// Generated by CoffeeScript 1.8.0
var lodheatmap;
lodheatmap = function() {
var axispos, cellSelect, chart, chrGap, colors, height, margin, rectcolor, rotate_ylab, title, titlepos, width, xlab, xscale, ylab, yscale, zlim, zscale, zthresh;
width = 1200;
height = 600;
margin = {
left: 100,
top: 40,
right: 40,
bottom: 40
};
axispos = {
xtitle: 25,
ytitle: 30,
xlabel: 5,
ylabel: 5
};
chrGap = 8;
titlepos = 20;
rectcolor = d3.rgb(230, 230, 230);
colors = ["slateblue", "white", "red"];
title = "";
xlab = "Chromosome";
ylab = "";
rotate_ylab = null;
zlim = null;
zthresh = null;
xscale = d3.scale.linear();
yscale = d3.scale.linear();
zscale = d3.scale.linear();
cellSelect = null;
chart = function(selection) {
return selection.each(function(data) {
var cells, celltip, chr, chr_ob, extent, g, gEnter, i, j, lod, lodcol, nlod, pos, rectHeight, svg, titlegrp, xLR, xaxis, yaxis, zmax, zmin, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _m, _ref, _ref1, _ref2, _ref3, _ref4;
data = reorgLodData(data);
data = chrscales(data, width, chrGap, margin.left, true);
xscale = data.xscale;
nlod = data.lodnames.length;
yscale.domain([-0.5, nlod - 0.5]).range([margin.top + height, margin.top]);
rectHeight = yscale(0) - yscale(1);
xLR = {};
_ref = data.chrnames;
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
chr = _ref[_i];
if (data.posByChr[chr[0]].length > 0){
xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]);
}
}
zmin = 0;
zmax = 0;
_ref1 = data.lodnames;
for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
lodcol = _ref1[_j];
extent = d3.extent(data[lodcol]);
if (extent[0] < zmin) {
zmin = extent[0];
}
if (extent[1] > zmax) {
zmax = extent[1];
}
}
if (-zmin > zmax) {
zmax = -zmin;
}
zlim = zlim != null ? zlim : [-zmax, 0, zmax];
if (zlim.length !== colors.length) {
console.log("zlim.length (" + zlim.length + ") != colors.length (" + colors.length + ")");
}
zscale.domain(zlim).range(colors);
zthresh = zthresh != null ? zthresh : zmin - 1;
data.cells = [];
_ref2 = data.chrnames;
for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
chr_ob = _ref2[_k];
chr = chr_ob[0];
_ref3 = data.posByChr[chr];
for (i = _l = 0, _len3 = _ref3.length; _l < _len3; i = ++_l) {
pos = _ref3[i];
_ref4 = data.lodByChr[chr][i];
for (j = _m = 0, _len4 = _ref4.length; _m < _len4; j = ++_m) {
lod = _ref4[j];
if (lod >= zthresh || lod <= -zthresh) {
data.cells.push({
z: lod,
left: (xscale[chr](pos) + xscale[chr](xLR[chr][pos].left)) / 2,
right: (xscale[chr](pos) + xscale[chr](xLR[chr][pos].right)) / 2,
lodindex: j,
chr: chr,
pos: pos
});
}
}
}
}
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("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
return "box" + d[0];
}).attr("x", function(d, i) {
return data.chrStart[i];
}).attr("y", function(d) {
return margin.top;
}).attr("height", height).attr("width", function(d, i) {
return data.chrEnd[i] - data.chrStart[i];
}).attr("fill", rectcolor).attr("stroke", "none");
titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title);
xaxis = g.append("g").attr("class", "x axis");
xaxis.selectAll("empty").data(data.chrnames).enter().append("text").attr("x", function(d, i) {
return (data.chrStart[i] + data.chrEnd[i]) / 2;
}).attr("y", margin.top + height + axispos.xlabel).text(function(d) {
return d[0];
});
xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab);
rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
yaxis = g.append("g").attr("class", "y axis");
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.selectAll("empty").data(data.lodnames).enter().append("text").attr("id", function(d, i) {
return "yaxis" + i;
}).attr("y", function(d, i) {
return yscale(i);
}).attr("x", margin.left - axispos.ylabel).text(function(d) {
return d;
}).attr("opacity", 0);
celltip = d3.tip().attr('class', 'd3-tip').html(function(d) {
var p, z;
z = d3.format(".2f")(Math.abs(d.z));
p = d3.format(".1f")(d.pos);
return "" + d.chr + "@" + p + " → " + z;
}).direction('e').offset([0, 10]);
svg.call(celltip);
cells = g.append("g").attr("id", "cells");
cellSelect = cells.selectAll("empty").data(data.cells).enter().append("rect").attr("x", function(d) {
return d.left;
}).attr("y", function(d) {
return yscale(d.lodindex) - rectHeight / 2;
}).attr("width", function(d) {
return d.right - d.left;
}).attr("height", rectHeight).attr("class", function(d, i) {
return "cell" + i;
}).attr("fill", function(d) {
return zscale(d.z);
}).attr("stroke", "none").attr("stroke-width", "1").on("mouseover.paneltip", function(d) {
yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 1);
d3.select(this).attr("stroke", "black");
return celltip.show(d, this);
}).on("mouseout.paneltip", function(d) {
yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 0);
d3.select(this).attr("stroke", "none");
return celltip.hide();
});
return g.append("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
return "box" + d;
}).attr("x", function(d, i) {
return data.chrStart[i];
}).attr("y", function(d) {
return margin.top;
}).attr("height", height).attr("width", function(d, i) {
return data.chrEnd[i] - data.chrStart[i];
}).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
});
};
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.axispos = function(value) {
if (!arguments.length) {
return axispos;
}
axispos = value;
return chart;
};
chart.titlepos = function(value) {
if (!arguments.length) {
return titlepos;
}
titlepos;
return chart;
};
chart.rectcolor = function(value) {
if (!arguments.length) {
return rectcolor;
}
rectcolor = value;
return chart;
};
chart.colors = function(value) {
if (!arguments.length) {
return colors;
}
colors = 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.zthresh = function(value) {
if (!arguments.length) {
return zthresh;
}
zthresh = value;
return chart;
};
chart.zlim = function(value) {
if (!arguments.length) {
return zlim;
}
zlim = value;
return chart;
};
chart.chrGap = function(value) {
if (!arguments.length) {
return chrGap;
}
chrGap = value;
return chart;
};
chart.xscale = function() {
return xscale;
};
chart.yscale = function() {
return yscale;
};
chart.zscale = function() {
return zscale;
};
chart.cellSelect = function() {
return cellSelect;
};
return chart;
};
