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-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
4 files changed, 33 insertions, 61 deletions
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
+};
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-28 02:08:48 +0000