diff options
Diffstat (limited to 'wqflask/wqflask/static/new/javascript/manhattan_plot.coffee')
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/manhattan_plot.coffee | 175 |
1 files changed, 88 insertions, 87 deletions
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee index 37226b8a..cc087493 100644 --- a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee +++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee @@ -32,8 +32,7 @@ lodchart = () -> ## the main function
chart = (selection) ->
selection.each (data) ->
-
- console.log("data:", data)
+
lodvarname = lodvarname ? data.lodnames[0]
data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values
@@ -68,6 +67,8 @@ lodchart = () -> # 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)
@@ -206,7 +207,7 @@ lodchart = () -> markertip = d3.tip()
.attr('class', 'd3-tip')
.html((d) ->
- [d.name, " LRS = #{d3.format('.2f')(d.lod)}"])
+ [d.name, " LOD = #{d3.format('.2f')(d.lod)}"])
.direction("e")
.offset([0,10])
svg.call(markertip)
@@ -374,90 +375,90 @@ lodchart = () -> # reorganize lod/pos by chromosome
# lodvarname==null -> case for multiple LOD columns (lodheatmap)
# lodvarname provided -> case for one LOD column (lodchart)
-reorgLodData = (data, lodvarname=null) ->
- data.posByChr = {}
- data.lodByChr = {}
-
- for chr,i in data.chrnames
- data.posByChr[chr[0]] = []
- data.lodByChr[chr[0]] = []
- for pos, j in data.pos
- if data.chr[j] == chr[0]
- data.posByChr[chr[0]].push(pos)
- data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)
- lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)
- data.lodByChr[chr[0]].push(lodval)
-
-
- if lodvarname?
- data.markers = []
- for marker,i in data.markernames
- if marker != ""
- data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]})
-
- data
+#reorgLodData = (data, lodvarname=null) ->
+# data.posByChr = {}
+# data.lodByChr = {}
+#
+# for chr,i in data.chrnames
+# data.posByChr[chr[0]] = []
+# data.lodByChr[chr[0]] = []
+# for pos, j in data.pos
+# if data.chr[j] == chr[0]
+# data.posByChr[chr[0]].push(pos)
+# data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)
+# lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)
+# data.lodByChr[chr[0]].push(lodval)
+#
+#
+# if lodvarname?
+# data.markers = []
+# for marker,i in data.markernames
+# if marker != ""
+# data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]})
+#
+# data
# calculate chromosome start/end + scales, for heat map
-chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
- # start and end of chromosome positions
- chrStart = []
- chrEnd = []
- chrLength = []
- totalChrLength = 0
- maxd = 0
- for chr in data.chrnames
- d = maxdiff(data.posByChr[chr[0]])
- maxd = d if d > maxd
-
- rng = d3.extent(data.posByChr[chr[0]])
- chrStart.push(rng[0])
- chrEnd.push(rng[1])
- L = rng[1] - rng[0]
- chrLength.push(L)
- totalChrLength += L
-
- # adjust lengths for heatmap
- if pad4heatmap
- data.recwidth = maxd
- chrStart = chrStart.map (x) -> x-maxd/2
- chrEnd = chrEnd.map (x) -> x+maxd/2
- chrLength = chrLength.map (x) -> x+maxd
- totalChrLength += (chrLength.length*maxd)
-
- # break up x axis into chromosomes by length, with gaps
- data.chrStart = []
- data.chrEnd = []
- cur = leftMargin
- cur += chrGap/2 unless pad4heatmap
- data.xscale = {}
- for chr,i in data.chrnames
- data.chrStart.push(cur)
- w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])
- data.chrEnd.push(cur + w)
- cur = data.chrEnd[i] + chrGap
- # x-axis scales, by chromosome
- data.xscale[chr[0]] = d3.scale.linear()
- .domain([chrStart[i], chrEnd[i]])
- .range([data.chrStart[i], data.chrEnd[i]])
-
- # return data with new stuff added
- data
-
-# maximum difference between adjacent values in a vector
-maxdiff = (x) ->
- return null if x.length < 2
- result = x[1] - x[0]
- return result if x.length < 3
- for i in [2...x.length]
- d = x[i] - x[i-1]
- result = d if d > result
- result
-
-# determine rounding of axis labels
-formatAxis = (d) ->
- d = d[1] - d[0]
- ndig = Math.floor( Math.log(d % 10) / Math.log(10) )
- ndig = 0 if ndig > 0
- ndig = Math.abs(ndig)
- d3.format(".#{ndig}f")
+#chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
+# # start and end of chromosome positions
+# chrStart = []
+# chrEnd = []
+# chrLength = []
+# totalChrLength = 0
+# maxd = 0
+# for chr in data.chrnames
+# d = maxdiff(data.posByChr[chr[0]])
+# maxd = d if d > maxd
+#
+# rng = d3.extent(data.posByChr[chr[0]])
+# chrStart.push(rng[0])
+# chrEnd.push(rng[1])
+# L = rng[1] - rng[0]
+# chrLength.push(L)
+# totalChrLength += L
+#
+# # adjust lengths for heatmap
+# if pad4heatmap
+# data.recwidth = maxd
+# chrStart = chrStart.map (x) -> x-maxd/2
+# chrEnd = chrEnd.map (x) -> x+maxd/2
+# chrLength = chrLength.map (x) -> x+maxd
+# totalChrLength += (chrLength.length*maxd)
+#
+# # break up x axis into chromosomes by length, with gaps
+# data.chrStart = []
+# data.chrEnd = []
+# cur = leftMargin
+# cur += chrGap/2 unless pad4heatmap
+# data.xscale = {}
+# for chr,i in data.chrnames
+# data.chrStart.push(cur)
+# w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])
+# data.chrEnd.push(cur + w)
+# cur = data.chrEnd[i] + chrGap
+# # x-axis scales, by chromosome
+# data.xscale[chr[0]] = d3.scale.linear()
+# .domain([chrStart[i], chrEnd[i]])
+# .range([data.chrStart[i], data.chrEnd[i]])
+#
+# # return data with new stuff added
+# data
+#
+## maximum difference between adjacent values in a vector
+#maxdiff = (x) ->
+# return null if x.length < 2
+# result = x[1] - x[0]
+# return result if x.length < 3
+# for i in [2...x.length]
+# d = x[i] - x[i-1]
+# result = d if d > result
+# result
+#
+## determine rounding of axis labels
+#formatAxis = (d) ->
+# d = d[1] - d[0]
+# ndig = Math.floor( Math.log(d % 10) / Math.log(10) )
+# ndig = 0 if ndig > 0
+# ndig = Math.abs(ndig)
+# d3.format(".#{ndig}f")
|