// Generated by CoffeeScript 1.9.2
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;
width = 800;
height = 500;
margin = {
left: 60,
top: 40,
right: 40,
bottom: 40,
inner: 5
};
axispos = {
xtitle: 25,
ytitle: 30,
xlabel: 5,
ylabel: 5
};
titlepos = 20;
manhattanPlot = false;
ylim = null;
additive_ylim = null;
nyticks = 5;
yticks = null;
additive_yticks = null;
chrGap = 8;
darkrect = "#F1F1F9";
lightrect = "#FBFBFF";
lodlinecolor = "darkslateblue";
additivelinecolor_plus = "red";
additivelinecolor_negative = "green";
linewidth = 2;
suggestivecolor = "gainsboro";
significantcolor = "#EBC7C7";
pointcolor = "#E9CFEC";
pointsize = 0;
pointstroke = "black";
title = "";
xlab = "Chromosome";
ylab = "LRS score";
additive_ylab = "Additive Effect";
rotate_ylab = null;
yscale = d3.scale.linear();
additive_yscale = d3.scale.linear();
xscale = null;
pad4heatmap = false;
lodcurve = null;
lodvarname = null;
markerSelect = null;
chrSelect = null;
pointsAtMarkers = true;
chart = function(selection) {
return selection.each(function(data) {
var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, j, k, len, len1, lodvarnum, markerpoints, markertip, redraw_plot, ref, ref1, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis;
if (manhattanPlot === true) {
pointcolor = "darkslateblue";
pointsize = 2;
}
lodvarname = lodvarname != null ? lodvarname : data.lodnames[0];
data[lodvarname] = (function() {
var j, len, ref, results;
ref = data[lodvarname];
results = [];
for (j = 0, len = ref.length; j < len; j++) {
x = ref[j];
results.push(Math.abs(x));
}
return results;
})();
ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
if ('additive' in data) {
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);
}
return results;
})();
additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])];
}
lodvarnum = data.lodnames.indexOf(lodvarname);
svg = d3.select(this).selectAll("svg").data([data]);
gEnter = svg.enter().append("svg").append("g");
svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom);
g = svg.select("g");
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) {
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);
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];
}).attr("x", function(d, i) {
if (i === 0 && pad4heatmap) {
return data.chrStart[i];
}
return data.chrStart[i] - chrGap / 2;
}).attr("width", function(d, i) {
if ((i === 0 || i + 1 === data.chrnames.length) && pad4heatmap) {
return data.chrEnd[i] - data.chrStart[i] + chrGap / 2;
}
return data.chrEnd[i] - data.chrStart[i] + chrGap;
}).attr("y", margin.top).attr("height", height).attr("fill", function(d, i) {
if (i % 2) {
return darkrect;
}
return lightrect;
}).attr("stroke", "none").on("click", function(d) {
console.log("d is:", d);
return redraw_plot(d);
});
xaxis = g.append("g").attr("class", "x axis");
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("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).attr("fill", "slateblue").text(xlab);
redraw_plot = function(chr_ob) {
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);
};
rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
yaxis = g.append("g").attr("class", "y axis");
yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) {
return yscale(d);
}).attr("y2", function(d) {
return yscale(d);
}).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").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) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue");
if ('additive' in data) {
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) {
return additive_yscale(d);
}).attr("y2", function(d) {
return additive_yscale(d);
}).attr("x1", margin.left + width).attr("x2", margin.left + width - 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("text").attr("y", function(d) {
return additive_yscale(d);
}).attr("x", function(d) {
return margin.left + width + axispos.ylabel + 20;
}).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) + ")" : "").attr("text-anchor", "middle").attr("fill", "green");
}
if ('suggestive' in data) {
suggestive_bar = g.append("g").attr("class", "suggestive");
suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) {
return yscale(d);
}).attr("y2", function(d) {
return yscale(d);
}).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", suggestivecolor).attr("stroke-width", 5).style("pointer-events", "none");
suggestive_bar = g.append("g").attr("class", "significant");
suggestive_bar.selectAll("empty").data([data.significant]).enter().append("line").attr("y1", function(d) {
return yscale(d);
}).attr("y2", function(d) {
return yscale(d);
}).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", significantcolor).attr("stroke-width", 5).style("pointer-events", "none");
}
if (manhattanPlot === false) {
lodcurve = function(chr, lodcolumn) {
return d3.svg.line().x(function(d) {
return xscale[chr](d);
}).y(function(d, i) {
return yscale(data.lodByChr[chr][i][lodcolumn]);
});
};
if ('additive' in data) {
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 xscale[chr](d);
}).y(function(d, i) {
return additive_yscale(Math.abs(data.additiveByChr[chr][i]));
})];
};
}
curves = g.append("g").attr("id", "curves");
ref = data.chrnames;
for (j = 0, len = ref.length; j < len; j++) {
chr = ref[j];
if (chr.indexOf(data['chr'])) {
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) {
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");
}
}
}
}
}
console.log("before pointsize");
if (pointsize > 0) {
console.log("pointsize > 0 !!!");
}
markerpoints = g.append("g").attr("id", "markerpoints_visible");
markerpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
return xscale[d.chr](d.pos);
}).attr("cy", function(d) {
return yscale(d.lod);
}).attr("r", pointsize).attr("fill", pointcolor).attr("stroke", pointstroke).attr("pointer-events", "hidden");
titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title);
g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", function() {
if (pad4heatmap) {
return data.chrEnd.slice(-1)[0] - margin.left;
}
return data.chrEnd.slice(-1)[0] - margin.left + chrGap / 2;
}).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
if (pointsAtMarkers) {
hiddenpoints = g.append("g").attr("id", "markerpoints_hidden");
markertip = d3.tip().attr('class', 'd3-tip').html(function(d) {
return [d.name, " LRS = " + (d3.format('.2f')(d.lod))];
}).direction("e").offset([0, 10]);
svg.call(markertip);
return markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
return xscale[d.chr](d.pos);
}).attr("cy", function(d) {
return yscale(d.lod);
}).attr("id", function(d) {
return d.name;
}).attr("r", d3.max([pointsize * 2, 3])).attr("opacity", 0).attr("fill", pointcolor).attr("stroke", pointstroke).attr("stroke-width", "1").on("mouseover.paneltip", function(d) {
d3.select(this).attr("opacity", 1);
return markertip.show(d);
}).on("mouseout.paneltip", function() {
return d3.select(this).attr("opacity", 0).call(markertip.hide);
});
}
});
};
chart.width = function(value) {
if (!arguments.length) {
return width;
}
width = value;
return chart;
};
chart.height = function(value) {
if (!arguments.length) {
return height;
}
height = value;
return chart;
};
chart.margin = function(value) {
if (!arguments.length) {
return margin;
}
margin = value;
return chart;
};
chart.titlepos = function(value) {
if (!arguments.length) {
return titlepos;
}
titlepos;
return chart;
};
chart.axispos = function(value) {
if (!arguments.length) {
return axispos;
}
axispos = value;
return chart;
};
chart.manhattanPlot = function(value) {
if (!arguments.length) {
return manhattanPlot;
}
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;
}
ylim = value;
return chart;
};
chart.additive_ylim = function(value) {
if (!arguments.length) {
return additive_ylim;
}
additive_ylim = value;
return chart;
};
chart.nyticks = function(value) {
if (!arguments.length) {
return nyticks;
}
nyticks = value;
return chart;
};
chart.yticks = function(value) {
if (!arguments.length) {
return yticks;
}
yticks = value;
return chart;
};
chart.chrGap = function(value) {
if (!arguments.length) {
return chrGap;
}
chrGap = value;
return chart;
};
chart.darkrect = function(value) {
if (!arguments.length) {
return darkrect;
}
darkrect = value;
return chart;
};
chart.lightrect = function(value) {
if (!arguments.length) {
return lightrect;
}
lightrect = value;
return chart;
};
chart.linecolor = function(value) {
var linecolor;
if (!arguments.length) {
return linecolor;
}
linecolor = value;
return chart;
};
chart.linewidth = function(value) {
if (!arguments.length) {
return linewidth;
}
linewidth = value;
return chart;
};
chart.pointcolor = function(value) {
if (!arguments.length) {
return pointcolor;
}
pointcolor = value;
return chart;
};
chart.pointsize = function(value) {
if (!arguments.length) {
return pointsize;
}
pointsize = value;
return chart;
};
chart.pointstroke = function(value) {
if (!arguments.length) {
return pointstroke;
}
pointstroke = value;
return chart;
};
chart.title = function(value) {
if (!arguments.length) {
return title;
}
title = value;
return chart;
};
chart.xlab = function(value) {
if (!arguments.length) {
return xlab;
}
xlab = value;
return chart;
};
chart.ylab = function(value) {
if (!arguments.length) {
return ylab;
}
ylab = value;
return chart;
};
chart.rotate_ylab = function(value) {
if (!arguments.length) {
return rotate_ylab;
}
rotate_ylab = value;
return chart;
};
chart.lodvarname = function(value) {
if (!arguments.length) {
return lodvarname;
}
lodvarname = value;
return chart;
};
chart.pad4heatmap = function(value) {
if (!arguments.length) {
return pad4heatmap;
}
pad4heatmap = value;
return chart;
};
chart.pointsAtMarkers = function(value) {
if (!arguments.length) {
return pointsAtMarkers;
}
pointsAtMarkers = value;
return chart;
};
chart.yscale = function() {
return yscale;
};
chart.additive_yscale = function() {
return additive_yscale;
};
chart.xscale = function() {
return xscale;
};
if (manhattanPlot === false) {
chart.lodcurve = function() {
return lodcurve;
};
}
chart.additivecurve = function() {
return additivecurve;
};
chart.markerSelect = function() {
return markerSelect;
};
chart.chrSelect = function() {
return chrSelect;
};
return chart;
};
