000000 --- a/wqflask/wqflask/correlation_matrix/.show_corr_matrix.py.swn +++ /dev/null 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(): |