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-rw-r--r--etc/default_settings.py3
-rw-r--r--wqflask/wqflask/static/new/javascript/biodalliance.js75
-rw-r--r--wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee1
-rw-r--r--wqflask/wqflask/static/new/javascript/chr_lod_chart.js31
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.coffee2
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.js60
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html45
-rw-r--r--wqflask/wqflask/views.py6
8 files changed, 158 insertions, 65 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py
index df734f7c..f3ca2e58 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -56,3 +56,6 @@ GENENETWORK_FILES = HOME+"/gn2_data"
PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
PLINK_COMMAND = str.strip(os.popen("which plink2").read())
GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
+
+
+BIODALLIANCE_PATH = os.environ['HOME']+"/dalliance"
diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js
new file mode 100644
index 00000000..2dde6365
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/biodalliance.js
@@ -0,0 +1,75 @@
+"use strict";
+
+var bd_browser = null;
+var bd_data = {};
+
+var getChrLen = function(chr) {
+ return js_data[chr * 1];
+};
+
+var createBDBrowser = function(chr, start, end, speciesName, sources) {
+ console.log("creating BD browser");
+ var b = new Browser({
+ chr: chr,
+ viewStart: start,
+ viewEnd: end,
+
+ coordSystem: {
+ speciesName: speciesName
+ },
+
+ sources: sources,
+
+ setDocumentTitle: false,
+ prefix: '/dalliance/',
+ noPersist: true,
+ pageName: 'bd_container'
+ });
+
+ console.log("created BD browser");
+ return b;
+};
+
+var showBDButton = function() {
+ $('#open_bd').show();
+ $('#close_bd').hide();
+};
+
+var hideBDButton = function() {
+ $('#close_bd').show();
+ $('#open_bd').hide();
+};
+
+
+var setBDData = function(chr, length) {
+ // bd_data = { chr: chr, length: length };
+ bd_data.chr = chr;
+ bd_data.length = length;
+};
+
+var setBDSpecies = function(species) {
+ bd_data.species = species;
+};
+
+
+var openBDBrowser = function() {
+ console.log("opening browser");
+ if (!bd_browser) {
+ bd_browser = createBDBrowser(bd_data.chr, 0, bd_data.length * 1000000, bd_data.species,
+ [{name: 'Genome',
+ twoBitURI: 'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit',
+ desc: 'Mouse reference genome build GRCm38',
+ tier_type: 'sequence',
+ provides_entrypoints: true},
+ {name: 'QTL',
+ tier_type: 'qtl',
+ uri: 'http://gsocbox:8880/static/qtl/lod2.csv',
+ stylesheet_uri: "http://gsocbox:8880/stylesheets/qtl-stylesheet.xml"
+ }]
+ );
+ } else {
+ bd_browser.setLocation(bd_data.chr, 0, bd_data.length * 1000000);
+ }
+
+ bd_browser.maxViewWidth = bd_data.length * 1000000;
+};
diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
index e00694be..d3c1ee7d 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
@@ -273,6 +273,7 @@ class Chr_Lod_Chart
$("#return_to_full_view").hide()
$('#topchart').remove()
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')
+ hideBDButton()
create_lod_chart()
show_marker_in_table: (marker_info) ->
diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
index c6cbd01b..0032858f 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
@@ -1,13 +1,12 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.10.0
var Chr_Lod_Chart;
Chr_Lod_Chart = (function() {
- function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) {
+ function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot) {
this.plot_height = plot_height;
this.plot_width = plot_width;
this.chr = chr;
this.manhattanPlot = manhattanPlot;
- this.mappingScale = mappingScale;
this.qtl_results = js_data.qtl_results;
console.log("qtl_results are:", this.qtl_results);
console.log("chr is:", this.chr);
@@ -66,6 +65,8 @@ Chr_Lod_Chart = (function() {
} else {
this_chr = result.chr;
}
+ console.log("this_chr is:", this_chr);
+ console.log("@chr[0] is:", parseInt(this.chr[0]));
if (this_chr > parseInt(this.chr[0])) {
break;
}
@@ -95,18 +96,11 @@ Chr_Lod_Chart = (function() {
Chr_Lod_Chart.prototype.create_coordinates = function() {
var i, len, ref, result, results;
ref = this.these_results;
- console.log("THESE_RESULTS:", ref)
results = [];
for (i = 0, len = ref.length; i < len; i++) {
result = ref[i];
this.x_coords.push(parseFloat(result.Mb));
- if (js_data.result_score_type == "LOD") {
- this.y_coords.push(result.lod_score);
- }
- else {
- console.log("LRS VALUE:", result['lrs_value'])
- this.y_coords.push(result['lrs_value']);
- }
+ this.y_coords.push(result.lod_score);
results.push(this.marker_names.push(result.name));
}
return results;
@@ -119,19 +113,7 @@ Chr_Lod_Chart = (function() {
};
Chr_Lod_Chart.prototype.create_scales = function() {
- if (this.mappingScale == "morgan") {
- max_pos = 0
- for (i = 0, len = this.these_results.length; i < len; i++) {
- marker = this.these_results[i]
- if (parseFloat(marker['Mb']) > max_pos){
- max_pos = parseFloat(marker.Mb)
- }
- }
- this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]);
- }
- else {
- this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
- }
+ this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
};
@@ -278,6 +260,7 @@ Chr_Lod_Chart = (function() {
$("#return_to_full_view").hide();
$('#topchart').remove();
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
+ hideBDButton();
return create_lod_chart();
};
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index 55ffdce0..2da2e5bb 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -123,6 +123,8 @@ lodchart = () ->
.on("click", (d) ->
console.log("d is:", d)
redraw_plot(d)
+ setBDData(d[0], d[1])
+ showBDButton()
)
# x-axis labels
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index 014bf59b..c6d1045c 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -1,8 +1,8 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.10.0
var lodchart;
lodchart = function() {
- var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
+ var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
width = 800;
height = 500;
margin = {
@@ -20,6 +20,7 @@ lodchart = function() {
};
titlepos = 20;
manhattanPlot = false;
+ additive = false;
ylim = null;
additive_ylim = null;
nyticks = 5;
@@ -29,8 +30,7 @@ lodchart = function() {
darkrect = "#F1F1F9";
lightrect = "#FBFBFF";
lodlinecolor = "darkslateblue";
- additivelinecolor_plus = "red";
- additivelinecolor_negative = "green";
+ additivelinecolor = "red";
linewidth = 2;
suggestivecolor = "gainsboro";
significantcolor = "#EBC7C7";
@@ -70,15 +70,14 @@ lodchart = function() {
return results;
})();
ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
-
- if ('additive' in data) {
+ if (additive) {
data['additive'] = (function() {
var j, len, ref, results;
ref = data['additive'];
results = [];
for (j = 0, len = ref.length; j < len; j++) {
x = ref[j];
- results.push(x);
+ results.push(Math.abs(x));
}
return results;
})();
@@ -92,12 +91,12 @@ lodchart = function() {
g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
yticks = yticks != null ? yticks : yscale.ticks(nyticks);
- if ('additive' in data) {
+ if (additive) {
additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]);
additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks);
}
reorgLodData(data, lodvarname);
- data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale);
+ data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
xscale = data.xscale;
chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
return "chrrect" + d[0];
@@ -118,7 +117,9 @@ lodchart = function() {
return lightrect;
}).attr("stroke", "none").on("click", function(d) {
console.log("d is:", d);
- return redraw_plot(d);
+ redraw_plot(d);
+ setBDData(d[0], d[1]);
+ return showBDButton();
});
xaxis = g.append("g").attr("class", "x axis");
xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) {
@@ -133,7 +134,7 @@ lodchart = function() {
var chr_plot;
$('#topchart').remove();
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
- return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale);
+ return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot);
};
rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
yaxis = g.append("g").attr("class", "y axis");
@@ -148,7 +149,7 @@ lodchart = function() {
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) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue");
- if ('additive' in data) {
+ if (additive) {
rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1;
additive_yaxis = g.append("g").attr("class", "y axis");
additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) {
@@ -187,19 +188,13 @@ lodchart = function() {
return yscale(data.lodByChr[chr][i][lodcolumn]);
});
};
- if ('additive' in data) {
+ if (additive) {
additivecurve = function(chr, lodcolumn) {
- if (data.additiveByChr[chr][0] < 0) {
- pos_neg = "negative"
- }
- else {
- pos_neg = "positive"
- }
- return [pos_neg, d3.svg.line().x(function(d) {
+ return d3.svg.line().x(function(d) {
return xscale[chr](d);
}).y(function(d, i) {
- return additive_yscale(Math.abs(data.additiveByChr[chr][i]));
- })];
+ return additive_yscale(data.additiveByChr[chr][i][lodcolumn]);
+ });
};
}
curves = g.append("g").attr("id", "curves");
@@ -210,17 +205,12 @@ lodchart = function() {
curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
}
}
- if ('additive' in data) {
+ if (additive) {
ref1 = data.chrnames;
for (k = 0, len1 = ref1.length; k < len1; k++) {
chr = ref1[k];
if (chr.indexOf(data['chr'])) {
- if (additivecurve(chr[0], lodvarnum)[0] == "negative") {
- curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_negative).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
- }
- else {
- curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_plus).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
- }
+ curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
}
}
}
@@ -305,13 +295,6 @@ lodchart = function() {
manhattanPlot = value;
return chart;
};
- chart.mappingScale = function(value) {
- if (!arguments.length) {
- return mappingScale;
- }
- mappingScale = value;
- return chart;
- };
chart.ylim = function(value) {
if (!arguments.length) {
return ylim;
@@ -449,6 +432,9 @@ lodchart = function() {
chart.yscale = function() {
return yscale;
};
+ chart.additive = function() {
+ return additive;
+ };
chart.additive_yscale = function() {
return additive_yscale;
};
@@ -470,4 +456,4 @@ lodchart = function() {
return chrSelect;
};
return chart;
-}; \ No newline at end of file
+};
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 978ea55f..efb80494 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -160,8 +160,23 @@
</div>
{% if mapping_method != "gemma" %}
<div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
- <div id="chart_container">
- <div class="qtlcharts" id="topchart"></div>
+ <div id="chart_container">
+ <div id="return_to_full_view" style="display:none">
+ Return to full view
+ </div>
+
+ <div id="open_bd" style="display:none">
+ Open BioDalliance view
+ </div>
+
+ <div id="close_bd" style="display:none">
+ Return to vector map
+ </div>
+
+ <div class="qtlcharts" id="topchart"></div>
+
+ <div id="bd_container" class="qtlcharts">
+ </div>
</div>
</div>
{% endif %}
@@ -269,10 +284,15 @@
<script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
+
+ <script language="javascript" type="text/javascript" src="/dalliance/dalliance-all.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/biodalliance.js"></script>
{% endif %}
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
+ setBDSpecies("{{ dataset.group.species }}");
+
console.time("Creating table");
$('#qtl_results').dataTable( {
"columns": [
@@ -316,9 +336,27 @@
});
$('#gn1_map_tab').click(function(){
- $('div#gn1_map_options').show();
+ $('#gn1_map_options').show();
+ $('div#bd_container').hide();
});
+ $('#close_bd').click(function() {
+ $('#open_bd').show();
+ $('#close_bd').hide();
+
+ $('#bd_container').hide();
+ $('#topchart').show();
+ });
+
+ $('#open_bd').click(function() {
+ $('#close_bd').show();
+ $('#open_bd').hide()
+
+ $('#topchart').hide();
+ $('#bd_container').show();
+
+ openBDBrowser();
+ })
});
chrView = function(this_chr, chr_mb_list) {
@@ -355,4 +393,3 @@
</script>
{% endblock %}
-
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 70e465d1..55efd7e4 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -106,6 +106,12 @@ def tmp_page(img_path):
img_base64 = bytesarray )
+@app.route("/dalliance/<path:filename>")
+def bd_files(filename):
+ bd_path = app.config['BIODALLIANCE_PATH']
+ return send_from_directory(bd_path, filename)
+
+
#@app.route("/data_sharing")
#def data_sharing_page():
# logger.info("In data_sharing")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 20:10:23 +0000