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Diffstat (limited to 'wqflask/wqflask/static/new/javascript/panelutil.coffee')
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.coffee | 356 |
1 files changed, 0 insertions, 356 deletions
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee deleted file mode 100644 index f7b51457..00000000 --- a/wqflask/wqflask/static/new/javascript/panelutil.coffee +++ /dev/null @@ -1,356 +0,0 @@ -# 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 - if data.chr.indexOf(chr[0]) - data.posByChr[chr[0]] = [] - data.lodByChr[chr[0]] = [] - for pos, j in data.pos - if data.chr[j].toString() == 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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