diff options
Diffstat (limited to 'wqflask/wqflask/static/new/javascript/panelutil.coffee')
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.coffee | 205 |
1 files changed, 205 insertions, 0 deletions
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee new file mode 100644 index 00000000..42636369 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/panelutil.coffee @@ -0,0 +1,205 @@ +# A variety of utility functions used by the different panel functions
+
+root = exports ? this
+
+# 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")
+
+# 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
+ data.posByChr[chr] = []
+ data.lodByChr[chr] = []
+ for pos,j in data.pos
+ if data.chr[j] == chr
+ 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], 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 [d3.rgb(190, 190, 190)] 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 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]
+ 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 if Array.isArray(x)
+ [x]
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