diff options
Diffstat (limited to 'wqflask/wqflask/static/new/javascript/manhattan_plot.coffee')
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/manhattan_plot.coffee | 372 |
1 files changed, 0 insertions, 372 deletions
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee deleted file mode 100644 index d637183d..00000000 --- a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee +++ /dev/null @@ -1,372 +0,0 @@ -lodchart = () -> - 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 - ylim = null - nyticks = 5 - yticks = null - chrGap = 8 - darkrect = "#F1F1F9" - lightrect = "#FBFBFF" - lodlinecolor = "darkslateblue" - linewidth = 2 - pointcolor = "darkslateblue" # pink - pointhover = "#E9CFEC" # pink - pointsize = 2 # default = no visible points at markers - pointstroke = "black" - title = "" - xlab = "Chromosome" - ylab = "LOD score" - rotate_ylab = null - yscale = d3.scale.linear() - xscale = null - pad4heatmap = false - lodcurve = null - lodvarname = null - markerSelect = null - chrSelect = null - pointsAtMarkers = true - - ## the main function - chart = (selection) -> - selection.each (data) -> - - - lodvarname = lodvarname ? data.lodnames[0] - data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values - ylim = ylim ? [0, d3.max(data[lodvarname])] - lodvarnum = data.lodnames.indexOf(lodvarname) - - # 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) - - # Update the inner dimensions. - g = svg.select("g") - - # box - 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]) - - # if yticks not provided, use nyticks to choose pretty ones - yticks = yticks ? yscale.ticks(nyticks) - - console.log("data:", data) - - # reorganize lod,pos by chromosomes - data = reorgLodData(data, lodvarname) - - # add chromosome scales (for x-axis) - data = chrscales(data, width, chrGap, margin.left, pad4heatmap) - xscale = data.xscale - - # chr rectangles - chrSelect = - g.append("g").attr("class", "chrRect") - .selectAll("empty") - .data(data.chrnames) - .enter() - .append("rect") - .attr("id", (d) -> "chrrect#{d[0]}") - .attr("x", (d,i) -> - return data.chrStart[i] if i==0 and pad4heatmap - data.chrStart[i]-chrGap/2) - .attr("width", (d,i) -> - return data.chrEnd[i] - data.chrStart[i]+chrGap/2 if (i==0 or i+1 == data.chrnames.length) and pad4heatmap - data.chrEnd[i] - data.chrStart[i]+chrGap) - .attr("y", margin.top) - .attr("height", height) - .attr("fill", (d,i) -> - return darkrect if i % 2 - lightrect) - .attr("stroke", "none") - .on("click", (d) -> - redraw_plot(d) - ) - - # x-axis labels - xaxis = g.append("g").attr("class", "x axis") - xaxis.selectAll("empty") - .data(data.chrnames) - .enter() - .append("text") - .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) - ) - - 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") - 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+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", (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") - .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 "") - .attr("text-anchor", "middle") - .attr("fill", "slateblue") - - - # points at markers - if pointsize > 0 - markerpoints = g.append("g").attr("id", "markerpoints_visible") - markerpoints.selectAll("empty") - .data(data.markers) - .enter() - .append("circle") - .attr("cx", (d) -> xscale[d.chr](d.pos)) - .attr("cy", (d) -> yscale(d.lod)) - .attr("r", pointsize) - .attr("fill", pointcolor) - .attr("stroke", pointstroke) - .attr("pointer-events", "hidden") - - # title - titlegrp = g.append("g").attr("class", "title") - .append("text") - .attr("x", margin.left+width/2) - .attr("y", margin.top-titlepos) - .text(title) - - # another box around edge - g.append("rect") - .attr("x", margin.left) - .attr("y", margin.top) - .attr("height", height) - .attr("width", () -> - return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap - data.chrEnd[-1..][0]-margin.left+chrGap/2) - .attr("fill", "none") - .attr("stroke", "black") - .attr("stroke-width", "none") - - if pointsAtMarkers - # these hidden points are what gets selected...a bit larger - hiddenpoints = g.append("g").attr("id", "markerpoints_hidden") - - markertip = d3.tip() - .attr('class', 'd3-tip') - .html((d) -> - [d.name, " LOD = #{d3.format('.2f')(d.lod)}"]) - .direction("e") - .offset([0,10]) - svg.call(markertip) - - markerSelect = - hiddenpoints.selectAll("empty") - .data(data.markers) - .enter() - .append("circle") - .attr("cx", (d) -> xscale[d.chr](d.pos)) - .attr("cy", (d) -> yscale(d.lod)) - .attr("id", (d) -> d.name) - .attr("r", d3.max([pointsize*2, 3])) - .attr("opacity", 0) - .attr("fill", pointhover) - .attr("stroke", pointstroke) - .attr("stroke-width", "1") - .on "mouseover.paneltip", (d) -> - d3.select(this).attr("opacity", 1) - markertip.show(d) - .on "mouseout.paneltip", -> - d3.select(this).attr("opacity", 0) - .call(markertip.hide) - - ## configuration parameters - chart.width = (value) -> - return width unless arguments.length - width = value - chart - - chart.height = (value) -> - return height unless arguments.length - height = value - chart - - chart.margin = (value) -> - return margin unless arguments.length - margin = value - chart - - chart.titlepos = (value) -> - return titlepos unless arguments.length - titlepos - chart - - chart.axispos = (value) -> - return axispos unless arguments.length - axispos = value - chart - - chart.ylim = (value) -> - return ylim unless arguments.length - ylim = value - chart - - chart.nyticks = (value) -> - return nyticks unless arguments.length - nyticks = value - chart - - chart.yticks = (value) -> - return yticks unless arguments.length - yticks = value - chart - - chart.chrGap = (value) -> - return chrGap unless arguments.length - chrGap = value - chart - - chart.darkrect = (value) -> - return darkrect unless arguments.length - darkrect = value - chart - - chart.lightrect = (value) -> - return lightrect unless arguments.length - lightrect = value - chart - - chart.linecolor = (value) -> - return linecolor unless arguments.length - linecolor = value - chart - - chart.linewidth = (value) -> - return linewidth unless arguments.length - linewidth = value - chart - - chart.pointcolor = (value) -> - return pointcolor unless arguments.length - pointcolor = value - chart - - chart.pointhover = (value) -> - return pointhover unless arguments.length - pointhover = value - chart - - chart.pointsize = (value) -> - return pointsize unless arguments.length - pointsize = value - chart - - chart.pointstroke = (value) -> - return pointstroke unless arguments.length - pointstroke = value - chart - - chart.title = (value) -> - return title unless arguments.length - title = value - chart - - chart.xlab = (value) -> - return xlab unless arguments.length - xlab = value - chart - - chart.ylab = (value) -> - return ylab unless arguments.length - ylab = value - chart - - chart.rotate_ylab = (value) -> - return rotate_ylab if !arguments.length - rotate_ylab = value - chart - - chart.lodvarname = (value) -> - return lodvarname unless arguments.length - lodvarname = value - chart - - chart.pad4heatmap = (value) -> - return pad4heatmap unless arguments.length - pad4heatmap = value - chart - - chart.pointsAtMarkers = (value) -> - return pointsAtMarkers unless arguments.length - pointsAtMarkers = value - chart - - chart.yscale = () -> - return yscale - - chart.xscale = () -> - return xscale - - #chart.lodcurve = () -> - # return lodcurve - - chart.markerSelect = () -> - return markerSelect - - chart.chrSelect = () -> - return chrSelect - - # return the chart function - chart |