diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/data_set.py | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/create_lodchart.coffee | 174 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.coffee | 712 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/base.html | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/collections/view.html | 35 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page.html | 20 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/new_security/login_user.html | 34 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait.html | 21 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_details.html | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_progress_bar.html | 39 |
13 files changed, 554 insertions, 497 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 685cd648..7e187802 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -79,7 +79,7 @@ class Dataset_Types(object): def __init__(self): self.datasets = {} - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" + file_name = "/home/zas1024/gene/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 7f215d9b..60221c05 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -513,7 +513,7 @@ class MarkerRegression(object): p_value = float(line_list[-1]) if threshold_p_value >= 0 and threshold_p_value <= 1: if p_value < threshold_p_value: - p_value_dict[snp] = p_value + p_value_dict[snp] = float(p_value) if plink_results.has_key(chr_name): value_list = plink_results[chr_name] diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee index 2d5e3acb..76be5490 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee @@ -1,87 +1,87 @@ -create_manhattan_plot = -> - h = 500 - w = 1200 - margin = {left:60, top:40, right:40, bottom: 40, inner:5} - halfh = (h+margin.top+margin.bottom) - totalh = halfh*2 - totalw = (w+margin.left+margin.right) - if 'additive' of js_data - additive = js_data.additive - else - additive = false - - console.log("js_data:", js_data) - - # simplest use - #d3.json "data.json", (data) -> - mychart = lodchart().lodvarname("lod.hk") - .height(h) - .width(w) - .margin(margin) - .ylab("LOD score") - .manhattanPlot(js_data.manhattan_plot) - #.additive(additive) - - data = js_data.json_data - - d3.select("div#topchart") - .datum(data) - .call(mychart) - - # grab chromosome rectangles; color pink on hover - chrrect = mychart.chrSelect() - chrrect.on "mouseover", -> - d3.select(this).attr("fill", "#E9CFEC") - .on "mouseout", (d,i) -> - d3.select(this).attr("fill", -> - return "#F1F1F9" if i % 2 - "#FBFBFF") - - # animate points at markers on click - mychart.markerSelect() - .on "click", (d) -> - r = d3.select(this).attr("r") - d3.select(this) - .transition().duration(500).attr("r", r*3) - .transition().duration(500).attr("r", r) - -create_manhattan_plot() - -$("#export").click => - #Get d3 SVG element - svg = $("#topchart").find("svg")[0] - - #Extract SVG text string - svg_xml = (new XMLSerializer).serializeToString(svg) - console.log("svg_xml:", svg_xml) - - #Set filename - filename = "manhattan_plot_" + js_data.this_trait - - #Make a form with the SVG data - form = $("#exportform") - form.find("#data").val(svg_xml) - form.find("#filename").val(filename) - form.submit() - -$("#export_pdf").click => - - #$('#topchart').remove() - #$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>') - #create_interval_map() - - #Get d3 SVG element - svg = $("#topchart").find("svg")[0] - - #Extract SVG text string - svg_xml = (new XMLSerializer).serializeToString(svg) - console.log("svg_xml:", svg_xml) - - #Set filename - filename = "manhattan_plot_" + js_data.this_trait - - #Make a form with the SVG data - form = $("#exportpdfform") - form.find("#data").val(svg_xml) - form.find("#filename").val(filename) - form.submit() +create_manhattan_plot = -> + h = 500 + w = 1200 + margin = {left:60, top:40, right:40, bottom: 40, inner:5} + halfh = (h+margin.top+margin.bottom) + totalh = halfh*2 + totalw = (w+margin.left+margin.right) + if 'additive' of js_data + additive = js_data.additive + else + additive = false + + console.log("js_data:", js_data) + + # simplest use + #d3.json "data.json", (data) -> + mychart = lodchart().lodvarname("lod.hk") + .height(h) + .width(w) + .margin(margin) + .ylab("LOD score") + .manhattanPlot(js_data.manhattan_plot) + #.additive(additive) + + data = js_data.json_data + + d3.select("div#topchart") + .datum(data) + .call(mychart) + + # grab chromosome rectangles; color pink on hover + chrrect = mychart.chrSelect() + chrrect.on "mouseover", -> + d3.select(this).attr("fill", "#E9CFEC") + .on "mouseout", (d,i) -> + d3.select(this).attr("fill", -> + return "#F1F1F9" if i % 2 + "#FBFBFF") + + # animate points at markers on click + mychart.markerSelect() + .on "click", (d) -> + r = d3.select(this).attr("r") + d3.select(this) + .transition().duration(500).attr("r", r*3) + .transition().duration(500).attr("r", r) + +create_manhattan_plot() + +$("#export").click => + #Get d3 SVG element + svg = $("#topchart").find("svg")[0] + + #Extract SVG text string + svg_xml = (new XMLSerializer).serializeToString(svg) + console.log("svg_xml:", svg_xml) + + #Set filename + filename = "manhattan_plot_" + js_data.this_trait + + #Make a form with the SVG data + form = $("#exportform") + form.find("#data").val(svg_xml) + form.find("#filename").val(filename) + form.submit() + +$("#export_pdf").click => + + #$('#topchart').remove() + #$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>') + #create_interval_map() + + #Get d3 SVG element + svg = $("#topchart").find("svg")[0] + + #Extract SVG text string + svg_xml = (new XMLSerializer).serializeToString(svg) + console.log("svg_xml:", svg_xml) + + #Set filename + filename = "manhattan_plot_" + js_data.this_trait + + #Make a form with the SVG data + form = $("#exportpdfform") + form.find("#data").val(svg_xml) + form.find("#filename").val(filename) + form.submit() 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) \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee index 8d56d04b..8b73b85d 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -134,7 +134,7 @@ $('input[name=display_all]').change(() => ) $("#pylmm_compute").click(() => - $("#progress_bar_container").modal() + $("#progress_bar_container").modal({show:true}) url = "/marker_regression" $('input[name=method]').val("pylmm") $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()) diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index e1ef8b63..92d3183a 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -132,7 +132,9 @@ $('input[name=display_all]').change((function(_this) { $("#pylmm_compute").click((function(_this) { return function() { var form_data, url; - $("#progress_bar_container").modal(); + $("#progress_bar_container").modal({ + show: true + }); url = "/marker_regression"; $('input[name=method]').val("pylmm"); $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()); diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 29fa0469..e032dfc5 100755 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -72,7 +72,7 @@ </div> <!-- Collect the nav links, forms, and other content for toggling --> - <div class="nav-collapse collapse"> + <div class="nav-collapse collapse in"> <ul class="nav navbar-nav"> <li class=""> <a href="/">Home</a> diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index eee22afe..1c94d61f 100755 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -16,14 +16,42 @@ <h2>{{ uc.name }}</h2> {% endif %} + <div class="form-group"> <form action="/collections/delete" method="post"> {% if uc %} <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> {% endif %} - <input type="submit" - class="btn btn-small btn-danger" - value="Delete this collection" /> + <div class="col-sm-2 controls"> + <input type="submit" class="btn btn-danger" value="Delete this collection" /> + </div> + </form> + <form action="/corr_matrix" method="post"> + {% if uc %} + <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> + {% endif %} + <input type="hidden" name="trait_list" id="trait_list" value= " + {% for this_trait in trait_obs %} + {{ this_trait.name }}:{{ this_trait.dataset.name }}, + {% endfor %}" > + <div class="col-sm-2 controls"> + <input type="submit" class="btn" value="Correlation Matrix" /> + </div> </form> + <form action="/heatmap" method="post"> + {% if uc %} + <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> + {% endif %} + <input type="hidden" name="trait_list" id="trait_list" value= " + {% for this_trait in trait_obs %} + {{ this_trait.name }}:{{ this_trait.dataset.name }}, + {% endfor %}" > + <div class="col-sm-2 controls"> + <input type="submit" class="btn" value="Heatmap" /> + </div> + </form> + </div> + + <!-- <form action="/corr_matrix" method="post"> {% if uc %} <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> @@ -48,6 +76,7 @@ class="btn btn-small" value="Heatmap" /> </form> + --> </div> diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 277acffa..fcaabce3 100755 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -226,8 +226,8 @@ <div class="form-group"> <label for="tfor" class="col-sm-1 control-label">Search:</label> - <div style="margin-left: 30px;" class="col-sm-6 controls"> - <input name="search_terms" type="text" class="form-control search-query" id="tfor"> + <div style="margin-left: 30px;" class="col-sm-10 controls"> + <textarea name="search_terms" rows="2" class="form-control search-query" id="tfor"></textarea> </div> </div> @@ -242,12 +242,18 @@ <!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH --> + <div class="form-group"> - <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search"> - - <input type="button" class="btn form-control btn-default" value="Make Default" id="make_default"> - - <input type="button" class="btn form-control btn-default" value="Advanced Search" onclick="javascript:window.open('/index3.html', '_self');"> + <div class="col-sm-3 controls"> + <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search"> + </div> + <div class="col-sm-4 controls"> + <input id="make_default" type="submit" class="btn btn-default form-control" value="Make Default"> + </div> + <div class="col-sm-5 controls"> + <input type="submit" class="btn btn-default form-control" value="Advanced Search"> + </div> + </div> <input type="hidden" name="FormID" value="searchResult" class="form-control"> <!--!<input type="hidden" name="RISet" value="BXD">--> diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 4e308c75..3378846a 100755 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -26,21 +26,18 @@ - <form class="form-horizontal" action="/n/login" - method="POST" name="login_user_form"> - <fieldset> - - - <div class="control-group"> - <label class="control-label" for="email_address">Email Address</label> - <div class="controls"> + <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form"> + <fieldset> + <div class="form-group"> + <label class="col-sm-2 control-label" for="email_address">Email Address</label> + <div class="col-sm-3 controls"> <input id="email_address" class="focused" name="email_address" type="text" value=""> </div> </div> - <div class="control-group"> - <label class="control-label" for="password">Password</label> - <div class="controls"> + <div class="form-group"> + <label class="col-sm-2 control-label" for="password">Password</label> + <div class="col-sm-3 controls"> <input id="password" name="password" type="password" value=""> <br /> <a href="/n/forgot_password">Forgot your password?</a><br/> @@ -48,22 +45,21 @@ </div> - <div class="control-group"> - <div class="controls"> + <div class="form-group"> + <label class="col-sm-2 control-label" for="remember"></label> + <div class="col-sm-3 controls"> <label class="checkbox"> <input id="remember" name="remember" type="checkbox" value="y"> Remember me </label> </div> + </div> - - <div class="control-group"> - <div class="controls"> + <div class="form-group"> + <label class="col-sm-2 control-label" for="submit"></label> + <div class="col-sm-3 controls"> <input id="next" name="next" type="hidden" value=""> - <input class="btn btn-primary" id="submit" name="submit" type="submit" value="Sign in"> </div> - - </div> </fieldset> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index af606600..5d0437df 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -18,13 +18,13 @@ <form method="post" action="/corr_compute" name="trait_page" id="trait_data_form" class="form-horizontal"> - <div id="hidden_inputs"> - {% for key in hddn %} - <input type="hidden" name="{{ key }}" value="{{ hddn[key] }}"> - {% endfor %} - </div> + <div id="hidden_inputs"> + {% for key in hddn %} + <input type="hidden" name="{{ key }}" value="{{ hddn[key] }}"> + {% endfor %} + </div> - <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}"> + <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}"> <div class="container"> <div class="page-header"> @@ -81,18 +81,19 @@ <div class="panel panel-default"> <div class="panel-heading"> <h3 class="panel-title"> - <a data-toggle="collapse" data-parent="#accordion" href="#collapseFour"> + <a data-toggle="collapse" data-parent="#accordion" href="#collapseFour" aria-expanded="true"> Review and Edit Data </a> </h3> </div> - <div id="collapseFour" class="panel-collapse collapse in"> + <div id="collapseFour" class="panel-collapse collapse" aria-expanded="true"> <div class="panel-body"> {% include 'show_trait_edit_data.html' %} </div> </div> </div> </div> + {% include 'show_trait_progress_bar.html' %} </div> </form> @@ -134,7 +135,7 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> - <script type="text/javascript" charset="utf-8"> + <script type="text/javascript" charset="utf-8"> function getValue(x) { if (x.indexOf('input') >= 0) { @@ -227,6 +228,6 @@ console.timeEnd("Creating table"); {% endif %} }); - </script> + </script> {% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 88fd74d9..0afac1f7 100755 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -19,11 +19,11 @@ BLAT Specifity </a> </dt> - <dd>{{ "%s" % (this_trait.probe_set_specificity) }}</dd> + <dd>{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}</dd> {% endif %} {% if this_trait.probe_set_blat_score %} <dt>BLAT Score</dt> - <dd>{{ "%s" % (this_trait.probe_set_blat_score) }}</dd> + <dd>{{ "%0.3f" | format(this_trait.probe_set_blat_score|float) }}</dd> {% endif %} </dl> diff --git a/wqflask/wqflask/templates/show_trait_progress_bar.html b/wqflask/wqflask/templates/show_trait_progress_bar.html index aebf64a4..99906338 100755 --- a/wqflask/wqflask/templates/show_trait_progress_bar.html +++ b/wqflask/wqflask/templates/show_trait_progress_bar.html @@ -1,17 +1,40 @@ -<div id="progress_bar_container" class="modal hide fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true"> - <div class="modal-header"> - <h3 id="progress_bar">Loading...</h3> +<div id="progress_bar_container" class="modal fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true"> + <div class="modal-dialog"> + <div class="modal-content"> + <div class="modal-header"> + <h3 id="progress_bar">Loading...</h3> + </div> + <div class="modal-body"> + <div class="progress"> + <div id="marker_regression_progress" class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width:0%;"> + </div> + </div> + <div id="time_remaining"> + </div> + </div> + </div> </div> - <div class="modal-body"> - <div class="progress active"> - <div id="marker_regression_progress" class="bar"></div> +</div> + +<div id="static_progress_bar_container" class="modal fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true"> + <div class="modal-dialog"> + <div class="modal-content"> + <div class="modal-header"> + <h3 id="progress_bar">Loading... (Estimated time ~10-15m)</h3> + </div> + <div class="modal-body"> + <div class="progress progress-striped active"> + <div id="marker_regression_progress" class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width:100%;"> + </div> </div> <div id="time_remaining"> </div> + </div> </div> + </div> </div> -<div id="static_progress_bar_container" class="modal hide fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true"> +<!--<div id="static_progress_bar_container" class="modal hide fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true"> <div class="modal-header"> <h3 id="progress_bar">Loading... (Estimated time ~10-15m)</h3> </div> @@ -22,4 +45,4 @@ <div id="time_remaining"> </div> </div> -</div> \ No newline at end of file +</div>--> \ No newline at end of file |