diff options
Diffstat (limited to 'wqflask/wqflask/static/new/javascript/panelutil.coffee')
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.coffee | 712 |
1 files changed, 356 insertions, 356 deletions
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee index d1eb83e5..a3bc0b44 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.coffee +++ b/wqflask/wqflask/static/new/javascript/panelutil.coffee @@ -1,357 +1,357 @@ -# A variety of utility functions used by the different panel functions
-
-# determine rounding of axis labels
-formatAxis = (d, extra_digits=0) ->
- d = d[1] - d[0]
- ndig = Math.floor( Math.log(d % 10) / Math.log(10) )
- ndig = 0 if ndig > 0
- ndig = Math.abs(ndig) + extra_digits
- d3.format(".#{ndig}f")
-
-# unique values of array (ignore nulls)
-unique = (x) ->
- output = {}
- output[v] = v for v in x when v
- output[v] for v of output
-
-# Pull out a variable (column) from a two-dimensional array
-pullVarAsArray = (data, variable) ->
- v = []
- for i of data
- v = v.concat data[i][variable]
- v
-
-
-# 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
- #console.log("chr:", chr)
- data.posByChr[chr[0]] = []
- data.lodByChr[chr[0]] = []
- for pos, j in data.pos
- if data.chr[j].toString() == chr[0]
- #console.log(data.chr[j] + " AND " + 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)
-
- #console.log("data.posByChr:", data.posByChr)
-
- 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
-
-
-# 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 = {}
-#
-# #console.log("data.chr", data.chr)
-# #console.log("data.chrnames:", data.chrnames)
-# the_chr = "0"
-# for chr,i in data.chrnames
-# data.posByChr[chr] = []
-# data.lodByChr[chr] = []
-# for pos,j in data.pos
-# console.log("data.chr[j][0]:", data.chr[j][0])
-# if data.chr[j][0] == chr
-# console.log("IS EQUAL")
-# data.posByChr[chr].push(pos)
-# data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)
-# lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)
-# data.lodByChr[chr].push(lodval)
-#
-# if lodvarname?
-# data.markers = []
-# for marker,i in data.markernames
-# if marker != ""
-# data.markers.push({name:marker, chr:data.chr[i][0], 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])
-# maxd = d if d > maxd
-#
-# rng = d3.extent(data.posByChr[chr])
-# 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] = d3.scale.linear()
-# .domain([chrStart[i], chrEnd[i]])
-# .range([data.chrStart[i], data.chrEnd[i]])
-#
-# # return data with new stuff added
-# data
-
-# Select a set of categorical colors
-# ngroup is positive integer
-# palette = "dark" or "pastel"
-selectGroupColors = (ngroup, palette) ->
- return [] if ngroup == 0
-
- if palette == "dark"
- return ["slateblue"] if ngroup == 1
- return ["MediumVioletRed", "slateblue"] if ngroup == 2
- return colorbrewer.Set1[ngroup] if ngroup <= 9
- return d3.scale.category20().range()[0...ngroup]
- else
- return ["#bebebe"] if ngroup == 1
- return ["lightpink", "lightblue"] if ngroup == 2
- return colorbrewer.Pastel1[ngroup] if ngroup <= 9
- # below is rough attempt to make _big_ pastel palette
- return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8",
- "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6",
- "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4",
- "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7",
- "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"][0...ngroup]
-
-# expand element/array (e.g., of colors) to a given length
-# single elment -> array, then repeated to length n
-expand2vector = (input, n) ->
- return input unless input? # return null if null
- return input if Array.isArray(input) and input.length >= n
- input = [input] unless Array.isArray(input)
- input = (input[0] for i of d3.range(n)) if input.length == 1 and n > 1
- input
-
-# median of a vector
-median = (x) ->
- return null if !x?
- n = x.length
- x.sort((a,b) -> a-b)
- if n % 2 == 1
- return x[(n-1)/2]
- (x[n/2] + x[(n/2)-1])/2
-
-# given a vector of x's, return hash with values to left and right, and the differences
-getLeftRight = (x) ->
- n = x.length
- x.sort( (a,b) -> a-b )
-
- xdif = []
- result = {}
- for v in x
- result[v] = {}
-
- for i in [1...n]
- #console.log("result:", result)
- xdif.push(x[i]-x[i-1])
- result[x[i]].left = x[i-1]
- for i in [0...(n-1)]
- result[x[i]].right = x[i+1]
-
- xdif = median(xdif)
- result.mediandiff = xdif
-
- result[x[0]].left = x[0]-xdif
- result[x[n-1]].right = x[n-1]+xdif
- result.extent = [x[0]-xdif/2, x[n-1]+xdif/2]
-
- result
-
-# 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
-
-# matrix extent, min max
-matrixMin = (mat) ->
- result = mat[0][0]
- for i of mat
- for j of mat[i]
- result = mat[i][j] if result > mat[i][j]
- result
-
-matrixMax = (mat) ->
- result = mat[0][0]
- for i of mat
- for j of mat[i]
- result = mat[i][j] if result < mat[i][j]
- result
-
-matrixMaxAbs = (mat) ->
- result = Math.abs(mat[0][0])
- for i of mat
- for j of mat[i]
- result = Math.abs(mat[i][j]) if result < mat[i][j]
- result
-
-matrixExtent = (mat) -> [matrixMin(mat), matrixMax(mat)]
-
-d3.selection.prototype.moveToFront = () ->
- this.each () -> this.parentNode.appendChild(this)
-
-d3.selection.prototype.moveToBack = () ->
- this.each () ->
- firstChild = this.parentNode.firstchild
- this.parentNode.insertBefore(this, firstChild) if firstChild
-
-forceAsArray = (x) ->
- return x unless x? # if null, return null
- return x if Array.isArray(x)
- [x]
-
-# any values in vec that appear in missing are made null
-missing2null = (vec, missingvalues=['NA', '']) ->
- vec.map (value) -> if missingvalues.indexOf(value) > -1 then null else value
-
-# display error at top of page
-displayError = (message) ->
- if d3.select("div.error").empty() # no errors yet
- d3.select("body")
- .insert("div", ":first-child")
- .attr("class", "error")
- d3.select("div.error")
- .append("p")
- .text(message)
-
-# sum values in an array
-sumArray = (vec) -> (vec.reduce (a,b) -> a+b)
-
-# calculate cross-tabulation
-calc_crosstab = (data) ->
- nrow = data.ycat.length
- ncol = data.xcat.length
-
- result = ((0 for col in [0..ncol]) for row in [0..nrow]) # matrix of 0's
-
- # count things up
- for i of data.x
- result[data.y[i]][data.x[i]] += 1
-
- # row and column sums
- rs = rowSums(result)
- cs = colSums(result)
-
- # fill in column sums
- for i in [0...ncol]
- result[nrow][i] = cs[i]
-
- # fill in row sums
- for i in [0...nrow]
- result[i][ncol] = rs[i]
-
- # fill in total
- result[nrow][ncol] = sumArray(rs)
-
- result
-
-# rowSums: the sums for each row
-rowSums = (mat) -> (sumArray(x) for x in mat)
-
-# transpose: matrix transpose
-transpose = (mat) -> ((mat[i][j] for i in [0...mat.length]) for j in [0...mat[0].length])
-
-# colSums = the sums for each column
-colSums = (mat) -> rowSums(transpose(mat))
-
-# log base 2
-log2 = (x) ->
- return(x) unless x?
- Math.log(x)/Math.log(2.0)
-
-# log base 10
-log10 = (x) ->
- return(x) unless x?
- Math.log(x)/Math.log(10.0)
-
-# absolute value, preserving nulls
-abs = (x) ->
- return(x) unless x?
+# A variety of utility functions used by the different panel functions + +# determine rounding of axis labels +formatAxis = (d, extra_digits=0) -> + d = d[1] - d[0] + ndig = Math.floor( Math.log(d % 10) / Math.log(10) ) + ndig = 0 if ndig > 0 + ndig = Math.abs(ndig) + extra_digits + d3.format(".#{ndig}f") + +# unique values of array (ignore nulls) +unique = (x) -> + output = {} + output[v] = v for v in x when v + output[v] for v of output + +# Pull out a variable (column) from a two-dimensional array +pullVarAsArray = (data, variable) -> + v = [] + for i of data + v = v.concat data[i][variable] + v + + +# 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 + #console.log("chr:", chr) + data.posByChr[chr[0]] = [] + data.lodByChr[chr[0]] = [] + for pos, j in data.pos + if data.chr[j].toString() == chr[0] + #console.log(data.chr[j] + " AND " + 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) + + #console.log("data.posByChr:", data.posByChr) + + 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 + + +# 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 = {} +# +# #console.log("data.chr", data.chr) +# #console.log("data.chrnames:", data.chrnames) +# the_chr = "0" +# for chr,i in data.chrnames +# data.posByChr[chr] = [] +# data.lodByChr[chr] = [] +# for pos,j in data.pos +# console.log("data.chr[j][0]:", data.chr[j][0]) +# if data.chr[j][0] == chr +# console.log("IS EQUAL") +# data.posByChr[chr].push(pos) +# data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames) +# lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) +# data.lodByChr[chr].push(lodval) +# +# if lodvarname? +# data.markers = [] +# for marker,i in data.markernames +# if marker != "" +# data.markers.push({name:marker, chr:data.chr[i][0], 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]) +# maxd = d if d > maxd +# +# rng = d3.extent(data.posByChr[chr]) +# 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] = d3.scale.linear() +# .domain([chrStart[i], chrEnd[i]]) +# .range([data.chrStart[i], data.chrEnd[i]]) +# +# # return data with new stuff added +# data + +# Select a set of categorical colors +# ngroup is positive integer +# palette = "dark" or "pastel" +selectGroupColors = (ngroup, palette) -> + return [] if ngroup == 0 + + if palette == "dark" + return ["slateblue"] if ngroup == 1 + return ["MediumVioletRed", "slateblue"] if ngroup == 2 + return colorbrewer.Set1[ngroup] if ngroup <= 9 + return d3.scale.category20().range()[0...ngroup] + else + return ["#bebebe"] if ngroup == 1 + return ["lightpink", "lightblue"] if ngroup == 2 + return colorbrewer.Pastel1[ngroup] if ngroup <= 9 + # below is rough attempt to make _big_ pastel palette + return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", + "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", + "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", + "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", + "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"][0...ngroup] + +# expand element/array (e.g., of colors) to a given length +# single elment -> array, then repeated to length n +expand2vector = (input, n) -> + return input unless input? # return null if null + return input if Array.isArray(input) and input.length >= n + input = [input] unless Array.isArray(input) + input = (input[0] for i of d3.range(n)) if input.length == 1 and n > 1 + input + +# median of a vector +median = (x) -> + return null if !x? + n = x.length + x.sort((a,b) -> a-b) + if n % 2 == 1 + return x[(n-1)/2] + (x[n/2] + x[(n/2)-1])/2 + +# given a vector of x's, return hash with values to left and right, and the differences +getLeftRight = (x) -> + n = x.length + x.sort( (a,b) -> a-b ) + + xdif = [] + result = {} + for v in x + result[v] = {} + + for i in [1...n] + #console.log("result:", result) + xdif.push(x[i]-x[i-1]) + result[x[i]].left = x[i-1] + for i in [0...(n-1)] + result[x[i]].right = x[i+1] + + xdif = median(xdif) + result.mediandiff = xdif + + result[x[0]].left = x[0]-xdif + result[x[n-1]].right = x[n-1]+xdif + result.extent = [x[0]-xdif/2, x[n-1]+xdif/2] + + result + +# 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 + +# matrix extent, min max +matrixMin = (mat) -> + result = mat[0][0] + for i of mat + for j of mat[i] + result = mat[i][j] if result > mat[i][j] + result + +matrixMax = (mat) -> + result = mat[0][0] + for i of mat + for j of mat[i] + result = mat[i][j] if result < mat[i][j] + result + +matrixMaxAbs = (mat) -> + result = Math.abs(mat[0][0]) + for i of mat + for j of mat[i] + result = Math.abs(mat[i][j]) if result < mat[i][j] + result + +matrixExtent = (mat) -> [matrixMin(mat), matrixMax(mat)] + +d3.selection.prototype.moveToFront = () -> + this.each () -> this.parentNode.appendChild(this) + +d3.selection.prototype.moveToBack = () -> + this.each () -> + firstChild = this.parentNode.firstchild + this.parentNode.insertBefore(this, firstChild) if firstChild + +forceAsArray = (x) -> + return x unless x? # if null, return null + return x if Array.isArray(x) + [x] + +# any values in vec that appear in missing are made null +missing2null = (vec, missingvalues=['NA', '']) -> + vec.map (value) -> if missingvalues.indexOf(value) > -1 then null else value + +# display error at top of page +displayError = (message) -> + if d3.select("div.error").empty() # no errors yet + d3.select("body") + .insert("div", ":first-child") + .attr("class", "error") + d3.select("div.error") + .append("p") + .text(message) + +# sum values in an array +sumArray = (vec) -> (vec.reduce (a,b) -> a+b) + +# calculate cross-tabulation +calc_crosstab = (data) -> + nrow = data.ycat.length + ncol = data.xcat.length + + result = ((0 for col in [0..ncol]) for row in [0..nrow]) # matrix of 0's + + # count things up + for i of data.x + result[data.y[i]][data.x[i]] += 1 + + # row and column sums + rs = rowSums(result) + cs = colSums(result) + + # fill in column sums + for i in [0...ncol] + result[nrow][i] = cs[i] + + # fill in row sums + for i in [0...nrow] + result[i][ncol] = rs[i] + + # fill in total + result[nrow][ncol] = sumArray(rs) + + result + +# rowSums: the sums for each row +rowSums = (mat) -> (sumArray(x) for x in mat) + +# transpose: matrix transpose +transpose = (mat) -> ((mat[i][j] for i in [0...mat.length]) for j in [0...mat[0].length]) + +# colSums = the sums for each column +colSums = (mat) -> rowSums(transpose(mat)) + +# log base 2 +log2 = (x) -> + return(x) unless x? + Math.log(x)/Math.log(2.0) + +# log base 10 +log10 = (x) -> + return(x) unless x? + Math.log(x)/Math.log(10.0) + +# absolute value, preserving nulls +abs = (x) -> + return(x) unless x? Math.abs(x)
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