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# lodheatmap: reuseable panel with heat map of LOD curves
lodheatmap = () ->
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", "black", "yellow"]
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
## the main function
chart = (selection) ->
selection.each (data) ->
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 = {}
#console.log("data.posByChr:", data.posByChr["2"])
#console.log("data.chrnames:", data.chrnames)
for chr in data.chrnames
#console.log("posByChr:", data.posByChr)
#console.log("chr is:", chr)
xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]])
#console.log("xLR:", xLR)
# z-axis (color) limits; if not provided, make symmetric about 0
zmin = 0
zmax = 0
for lodcol in data.lodnames
extent = d3.extent(data[lodcol])
zmin = extent[0] if extent[0] < zmin
zmax = extent[1] if extent[1] > zmax
zmax = -zmin if -zmin > zmax
zlim = 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 ? zmin - 1
data.cells = []
for chr_ob in data.chrnames
chr = chr_ob[0]
#console.log("xLR[chr]:", xLR[chr])
for pos, i in data.posByChr[chr]
for lod,j in data.lodByChr[chr][i]
if lod >= zthresh or 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})
# 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)
g = svg.select("g")
# boxes
g.append("g").attr("id", "boxes").selectAll("empty")
.data(data.chrnames)
.enter()
.append("rect")
.attr("id", (d) -> "box#{d[0]}")
.attr("x", (d,i) -> data.chrStart[i])
.attr("y", (d) -> margin.top)
.attr("height", height)
.attr("width", (d,i) -> data.chrEnd[i] - data.chrStart[i])
.attr("fill", rectcolor)
.attr("stroke", "none")
# title
titlegrp = g.append("g").attr("class", "title")
.append("text")
.attr("x", margin.left + width/2)
.attr("y", margin.top - titlepos)
.text(title)
# x-axis
xaxis = g.append("g").attr("class", "x axis")
xaxis.selectAll("empty")
.data(data.chrnames)
.enter()
.append("text")
.attr("x", (d,i) -> (data.chrStart[i] + data.chrEnd[i])/2)
.attr("y", margin.top+height+axispos.xlabel)
.text((d) -> d[0])
xaxis.append("text").attr("class", "title")
.attr("x", margin.left+width/2)
.attr("y", margin.top+height+axispos.xtitle)
.text(xlab)
# y-axis
rotate_ylab = 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", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "")
yaxis.selectAll("empty")
.data(data.lodnames)
.enter()
.append("text")
.attr("id", (d,i) -> "yaxis#{i}")
.attr("y", (d,i) -> yscale(i))
.attr("x", margin.left-axispos.ylabel)
.text((d) -> d)
.attr("opacity", 0)
celltip = d3.tip()
.attr('class', 'd3-tip')
.html((d) ->
z = d3.format(".2f")(Math.abs(d.z))
p = d3.format(".1f")(d.pos)
"#{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", (d) -> d.left)
.attr("y", (d) -> yscale(d.lodindex)-rectHeight/2)
.attr("width", (d) -> d.right - d.left)
.attr("height", rectHeight)
.attr("class", (d,i) -> "cell#{i}")
.attr("fill", (d) -> zscale(d.z))
.attr("stroke", "none")
.attr("stroke-width", "1")
.on("mouseover.paneltip", (d) ->
yaxis.select("text#yaxis#{d.lodindex}").attr("opacity", 1)
d3.select(this).attr("stroke", "black")
celltip.show(d))
.on("mouseout.paneltip", (d) ->
yaxis.select("text#yaxis#{d.lodindex}").attr("opacity", 0)
d3.select(this).attr("stroke", "none")
celltip.hide())
# boxes
g.append("g").attr("id", "boxes").selectAll("empty")
.data(data.chrnames)
.enter()
.append("rect")
.attr("id", (d) -> "box#{d}")
.attr("x", (d,i) -> data.chrStart[i])
.attr("y", (d) -> margin.top)
.attr("height", height)
.attr("width", (d,i) -> data.chrEnd[i] - data.chrStart[i])
.attr("fill", "none")
.attr("stroke", "black")
.attr("stroke-width", "none")
## configuration parameters
chart.width = (value) ->
return width if !arguments.length
width = value
chart
chart.height = (value) ->
return height if !arguments.length
height = value
chart
chart.margin = (value) ->
return margin if !arguments.length
margin = value
chart
chart.axispos = (value) ->
return axispos if !arguments.length
axispos = value
chart
chart.titlepos = (value) ->
return titlepos if !arguments.length
titlepos
chart
chart.rectcolor = (value) ->
return rectcolor if !arguments.length
rectcolor = value
chart
chart.colors = (value) ->
return colors if !arguments.length
colors = value
chart
chart.title = (value) ->
return title if !arguments.length
title = value
chart
chart.xlab = (value) ->
return xlab if !arguments.length
xlab = value
chart
chart.ylab = (value) ->
return ylab if !arguments.length
ylab = value
chart
chart.rotate_ylab = (value) ->
return rotate_ylab if !arguments.length
rotate_ylab = value
chart
chart.zthresh = (value) ->
return zthresh if !arguments.length
zthresh = value
chart
chart.zlim = (value) ->
return zlim if !arguments.length
zlim = value
chart
chart.chrGap = (value) ->
return chrGap if !arguments.length
chrGap = value
chart
chart.xscale = () ->
return xscale
chart.yscale = () ->
return yscale
chart.zscale = () ->
return zscale
chart.cellSelect = () ->
return cellSelect
# return the chart function
chart
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