diff options
| author | Zachary Sloan | 2014-07-25 16:28:51 +0000 |
|---|---|---|
| committer | Zachary Sloan | 2014-07-25 16:28:51 +0000 |
| commit | e69c346553bc26c2f1ba8b0d9fc394add9f6784f (patch) | |
| tree | 1eec23a32cf658d303b28aaba7b4782cc9e38023 | |
| parent | b3058f8c3710c65288d88ed777aa0fcad8429aef (diff) | |
| download | genenetwork2-e69c346553bc26c2f1ba8b0d9fc394add9f6784f.tar.gz | |
Got the heatmap/lodchart combo working
Started working on getting rqtl working as another mapping method
16 files changed, 1409 insertions, 447 deletions
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 8f910fa9..0433bf17 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -55,6 +55,8 @@ class Heatmap(object): helper_functions.get_trait_db_obs(self, trait_db_list) + self.temp_uuid = temp_uuid + self.num_permutations = 5000 self.dataset = self.trait_list[0][1] self.json_data = {} #The dictionary that will be used to create the json object that contains all the data needed to create the figure @@ -86,6 +88,135 @@ class Heatmap(object): #self.sample_data[this_trait.name].append('') self.sample_data.append(this_trait_vals) + self.gen_reaper_results() + #self.gen_pylmm_results() + + chrnames = [] + lodnames = [] + chr_pos = [] + pos = [] + markernames = [] + + for trait in self.trait_results.keys(): + lodnames.append(trait) + + for marker in self.dataset.group.markers.markers: + if marker['chr'] not in chrnames: + chrnames.append(marker['chr']) + chr_pos.append(marker['chr']) + pos.append(marker['Mb']) + markernames.append(marker['name']) + + self.json_data['chrnames'] = chrnames + self.json_data['lodnames'] = lodnames + self.json_data['chr'] = chr_pos + self.json_data['pos'] = pos + self.json_data['markernames'] = markernames + + for trait in self.trait_results: + self.json_data[trait] = self.trait_results[trait] + + self.js_data = dict( + json_data = self.json_data + ) + + print("self.js_data:", self.js_data) + + + def gen_reaper_results(self): + self.trait_results = {} + for trait_db in self.trait_list: + self.dataset.group.get_markers() + this_trait = trait_db[0] + #this_db = trait_db[1] + genotype = self.dataset.group.read_genotype_file() + samples, values, variances = this_trait.export_informative() + + trimmed_samples = [] + trimmed_values = [] + for i in range(0, len(samples)): + if samples[i] in self.dataset.group.samplelist: + trimmed_samples.append(samples[i]) + trimmed_values.append(values[i]) + + self.lrs_array = genotype.permutation(strains = trimmed_samples, + trait = trimmed_values, + nperm= self.num_permutations) + + #self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)] + #self.significant = self.lrs_array[int(self.num_permutations*0.95-1)] + + reaper_results = genotype.regression(strains = trimmed_samples, + trait = trimmed_values) + + + lrs_values = [float(qtl.lrs) for qtl in reaper_results] + print("lrs_values:", lrs_values) + #self.dataset.group.markers.add_pvalues(p_values) + + self.trait_results[this_trait.name] = [] + for qtl in reaper_results: + if qtl.additive > 0: + self.trait_results[this_trait.name].append(-float(qtl.lrs)) + else: + self.trait_results[this_trait.name].append(float(qtl.lrs)) + #for lrs in lrs_values: + # if + # self.trait_results[this_trait.name].append(lrs) + + + #this_db_samples = self.dataset.group.samplelist + #this_sample_data = this_trait.data + ##print("this_sample_data", this_sample_data) + #this_trait_vals = [] + #for index, sample in enumerate(this_db_samples): + # if sample in this_sample_data: + # sample_value = this_sample_data[sample].value + # this_trait_vals.append(sample_value) + # else: + # this_trait_vals.append("x") + + #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) + + #key = "pylmm:input:" + str(self.temp_uuid) + #print("key is:", pf(key)) + + #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + + #no_val_samples = self.identify_empty_samples(this_trait_vals) + #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + + #genotype_matrix = np.array(trimmed_genotype_data).T + + #print("genotype_matrix:", str(genotype_matrix.tolist())) + #print("pheno_vector:", str(pheno_vector.tolist())) + + #params = dict(pheno_vector = pheno_vector.tolist(), + # genotype_matrix = genotype_matrix.tolist(), + # restricted_max_likelihood = True, + # refit = False, + # temp_uuid = str(self.temp_uuid), + # + # # meta data + # timestamp = datetime.datetime.now().isoformat(), + # ) + # + #json_params = json.dumps(params) + ##print("json_params:", json_params) + #Redis.set(key, json_params) + #Redis.expire(key, 60*60) + #print("before printing command") + # + #command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key, + # "other") + #print("command is:", command) + #print("after printing command") + # + #os.system(command) + # + #json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) + + def gen_pylmm_results(self): self.trait_results = {} for trait_db in self.trait_list: this_trait = trait_db[0] @@ -105,7 +236,7 @@ class Heatmap(object): pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) - key = "pylmm:input:" + str(temp_uuid) + key = "pylmm:input:" + str(self.temp_uuid) #print("key is:", pf(key)) genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] @@ -122,7 +253,7 @@ class Heatmap(object): genotype_matrix = genotype_matrix.tolist(), restricted_max_likelihood = True, refit = False, - temp_uuid = str(temp_uuid), + temp_uuid = str(self.temp_uuid), # meta data timestamp = datetime.datetime.now().isoformat(), @@ -141,7 +272,7 @@ class Heatmap(object): os.system(command) - json_results = Redis.blpop("pylmm:results:" + str(temp_uuid), 45*60) + json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) results = json.loads(json_results[1]) p_values = [float(result) for result in results['p_values']] #print("p_values:", p_values) @@ -150,40 +281,8 @@ class Heatmap(object): self.trait_results[this_trait.name] = [] for marker in self.dataset.group.markers.markers: self.trait_results[this_trait.name].append(marker['lod_score']) + - #print("self.trait_results:", self.trait_results) - - chrnames = [] - lodnames = [] - chr_pos = [] - pos = [] - markernames = [] - - for trait in self.trait_results.keys(): - lodnames.append(trait) - - for marker in self.dataset.group.markers.markers: - if marker['chr'] not in chrnames: - chrnames.append(marker['chr']) - chr_pos.append(marker['chr']) - pos.append(marker['Mb']) - markernames.append(marker['name']) - - self.json_data['chrnames'] = chrnames - self.json_data['lodnames'] = lodnames - self.json_data['chr'] = chr_pos - self.json_data['pos'] = pos - self.json_data['markernames'] = markernames - - for trait in self.trait_results: - self.json_data[trait] = self.trait_results[trait] - - self.js_data = dict( - json_data = self.json_data - ) - - print("self.js_data:", self.js_data) - def identify_empty_samples(self, values): no_val_samples = [] for sample_count, val in enumerate(values): diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 0a83f9f8..648cb49b 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -186,10 +186,18 @@ class MarkerRegression(object): # # - #def run_rqtl(self): - # os.chdir("/home/zas1024/plink") - # - + def run_rqtl(self): + os.chdir("/home/zas1024/plink") + + output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name)) + + self.gen_pheno_txt_file_plink(pheno_filename = output_filename) + + rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename) + + os.system(rqtl_command) + + count, p_values = self.parse_rqtl_output(plink_output_filename) def run_plink(self): @@ -317,6 +325,9 @@ class MarkerRegression(object): # return ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList + def parse_rqtl_output(self, output_filename): + return True + def parse_plink_output(self, output_filename): plink_results={} diff --git a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js index df1e62b6..b06c70f4 100755 --- a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js +++ b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js @@ -1,77 +1,73 @@ -// Generated by CoffeeScript 1.6.1 -(function() { - var Scatter_Plot, root; +// Generated by CoffeeScript 1.7.1 +var Scatter_Plot, root; - root = typeof exports !== "undefined" && exports !== null ? exports : this; +root = typeof exports !== "undefined" && exports !== null ? exports : this; - Scatter_Plot = (function() { - - function Scatter_Plot() { - var chart, data, g, height, i, main, margin, maxx, maxy, minx, miny, sample1, sample2, samplename, samples_1, samples_2, text, width, x, xAxis, y, yAxis; - data = new Array(); - samples_1 = js_data.samples_1; - samples_2 = js_data.samples_2; - i = 0; - for (samplename in samples_1) { - sample1 = samples_1[samplename]; - sample2 = samples_2[samplename]; - data[i++] = [sample1.value, sample2.value]; - } - margin = { - top: 100, - right: 15, - bottom: 60, - left: 60 - }; - width = js_data.width - margin.left - margin.right; - height = js_data.height - margin.top - margin.bottom; - minx = d3.min(data, function(d) { - return d[0]; - }) * 0.95; - maxx = d3.max(data, function(d) { - return d[0]; - }) * 1.05; - miny = d3.min(data, function(d) { - return d[1]; - }) * 0.95; - maxy = d3.max(data, function(d) { - return d[1]; - }) * 1.05; - x = d3.scale.linear().domain([minx, maxx]).range([0, width]); - y = d3.scale.linear().domain([miny, maxy]).range([height, 0]); - chart = d3.select("#scatter_plot").append("svg:svg").attr("width", width + margin.right + margin.left).attr("height", height + margin.top + margin.bottom).attr("class", "chart"); - main = chart.append("g").attr("transform", "translate(" + margin.left + "," + margin.top + ")").attr("width", width).attr("height", height).attr("class", "main"); - xAxis = d3.svg.axis().scale(x).orient("bottom"); - main.append("g").attr("transform", "translate(0," + height + ")").attr("class", "main axis date").call(xAxis); - yAxis = d3.svg.axis().scale(y).orient("left"); - main.append("g").attr("transform", "translate(0,0)").attr("class", "main axis date").call(yAxis); - g = main.append("svg:g"); - g.selectAll("scatter-dots").data(data).enter().append("svg:circle").attr("cx", function(d) { - return x(d[0]); - }).attr("cy", function(d) { - return y(d[1]); - }).attr("fill", js_data.circle_color).attr("r", js_data.circle_radius); - main.append("line").attr("x1", x(minx)).attr("y1", y(js_data.slope * minx + js_data.intercept)).attr("x2", x(maxx * 0.995)).attr("y2", y(js_data.slope * maxx * 0.995 + js_data.intercept)).style("stroke", js_data.line_color).style("stroke-width", js_data.line_width); - chart.append("text").attr("x", width / 2).attr("y", margin.top / 2 - 25).text("Sample Correlation Scatterplot"); - text = ""; - text += "N=" + js_data.num_overlap; - chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 - 5).text(text); - text = ""; - text += "r=" + js_data.r_value + "\t"; - text += "p(r)=" + js_data.p_value; - chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 15).text(text); - text = ""; - text += "slope=" + js_data.slope + "\t"; - text += "intercept=" + js_data.intercept; - chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 35).text(text); - chart.append("text").attr("x", width / 2).attr("y", height + margin.top + 35).text(js_data.trait_1); - chart.append("text").attr("x", 20).attr("y", height / 2 + margin.top + 30).attr("transform", "rotate(-90 20," + (height / 2 + margin.top + 30) + ")").text(js_data.trait_2); +Scatter_Plot = (function() { + function Scatter_Plot() { + var chart, data, g, height, i, main, margin, maxx, maxy, minx, miny, sample1, sample2, samplename, samples_1, samples_2, text, width, x, xAxis, y, yAxis; + data = new Array(); + samples_1 = js_data.samples_1; + samples_2 = js_data.samples_2; + i = 0; + for (samplename in samples_1) { + sample1 = samples_1[samplename]; + sample2 = samples_2[samplename]; + data[i++] = [sample1.value, sample2.value]; } + margin = { + top: 100, + right: 15, + bottom: 60, + left: 60 + }; + width = js_data.width - margin.left - margin.right; + height = js_data.height - margin.top - margin.bottom; + minx = d3.min(data, function(d) { + return d[0]; + }) * 0.95; + maxx = d3.max(data, function(d) { + return d[0]; + }) * 1.05; + miny = d3.min(data, function(d) { + return d[1]; + }) * 0.95; + maxy = d3.max(data, function(d) { + return d[1]; + }) * 1.05; + x = d3.scale.linear().domain([minx, maxx]).range([0, width]); + y = d3.scale.linear().domain([miny, maxy]).range([height, 0]); + chart = d3.select("#scatter_plot").append("svg:svg").attr("width", width + margin.right + margin.left).attr("height", height + margin.top + margin.bottom).attr("class", "chart"); + main = chart.append("g").attr("transform", "translate(" + margin.left + "," + margin.top + ")").attr("width", width).attr("height", height).attr("class", "main"); + xAxis = d3.svg.axis().scale(x).orient("bottom"); + main.append("g").attr("transform", "translate(0," + height + ")").attr("class", "main axis date").call(xAxis); + yAxis = d3.svg.axis().scale(y).orient("left"); + main.append("g").attr("transform", "translate(0,0)").attr("class", "main axis date").call(yAxis); + g = main.append("svg:g"); + g.selectAll("scatter-dots").data(data).enter().append("svg:circle").attr("cx", function(d) { + return x(d[0]); + }).attr("cy", function(d) { + return y(d[1]); + }).attr("fill", js_data.circle_color).attr("r", js_data.circle_radius); + main.append("line").attr("x1", x(minx)).attr("y1", y(js_data.slope * minx + js_data.intercept)).attr("x2", x(maxx * 0.995)).attr("y2", y(js_data.slope * maxx * 0.995 + js_data.intercept)).style("stroke", js_data.line_color).style("stroke-width", js_data.line_width); + chart.append("text").attr("x", width / 2).attr("y", margin.top / 2 - 25).text("Sample Correlation Scatterplot"); + text = ""; + text += "N=" + js_data.num_overlap; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 - 5).text(text); + text = ""; + text += "r=" + js_data.r_value + "\t"; + text += "p(r)=" + js_data.p_value; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 15).text(text); + text = ""; + text += "slope=" + js_data.slope + "\t"; + text += "intercept=" + js_data.intercept; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 35).text(text); + chart.append("text").attr("x", width / 2).attr("y", height + margin.top + 35).text(js_data.trait_1); + chart.append("text").attr("x", 20).attr("y", height / 2 + margin.top + 30).attr("transform", "rotate(-90 20," + (height / 2 + margin.top + 30) + ")").text(js_data.trait_2); + } - return Scatter_Plot; - - })(); + return Scatter_Plot; - root.Scatter_Plot = Scatter_Plot; +})(); -}).call(this); +root.Scatter_Plot = Scatter_Plot; diff --git a/wqflask/wqflask/static/new/javascript/create_heatmap.coffee b/wqflask/wqflask/static/new/javascript/create_heatmap.coffee index 51ca5e8f..d3f9fb09 100644 --- a/wqflask/wqflask/static/new/javascript/create_heatmap.coffee +++ b/wqflask/wqflask/static/new/javascript/create_heatmap.coffee @@ -1,11 +1,11 @@ create_heatmap = () -> - h = 700 - w = 1000 + h = 500 + w = 1200 mychart = lodheatmap().height(h) .width(w) - .zthresh(0.5) + #.zthresh(1) data = js_data.json_data diff --git a/wqflask/wqflask/static/new/javascript/create_heatmap.js b/wqflask/wqflask/static/new/javascript/create_heatmap.js index 7d6f7a9d..df8f9673 100644 --- a/wqflask/wqflask/static/new/javascript/create_heatmap.js +++ b/wqflask/wqflask/static/new/javascript/create_heatmap.js @@ -3,9 +3,9 @@ var create_heatmap; create_heatmap = function() { var data, h, mychart, w; - h = 700; - w = 1000; - mychart = lodheatmap().height(h).width(w).zthresh(0.5); + h = 500; + w = 1200; + mychart = lodheatmap().height(h).width(w); data = js_data.json_data; console.log("data:", data); return d3.select("div#chart").datum(data).call(mychart); diff --git a/wqflask/wqflask/static/new/javascript/curvechart.coffee b/wqflask/wqflask/static/new/javascript/curvechart.coffee new file mode 100644 index 00000000..7ed4359a --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/curvechart.coffee @@ -0,0 +1,335 @@ +# curvechart: reuseable chart with many curves + +curvechart = () -> + width = 800 + height = 500 + margin = {left:60, top:40, right:40, bottom: 40, inner:5} + axispos = {xtitle:25, ytitle:30, xlabel:5, ylabel:5} + titlepos = 20 + xlim = null + ylim = null + nxticks = 5 + xticks = null + nyticks = 5 + yticks = null + rectcolor = "#e6e6e6" + strokecolor = null + strokecolorhilit = null + strokewidth = 2 + strokewidthhilit = 2 + title = "" + xlab = "X" + ylab = "Y" + rotate_ylab = null + yscale = d3.scale.linear() + xscale = d3.scale.linear() + curvesSelect = null + commonX = true + + ## the main function + chart = (selection) -> + selection.each (data) -> + + # grab indID if it's there + # if no indID, create a vector of them + indID = data?.indID ? null + indID = indID ? [1..data.data.length] + + # groups of colors + group = data?.group ? (1 for i of data.data) + ngroup = d3.max(group) + group = (g-1 for g in group) # changed from (1,2,3,...) to (0,1,2,...) + + # default light stroke colors + strokecolor = strokecolor ? selectGroupColors(ngroup, "pastel") + strokecolor = expand2vector(strokecolor, ngroup) + + # default dark stroke colors + strokecolorhilit = strokecolorhilit ? selectGroupColors(ngroup, "dark") + strokecolorhilit = expand2vector(strokecolorhilit, ngroup) + + # reorganize data? + if commonX # reorganize data + data = ({x:data.x, y:data.data[i]} for i of data.data) + else + data = data.data + + xlim = xlim ? d3.extent(pullVarAsArray(data, "x")) + ylim = ylim ? d3.extent(pullVarAsArray(data, "y")) + + # reorganize again + for i of data + tmp = data[i] + data[i] = [] + for j of tmp.x + data[i].push({x:tmp.x[j], y:tmp.y[j]}) unless !tmp.x[j]? or !tmp.y[j]? + + # Select the svg element, if it exists. + svg = d3.select(this).selectAll("svg").data([data]) + + # Otherwise, create the skeletal chart. + gEnter = svg.enter().append("svg").append("g") + + # Update the outer dimensions. + svg.attr("width", width+margin.left+margin.right) + .attr("height", height+margin.top+margin.bottom) + + g = svg.select("g") + + # box + g.append("rect") + .attr("x", margin.left) + .attr("y", margin.top) + .attr("height", height) + .attr("width", width) + .attr("fill", rectcolor) + .attr("stroke", "none") + + # scales + xrange = [margin.left+margin.inner, margin.left+width-margin.inner] + yrange = [margin.top+height-margin.inner, margin.top+margin.inner] + xscale.domain(xlim).range(xrange) + yscale.domain(ylim).range(yrange) + xs = d3.scale.linear().domain(xlim).range(xrange) + ys = d3.scale.linear().domain(ylim).range(yrange) + + # if yticks not provided, use nyticks to choose pretty ones + yticks = yticks ? ys.ticks(nyticks) + xticks = xticks ? xs.ticks(nxticks) + + # title + titlegrp = g.append("g").attr("class", "title") + .append("text") + .attr("x", margin.left + width/2) + .attr("y", margin.top - titlepos) + .text(title) + + # x-axis + xaxis = g.append("g").attr("class", "x axis") + xaxis.selectAll("empty") + .data(xticks) + .enter() + .append("line") + .attr("x1", (d) -> xscale(d)) + .attr("x2", (d) -> xscale(d)) + .attr("y1", margin.top) + .attr("y2", margin.top+height) + .attr("fill", "none") + .attr("stroke", "white") + .attr("stroke-width", 1) + .style("pointer-events", "none") + xaxis.selectAll("empty") + .data(xticks) + .enter() + .append("text") + .attr("x", (d) -> xscale(d)) + .attr("y", margin.top+height+axispos.xlabel) + .text((d) -> formatAxis(xticks)(d)) + xaxis.append("text").attr("class", "title") + .attr("x", margin.left+width/2) + .attr("y", margin.top+height+axispos.xtitle) + .text(xlab) + + # y-axis + rotate_ylab = rotate_ylab ? (ylab.length > 1) + yaxis = g.append("g").attr("class", "y axis") + yaxis.selectAll("empty") + .data(yticks) + .enter() + .append("line") + .attr("y1", (d) -> yscale(d)) + .attr("y2", (d) -> yscale(d)) + .attr("x1", margin.left) + .attr("x2", margin.left+width) + .attr("fill", "none") + .attr("stroke", "white") + .attr("stroke-width", 1) + .style("pointer-events", "none") + yaxis.selectAll("empty") + .data(yticks) + .enter() + .append("text") + .attr("y", (d) -> yscale(d)) + .attr("x", margin.left-axispos.ylabel) + .text((d) -> formatAxis(yticks)(d)) + yaxis.append("text").attr("class", "title") + .attr("y", margin.top+height/2) + .attr("x", margin.left-axispos.ytitle) + .text(ylab) + .attr("transform", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "") + + indtip = d3.tip() + .attr('class', 'd3-tip') + .html((d) -> indID[d]) + .direction('e') + .offset([0,10]) + svg.call(indtip) + + curve = d3.svg.line() + .x((d) -> xscale(d.x)) + .y((d) -> yscale(d.y)) + + curves = g.append("g").attr("id", "curves") + curvesSelect = + curves.selectAll("empty") + .data(d3.range(data.length)) + .enter() + .append("path") + .datum((d) -> data[d]) + .attr("d", curve) + .attr("class", (d,i) -> "path#{i}") + .attr("fill", "none") + .attr("stroke", (d,i) -> strokecolor[group[i]]) + .attr("stroke-width", strokewidth) + .on "mouseover.panel", (d,i) -> + d3.select(this).attr("stroke", strokecolorhilit[group[i]]).moveToFront() + circle = d3.select("circle#hiddenpoint#{i}") + indtip.show(i, circle.node()) + .on "mouseout.panel", (d,i) -> + d3.select(this).attr("stroke", strokecolor[group[i]]).moveToBack() + indtip.hide() + + # grab the last non-null point from each curve + lastpoint = ({x:null, y:null} for i of data) + for i of data + for v in data[i] + lastpoint[i] = v if v.x? and v.y? + + pointsg = g.append("g").attr("id", "invisiblepoints") + points = pointsg.selectAll("empty") + .data(lastpoint) + .enter() + .append("circle") + .attr("id", (d,i) -> "hiddenpoint#{i}") + .attr("cx", (d) -> xscale(d.x)) + .attr("cy", (d) -> yscale(d.y)) + .attr("r", 1) + .attr("opacity", 0) + + # box + g.append("rect") + .attr("x", margin.left) + .attr("y", margin.top) + .attr("height", height) + .attr("width", width) + .attr("fill", "none") + .attr("stroke", "black") + .attr("stroke-width", "none") + + ## configuration parameters + chart.width = (value) -> + return width if !arguments.length + width = value + chart + + chart.height = (value) -> + return height if !arguments.length + height = value + chart + + chart.margin = (value) -> + return margin if !arguments.length + margin = value + chart + + chart.axispos = (value) -> + return axispos if !arguments.length + axispos = value + chart + + chart.titlepos = (value) -> + return titlepos if !arguments.length + titlepos + chart + + chart.xlim = (value) -> + return xlim if !arguments.length + xlim = value + chart + + chart.nxticks = (value) -> + return nxticks if !arguments.length + nxticks = value + chart + + chart.xticks = (value) -> + return xticks if !arguments.length + xticks = value + chart + + chart.ylim = (value) -> + return ylim if !arguments.length + ylim = value + chart + + chart.nyticks = (value) -> + return nyticks if !arguments.length + nyticks = value + chart + + chart.yticks = (value) -> + return yticks if !arguments.length + yticks = value + chart + + chart.rectcolor = (value) -> + return rectcolor if !arguments.length + rectcolor = value + chart + + chart.strokecolor = (value) -> + return strokecolor if !arguments.length + strokecolor = value + chart + + chart.strokecolorhilit = (value) -> + return strokecolorhilit if !arguments.length + strokecolorhilit = value + chart + + chart.strokewidth = (value) -> + return strokewidth if !arguments.length + strokewidth = value + chart + + chart.strokewidthhilit = (value) -> + return strokewidthhilit if !arguments.length + strokewidthhilit = value + chart + + chart.commonX = (value) -> + return commonX if !arguments.length + commonX = value + chart + + chart.title = (value) -> + return title if !arguments.length + title = value + chart + + chart.xlab = (value) -> + return xlab if !arguments.length + xlab = value + chart + + chart.ylab = (value) -> + return ylab if !arguments.length + ylab = value + chart + + chart.rotate_ylab = (value) -> + return rotate_ylab if !arguments.length + rotate_ylab = value + chart + + chart.yscale = () -> + return yscale + + chart.xscale = () -> + return xscale + + chart.curvesSelect = () -> + return curvesSelect + + # return the chart function + chart \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/curvechart.js b/wqflask/wqflask/static/new/javascript/curvechart.js new file mode 100644 index 00000000..48526c41 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/curvechart.js @@ -0,0 +1,353 @@ +// Generated by CoffeeScript 1.7.1 +var curvechart; + +curvechart = function() { + var axispos, chart, commonX, curvesSelect, height, margin, nxticks, nyticks, rectcolor, rotate_ylab, strokecolor, strokecolorhilit, strokewidth, strokewidthhilit, title, titlepos, width, xlab, xlim, xscale, xticks, ylab, ylim, yscale, yticks; + width = 800; + height = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = 20; + xlim = null; + ylim = null; + nxticks = 5; + xticks = null; + nyticks = 5; + yticks = null; + rectcolor = "#e6e6e6"; + strokecolor = null; + strokecolorhilit = null; + strokewidth = 2; + strokewidthhilit = 2; + title = ""; + xlab = "X"; + ylab = "Y"; + rotate_ylab = null; + yscale = d3.scale.linear(); + xscale = d3.scale.linear(); + curvesSelect = null; + commonX = true; + chart = function(selection) { + return selection.each(function(data) { + var curve, curves, g, gEnter, group, i, indID, indtip, j, lastpoint, ngroup, points, pointsg, svg, titlegrp, tmp, v, xaxis, xrange, xs, yaxis, yrange, ys, _i, _j, _len, _ref, _ref1, _ref2, _ref3, _results; + indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null; + indID = indID != null ? indID : (function() { + _results = []; + for (var _i = 1, _ref1 = data.data.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); } + return _results; + }).apply(this); + group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() { + var _results1; + _results1 = []; + for (i in data.data) { + _results1.push(1); + } + return _results1; + })(); + ngroup = d3.max(group); + group = (function() { + var _j, _len, _results1; + _results1 = []; + for (_j = 0, _len = group.length; _j < _len; _j++) { + g = group[_j]; + _results1.push(g - 1); + } + return _results1; + })(); + strokecolor = strokecolor != null ? strokecolor : selectGroupColors(ngroup, "pastel"); + strokecolor = expand2vector(strokecolor, ngroup); + strokecolorhilit = strokecolorhilit != null ? strokecolorhilit : selectGroupColors(ngroup, "dark"); + strokecolorhilit = expand2vector(strokecolorhilit, ngroup); + if (commonX) { + data = (function() { + var _results1; + _results1 = []; + for (i in data.data) { + _results1.push({ + x: data.x, + y: data.data[i] + }); + } + return _results1; + })(); + } else { + data = data.data; + } + xlim = xlim != null ? xlim : d3.extent(pullVarAsArray(data, "x")); + ylim = ylim != null ? ylim : d3.extent(pullVarAsArray(data, "y")); + for (i in data) { + tmp = data[i]; + data[i] = []; + for (j in tmp.x) { + if (!((tmp.x[j] == null) || (tmp.y[j] == null))) { + data[i].push({ + x: tmp.x[j], + y: tmp.y[j] + }); + } + } + } + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", rectcolor).attr("stroke", "none"); + xrange = [margin.left + margin.inner, margin.left + width - margin.inner]; + yrange = [margin.top + height - margin.inner, margin.top + margin.inner]; + xscale.domain(xlim).range(xrange); + yscale.domain(ylim).range(yrange); + xs = d3.scale.linear().domain(xlim).range(xrange); + ys = d3.scale.linear().domain(ylim).range(yrange); + yticks = yticks != null ? yticks : ys.ticks(nyticks); + xticks = xticks != null ? xticks : xs.ticks(nxticks); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) { + return xscale(d); + }).attr("x2", function(d) { + return xscale(d); + }).attr("y1", margin.top).attr("y2", margin.top + height).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + xaxis.selectAll("empty").data(xticks).enter().append("text").attr("x", function(d) { + return xscale(d); + }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { + return formatAxis(xticks)(d); + }); + xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab); + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) { + return yscale(d); + }).attr("x", margin.left - axispos.ylabel).text(function(d) { + return formatAxis(yticks)(d); + }); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : ""); + indtip = d3.tip().attr('class', 'd3-tip').html(function(d) { + return indID[d]; + }).direction('e').offset([0, 10]); + svg.call(indtip); + curve = d3.svg.line().x(function(d) { + return xscale(d.x); + }).y(function(d) { + return yscale(d.y); + }); + curves = g.append("g").attr("id", "curves"); + curvesSelect = curves.selectAll("empty").data(d3.range(data.length)).enter().append("path").datum(function(d) { + return data[d]; + }).attr("d", curve).attr("class", function(d, i) { + return "path" + i; + }).attr("fill", "none").attr("stroke", function(d, i) { + return strokecolor[group[i]]; + }).attr("stroke-width", strokewidth).on("mouseover.panel", function(d, i) { + var circle; + d3.select(this).attr("stroke", strokecolorhilit[group[i]]).moveToFront(); + circle = d3.select("circle#hiddenpoint" + i); + return indtip.show(i, circle.node()); + }).on("mouseout.panel", function(d, i) { + d3.select(this).attr("stroke", strokecolor[group[i]]).moveToBack(); + return indtip.hide(); + }); + lastpoint = (function() { + var _results1; + _results1 = []; + for (i in data) { + _results1.push({ + x: null, + y: null + }); + } + return _results1; + })(); + for (i in data) { + _ref3 = data[i]; + for (_j = 0, _len = _ref3.length; _j < _len; _j++) { + v = _ref3[_j]; + if ((v.x != null) && (v.y != null)) { + lastpoint[i] = v; + } + } + } + pointsg = g.append("g").attr("id", "invisiblepoints"); + points = pointsg.selectAll("empty").data(lastpoint).enter().append("circle").attr("id", function(d, i) { + return "hiddenpoint" + i; + }).attr("cx", function(d) { + return xscale(d.x); + }).attr("cy", function(d) { + return yscale(d.y); + }).attr("r", 1).attr("opacity", 0); + return g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.xlim = function(value) { + if (!arguments.length) { + return xlim; + } + xlim = value; + return chart; + }; + chart.nxticks = function(value) { + if (!arguments.length) { + return nxticks; + } + nxticks = value; + return chart; + }; + chart.xticks = function(value) { + if (!arguments.length) { + return xticks; + } + xticks = value; + return chart; + }; + chart.ylim = function(value) { + if (!arguments.length) { + return ylim; + } + ylim = value; + return chart; + }; + chart.nyticks = function(value) { + if (!arguments.length) { + return nyticks; + } + nyticks = value; + return chart; + }; + chart.yticks = function(value) { + if (!arguments.length) { + return yticks; + } + yticks = value; + return chart; + }; + chart.rectcolor = function(value) { + if (!arguments.length) { + return rectcolor; + } + rectcolor = value; + return chart; + }; + chart.strokecolor = function(value) { + if (!arguments.length) { + return strokecolor; + } + strokecolor = value; + return chart; + }; + chart.strokecolorhilit = function(value) { + if (!arguments.length) { + return strokecolorhilit; + } + strokecolorhilit = value; + return chart; + }; + chart.strokewidth = function(value) { + if (!arguments.length) { + return strokewidth; + } + strokewidth = value; + return chart; + }; + chart.strokewidthhilit = function(value) { + if (!arguments.length) { + return strokewidthhilit; + } + strokewidthhilit = value; + return chart; + }; + chart.commonX = function(value) { + if (!arguments.length) { + return commonX; + } + commonX = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.yscale = function() { + return yscale; + }; + chart.xscale = function() { + return xscale; + }; + chart.curvesSelect = function() { + return curvesSelect; + }; + return chart; +}; diff --git a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee new file mode 100644 index 00000000..6aa301a0 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee @@ -0,0 +1,192 @@ +# iplotMScanone_noeff: image of lod curves linked to plot of lod curves +# Karl W Broman + +iplotMScanone_noeff = (lod_data, times, chartOpts) -> + + # chartOpts start + wleft = chartOpts?.wleft ? 1000 # width of left panels in pixels + wright = chartOpts?.wright ? 500 # width of right panel in pixels + htop = chartOpts?.htop ? 350 # height of top panels in pixels + hbot = chartOpts?.hbot ? 350 # height of bottom panel in pixels + margin = chartOpts?.margin ? {left:100, top:40, right:40, bottom: 40, inner:5} # margins in pixels (left, top, right, bottom, inner) + axispos = chartOpts?.axispos ? {xtitle:25, ytitle:30, xlabel:5, ylabel:5} # position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel) + titlepos = chartOpts?.titlepos ? 20 # position of chart title in pixels + chrGap = chartOpts?.chrGap ? 8 # gap between chromosomes in pixels + darkrect = chartOpts?.darkrect ? "#C8C8C8" # color of darker background rectangle + lightrect = chartOpts?.lightrect ? "#E6E6E6" # color of lighter background rectangle + nullcolor = chartOpts?.nullcolor ? "#E6E6E6" # color for pixels with null values + colors = chartOpts?.colors ? ["slateblue", "white", "crimson"] # heat map colors + zlim = chartOpts?.zlim ? null # z-axis limits + zthresh = chartOpts?.zthresh ? null # lower z-axis threshold for display in heat map + lod_ylab = chartOpts?.lod_ylab ? "" # y-axis label for LOD heatmap (also used as x-axis label on effect plot) + linecolor = chartOpts?.linecolor ? "darkslateblue" # color of lines + linewidth = chartOpts?.linewidth ? 2 # width of lines + nxticks = chartOpts?.nxticks ? 5 # no. ticks in x-axis on right-hand panel, if quantitative scale + xticks = chartOpts?.xticks ? null # tick positions in x-axis on right-hand panel, if quantitative scale + lod_labels = chartOpts?.lod_labels ? null # optional vector of strings, for LOD column labels + # chartOpts end + chartdivid = chartOpts?.chartdivid ? 'chart' + + totalh = htop + hbot + 2*(margin.top + margin.bottom) + totalw = wleft + wright + 2*(margin.left + margin.right) + + # if quant scale, use times as labels; otherwise use lod_data.lodnames + unless lod_labels? + lod_labels = if times? then (formatAxis(times, extra_digits=1)(x) for x in times) else lod_data.lodnames + + mylodheatmap = lodheatmap().height(htop) + .width(wleft) + .margin(margin) + .axispos(axispos) + #.titlepos(titlepos) + #.chrGap(chrGap) + #.rectcolor(lightrect) + #.colors(colors) + #.zlim(zlim) + #.zthresh(zthresh) + #.quantScale(times) + #.lod_labels(lod_labels) + #.ylab(lod_ylab) + #.nullcolor(nullcolor) + + svg = d3.select("div##{chartdivid}") + .append("svg") + .attr("height", totalh) + .attr("width", totalw) + + g_heatmap = svg.append("g") + .attr("id", "heatmap") + .datum(lod_data) + .call(mylodheatmap) + + mylodchart = lodchart().height(hbot) + .width(wleft) + .margin(margin) + .axispos(axispos) + .titlepos(titlepos) + .chrGap(chrGap) + .linecolor("none") + .pad4heatmap(true) + .darkrect(darkrect) + .lightrect(lightrect) + .ylim([0, d3.max(mylodheatmap.zlim())]) + .pointsAtMarkers(false) + + g_lodchart = svg.append("g") + .attr("transform", "translate(0,#{htop+margin.top+margin.bottom})") + .attr("id", "lodchart") + .datum(lod_data) + .call(mylodchart) + + # function for lod curve path + lodcurve = (chr, lodcolumn) -> + d3.svg.line() + .x((d) -> mylodchart.xscale()[chr](d)) + .y((d,i) -> mylodchart.yscale()(Math.abs(lod_data.lodByChr[chr][i][lodcolumn]))) + + # plot lod curves for selected lod column + lodchart_curves = null + plotLodCurve = (lodcolumn) -> + lodchart_curves = g_lodchart.append("g").attr("id", "lodcurves") + for chr in lod_data.chrnames + lodchart_curves.append("path") + .datum(lod_data.posByChr[chr]) + .attr("d", lodcurve(chr, lodcolumn)) + .attr("stroke", linecolor) + .attr("fill", "none") + .attr("stroke-width", linewidth) + .style("pointer-events", "none") + + # rearrange data for curves of time x LOD + lod4curves = {data:[]} + for pos of lod_data.pos + y = (Math.abs(lod_data[lodcolumn][pos]) for lodcolumn in lod_data.lodnames) + x = (+i for i of lod_data.lodnames) + lod4curves.data.push({x:x, y:y}) + + #mycurvechart = curvechart().height(htop) + # .width(wright) + # .margin(margin) + # .axispos(axispos) + # .titlepos(titlepos) + # .xlab(lod_ylab) + # .ylab("LOD score") + # .strokecolor("none") + # .rectcolor(lightrect) + # .xlim([-0.5, lod_data.lodnames.length-0.5]) + # .ylim([0, d3.max(mylodheatmap.zlim())]) + # .nxticks(0) + # .commonX(false) + # + #g_curvechart = svg.append("g") + # .attr("transform", "translate(#{wleft+margin.top+margin.bottom},0)") + # .attr("id", "curvechart") + # .datum(lod4curves) + # .call(mycurvechart) + # + ## add X axis + #if times? # use quantitative axis + # xscale = d3.scale.linear().range(mycurvechart.xscale().range()) + # xscale.domain([times[0], times[times.length-1]]) + # xticks = xticks ? xscale.ticks(nxticks) + # curvechart_xaxis = g_curvechart.select("g.x.axis") + # curvechart_xaxis.selectAll("empty") + # .data(xticks) + # .enter() + # .append("line") + # .attr("x1", (d) -> xscale(d)) + # .attr("x2", (d) -> xscale(d)) + # .attr("y1", margin.top) + # .attr("y2", margin.top+htop) + # .attr("fill", "none") + # .attr("stroke", "white") + # .attr("stroke-width", 1) + # .style("pointer-events", "none") + # curvechart_xaxis.selectAll("empty") + # .data(xticks) + # .enter() + # .append("text") + # .attr("x", (d) -> xscale(d)) + # .attr("y", margin.top+htop+axispos.xlabel) + # .text((d) -> formatAxis(xticks)(d)) + #else # qualitative axis + # curvechart_xaxis = g_curvechart.select("g.x.axis") + # .selectAll("empty") + # .data(lod_labels) + # .enter() + # .append("text") + # .attr("id", (d,i) -> "xaxis#{i}") + # .attr("x", (d,i) -> mycurvechart.xscale()(i)) + # .attr("y", margin.top+htop+axispos.xlabel) + # .text((d) -> d) + # .attr("opacity", 0) + + # hash for [chr][pos] -> posindex + #posindex = {} + #curindex = 0 + #for chr in lod_data.chrnames + # posindex[chr] = {} + # for pos in lod_data.posByChr[chr] + # posindex[chr][pos] = curindex + # curindex += 1 + + #mycurvechart.curvesSelect() + # .on("mouseover.panel", null) + # .on("mouseout.panel", null) + # + mylodheatmap.cellSelect() + .on "mouseover", (d) -> + plotLodCurve(d.lodindex) + g_lodchart.select("g.title text").text("#{lod_labels[d.lodindex]}") + #g_curvechart.selectAll("path.path#{posindex[d.chr][d.pos]}").attr("stroke", linecolor) + p = d3.format(".1f")(d.pos) + #g_curvechart.select("g.title text").text("#{d.chr}@#{p}") + #g_curvechart.select("text#xaxis#{d.lodindex}").attr("opacity", 1) unless times? + .on "mouseout", (d) -> + lodchart_curves.remove() + g_lodchart.select("g.title text").text("") + #g_curvechart.selectAll("path.path#{posindex[d.chr][d.pos]}").attr("stroke", null) + #g_curvechart.select("g.title text").text("") + #g_curvechart.select("text#xaxis#{d.lodindex}").attr("opacity", 0) unless times? + +iplotMScanone_noeff(lod_data = js_data.json_data) \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js new file mode 100644 index 00000000..e539d353 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js @@ -0,0 +1,113 @@ +// Generated by CoffeeScript 1.7.1 +var iplotMScanone_noeff, lod_data; + +iplotMScanone_noeff = function(lod_data, times, chartOpts) { + var axispos, chartdivid, chrGap, colors, darkrect, extra_digits, g_heatmap, g_lodchart, hbot, htop, i, lightrect, linecolor, linewidth, lod4curves, lod_labels, lod_ylab, lodchart_curves, lodcolumn, lodcurve, margin, mylodchart, mylodheatmap, nullcolor, nxticks, plotLodCurve, pos, svg, titlepos, totalh, totalw, wleft, wright, x, xticks, y, zlim, zthresh, _ref, _ref1, _ref10, _ref11, _ref12, _ref13, _ref14, _ref15, _ref16, _ref17, _ref18, _ref19, _ref2, _ref20, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9; + wleft = (_ref = chartOpts != null ? chartOpts.wleft : void 0) != null ? _ref : 1000; + wright = (_ref1 = chartOpts != null ? chartOpts.wright : void 0) != null ? _ref1 : 500; + htop = (_ref2 = chartOpts != null ? chartOpts.htop : void 0) != null ? _ref2 : 350; + hbot = (_ref3 = chartOpts != null ? chartOpts.hbot : void 0) != null ? _ref3 : 350; + margin = (_ref4 = chartOpts != null ? chartOpts.margin : void 0) != null ? _ref4 : { + left: 100, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = (_ref5 = chartOpts != null ? chartOpts.axispos : void 0) != null ? _ref5 : { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = (_ref6 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? _ref6 : 20; + chrGap = (_ref7 = chartOpts != null ? chartOpts.chrGap : void 0) != null ? _ref7 : 8; + darkrect = (_ref8 = chartOpts != null ? chartOpts.darkrect : void 0) != null ? _ref8 : "#C8C8C8"; + lightrect = (_ref9 = chartOpts != null ? chartOpts.lightrect : void 0) != null ? _ref9 : "#E6E6E6"; + nullcolor = (_ref10 = chartOpts != null ? chartOpts.nullcolor : void 0) != null ? _ref10 : "#E6E6E6"; + colors = (_ref11 = chartOpts != null ? chartOpts.colors : void 0) != null ? _ref11 : ["slateblue", "white", "crimson"]; + zlim = (_ref12 = chartOpts != null ? chartOpts.zlim : void 0) != null ? _ref12 : null; + zthresh = (_ref13 = chartOpts != null ? chartOpts.zthresh : void 0) != null ? _ref13 : null; + lod_ylab = (_ref14 = chartOpts != null ? chartOpts.lod_ylab : void 0) != null ? _ref14 : ""; + linecolor = (_ref15 = chartOpts != null ? chartOpts.linecolor : void 0) != null ? _ref15 : "darkslateblue"; + linewidth = (_ref16 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? _ref16 : 2; + nxticks = (_ref17 = chartOpts != null ? chartOpts.nxticks : void 0) != null ? _ref17 : 5; + xticks = (_ref18 = chartOpts != null ? chartOpts.xticks : void 0) != null ? _ref18 : null; + lod_labels = (_ref19 = chartOpts != null ? chartOpts.lod_labels : void 0) != null ? _ref19 : null; + chartdivid = (_ref20 = chartOpts != null ? chartOpts.chartdivid : void 0) != null ? _ref20 : 'chart'; + totalh = htop + hbot + 2 * (margin.top + margin.bottom); + totalw = wleft + wright + 2 * (margin.left + margin.right); + if (lod_labels == null) { + lod_labels = times != null ? (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = times.length; _i < _len; _i++) { + x = times[_i]; + _results.push(formatAxis(times, extra_digits = 1)(x)); + } + return _results; + })() : lod_data.lodnames; + } + mylodheatmap = lodheatmap().height(htop).width(wleft).margin(margin).axispos(axispos); + svg = d3.select("div#" + chartdivid).append("svg").attr("height", totalh).attr("width", totalw); + g_heatmap = svg.append("g").attr("id", "heatmap").datum(lod_data).call(mylodheatmap); + mylodchart = lodchart().height(hbot).width(wleft).margin(margin).axispos(axispos).titlepos(titlepos).chrGap(chrGap).linecolor("none").pad4heatmap(true).darkrect(darkrect).lightrect(lightrect).ylim([0, d3.max(mylodheatmap.zlim())]).pointsAtMarkers(false); + g_lodchart = svg.append("g").attr("transform", "translate(0," + (htop + margin.top + margin.bottom) + ")").attr("id", "lodchart").datum(lod_data).call(mylodchart); + lodcurve = function(chr, lodcolumn) { + return d3.svg.line().x(function(d) { + return mylodchart.xscale()[chr](d); + }).y(function(d, i) { + return mylodchart.yscale()(Math.abs(lod_data.lodByChr[chr][i][lodcolumn])); + }); + }; + lodchart_curves = null; + plotLodCurve = function(lodcolumn) { + var chr, _i, _len, _ref21, _results; + lodchart_curves = g_lodchart.append("g").attr("id", "lodcurves"); + _ref21 = lod_data.chrnames; + _results = []; + for (_i = 0, _len = _ref21.length; _i < _len; _i++) { + chr = _ref21[_i]; + _results.push(lodchart_curves.append("path").datum(lod_data.posByChr[chr]).attr("d", lodcurve(chr, lodcolumn)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none")); + } + return _results; + }; + lod4curves = { + data: [] + }; + for (pos in lod_data.pos) { + y = (function() { + var _i, _len, _ref21, _results; + _ref21 = lod_data.lodnames; + _results = []; + for (_i = 0, _len = _ref21.length; _i < _len; _i++) { + lodcolumn = _ref21[_i]; + _results.push(Math.abs(lod_data[lodcolumn][pos])); + } + return _results; + })(); + x = (function() { + var _results; + _results = []; + for (i in lod_data.lodnames) { + _results.push(+i); + } + return _results; + })(); + lod4curves.data.push({ + x: x, + y: y + }); + } + return mylodheatmap.cellSelect().on("mouseover", function(d) { + var p; + plotLodCurve(d.lodindex); + g_lodchart.select("g.title text").text("" + lod_labels[d.lodindex]); + return p = d3.format(".1f")(d.pos); + }).on("mouseout", function(d) { + lodchart_curves.remove(); + return g_lodchart.select("g.title text").text(""); + }); +}; + +iplotMScanone_noeff(lod_data = js_data.json_data); diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee index 8794625a..c9b277cc 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee @@ -43,9 +43,11 @@ lodchart = () -> lodvarname = lodvarname ? data.lodnames[0] data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values - data['additive'] = (Math.abs(x) for x in data['additive']) + if 'additive' of data + data['additive'] = (Math.abs(x) for x in data['additive']) ylim = ylim ? [0, d3.max(data[lodvarname])] - if data['additive'].length > 0 + if 'additive' of data + #if data['additive'].length > 0 additive_ylim = additive_ylim ? [0, d3.max(data['additive'])] lodvarnum = data.lodnames.indexOf(lodvarname) @@ -74,13 +76,15 @@ lodchart = () -> yscale.domain(ylim) .range([height+margin.top, margin.top+margin.inner]) - if data['additive'].length > 0 + #if data['additive'].length > 0 + if 'additive' of data additive_yscale.domain(additive_ylim) .range([height+margin.top, margin.top+margin.inner + height/2]) # if yticks not provided, use nyticks to choose pretty ones yticks = yticks ? yscale.ticks(nyticks) - if data['additive'].length > 0 + #if data['additive'].length > 0 + if 'additive' of data additive_yticks = additive_yticks ? additive_yscale.ticks(nyticks) # reorganize lod,pos by chromosomes @@ -179,7 +183,8 @@ lodchart = () -> .attr("text-anchor", "middle") .attr("fill", "slateblue") - if data['additive'].length > 0 + #if data['additive'].length > 0 + if 'additive' of data rotate_additive_ylab = rotate_additive_ylab ? (additive_ylab.length > 1) additive_yaxis = g.append("g").attr("class", "y axis") additive_yaxis.selectAll("empty") @@ -214,33 +219,34 @@ lodchart = () -> .attr("text-anchor", "middle") .attr("fill", "green") - suggestive_bar = g.append("g").attr("class", "suggestive") - suggestive_bar.selectAll("empty") - .data([data.suggestive]) - .enter() - .append("line") - .attr("y1", (d) -> yscale(d)) - .attr("y2", (d) -> yscale(d)) - .attr("x1", margin.left) - .attr("x2", margin.left+width) - .attr("fill", "none") - .attr("stroke", suggestivecolor) - .attr("stroke-width", 5) - .style("pointer-events", "none") - - suggestive_bar = g.append("g").attr("class", "significant") - suggestive_bar.selectAll("empty") - .data([data.significant]) - .enter() - .append("line") - .attr("y1", (d) -> yscale(d)) - .attr("y2", (d) -> yscale(d)) - .attr("x1", margin.left) - .attr("x2", margin.left+width) - .attr("fill", "none") - .attr("stroke", significantcolor) - .attr("stroke-width", 5) - .style("pointer-events", "none") + if 'suggestive' of data + suggestive_bar = g.append("g").attr("class", "suggestive") + suggestive_bar.selectAll("empty") + .data([data.suggestive]) + .enter() + .append("line") + .attr("y1", (d) -> yscale(d)) + .attr("y2", (d) -> yscale(d)) + .attr("x1", margin.left) + .attr("x2", margin.left+width) + .attr("fill", "none") + .attr("stroke", suggestivecolor) + .attr("stroke-width", 5) + .style("pointer-events", "none") + + suggestive_bar = g.append("g").attr("class", "significant") + suggestive_bar.selectAll("empty") + .data([data.significant]) + .enter() + .append("line") + .attr("y1", (d) -> yscale(d)) + .attr("y2", (d) -> yscale(d)) + .attr("x1", margin.left) + .attr("x2", margin.left+width) + .attr("fill", "none") + .attr("stroke", significantcolor) + .attr("stroke-width", 5) + .style("pointer-events", "none") # lod curves by chr lodcurve = (chr, lodcolumn) -> @@ -248,7 +254,8 @@ lodchart = () -> .x((d) -> xscale[chr](d)) .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn])) - if data['additive'].length > 0 + #if data['additive'].length > 0 + if 'additive' of data additivecurve = (chr, lodcolumn) -> d3.svg.line() .x((d) -> xscale[chr](d)) @@ -256,16 +263,17 @@ lodchart = () -> curves = g.append("g").attr("id", "curves") - for chr in data.chrnames - curves.append("path") - .datum(data.posByChr[chr[0]]) - .attr("d", lodcurve(chr[0], lodvarnum)) - .attr("stroke", lodlinecolor) - .attr("fill", "none") - .attr("stroke-width", linewidth) - .style("pointer-events", "none") + #for chr in data.chrnames + # curves.append("path") + # .datum(data.posByChr[chr[0]]) + # .attr("d", lodcurve(chr[0], lodvarnum)) + # .attr("stroke", lodlinecolor) + # .attr("fill", "none") + # .attr("stroke-width", linewidth) + # .style("pointer-events", "none") - if data['additive'].length > 0 + #if data['additive'].length > 0 + if 'additive' of data for chr in data.chrnames curves.append("path") .datum(data.posByChr[chr[0]]) @@ -493,95 +501,96 @@ 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 = {} - data.additiveByChr = {} - - for chr,i in data.chrnames - data.posByChr[chr[0]] = [] - data.lodByChr[chr[0]] = [] - data.additiveByChr[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) - if data['additive'].length > 0 - additiveval = (data['additive'][j] for lodcolumn in data.lodnames) - lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) - data.additiveByChr[chr[0]].push(additiveval) - 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 = {} +# data.additiveByChr = {} +# +# for chr,i in data.chrnames +# data.posByChr[chr[0]] = [] +# data.lodByChr[chr[0]] = [] +# data.additiveByChr[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) +# if 'additive' of data +# #if data['additive'].length > 0 +# additiveval = (data['additive'][j] for lodcolumn in data.lodnames) +# lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) +# data.additiveByChr[chr[0]].push(additiveval) +# 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 +#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") +#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") diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js index 75adc792..0f91fc71 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/lod_chart.js @@ -1,5 +1,5 @@ // Generated by CoffeeScript 1.7.1 -var chrscales, formatAxis, lodchart, maxdiff, reorgLodData; +var lodchart; lodchart = function() { var additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; @@ -51,7 +51,7 @@ lodchart = function() { pointsAtMarkers = true; chart = function(selection) { return selection.each(function(data) { - var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _j, _len, _len1, _ref, _ref1; + var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _len, _ref; console.log("data:", data); lodvarname = lodvarname != null ? lodvarname : data.lodnames[0]; data[lodvarname] = (function() { @@ -64,18 +64,20 @@ lodchart = function() { } return _results; })(); - data['additive'] = (function() { - var _i, _len, _ref, _results; - _ref = data['additive']; - _results = []; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - x = _ref[_i]; - _results.push(Math.abs(x)); - } - return _results; - })(); + if ('additive' in data) { + data['additive'] = (function() { + var _i, _len, _ref, _results; + _ref = data['additive']; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + x = _ref[_i]; + _results.push(Math.abs(x)); + } + return _results; + })(); + } ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])]; - if (data['additive'].length > 0) { + if ('additive' in data) { additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])]; } lodvarnum = data.lodnames.indexOf(lodvarname); @@ -85,11 +87,11 @@ lodchart = function() { g = svg.select("g"); g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none"); yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]); - if (data['additive'].length > 0) { + if ('additive' in data) { additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]); } yticks = yticks != null ? yticks : yscale.ticks(nyticks); - if (data['additive'].length > 0) { + if ('additive' in data) { additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks); } data = reorgLodData(data, lodvarname); @@ -145,7 +147,7 @@ lodchart = function() { return formatAxis(yticks)(d); }); yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue"); - if (data['additive'].length > 0) { + if ('additive' in data) { rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1; additive_yaxis = g.append("g").attr("class", "y axis"); additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) { @@ -162,18 +164,20 @@ lodchart = function() { }); additive_yaxis.append("text").attr("class", "title").attr("y", margin.top + 1.5 * height).attr("x", margin.left + width + axispos.ytitle).text(additive_ylab).attr("transform", rotate_additive_ylab ? "rotate(270," + (margin.left + width + axispos.ytitle) + ", " + (margin.top + height * 1.5) + ")" : "").attr("text-anchor", "middle").attr("fill", "green"); } - suggestive_bar = g.append("g").attr("class", "suggestive"); - suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) { - return yscale(d); - }).attr("y2", function(d) { - return yscale(d); - }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", suggestivecolor).attr("stroke-width", 5).style("pointer-events", "none"); - suggestive_bar = g.append("g").attr("class", "significant"); - suggestive_bar.selectAll("empty").data([data.significant]).enter().append("line").attr("y1", function(d) { - return yscale(d); - }).attr("y2", function(d) { - return yscale(d); - }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", significantcolor).attr("stroke-width", 5).style("pointer-events", "none"); + if ('suggestive' in data) { + suggestive_bar = g.append("g").attr("class", "suggestive"); + suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", suggestivecolor).attr("stroke-width", 5).style("pointer-events", "none"); + suggestive_bar = g.append("g").attr("class", "significant"); + suggestive_bar.selectAll("empty").data([data.significant]).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", significantcolor).attr("stroke-width", 5).style("pointer-events", "none"); + } lodcurve = function(chr, lodcolumn) { return d3.svg.line().x(function(d) { return xscale[chr](d); @@ -181,7 +185,7 @@ lodchart = function() { return yscale(data.lodByChr[chr][i][lodcolumn]); }); }; - if (data['additive'].length > 0) { + if ('additive' in data) { additivecurve = function(chr, lodcolumn) { return d3.svg.line().x(function(d) { return xscale[chr](d); @@ -191,15 +195,10 @@ lodchart = function() { }; } curves = g.append("g").attr("id", "curves"); - _ref = data.chrnames; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - chr = _ref[_i]; - curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none"); - } - if (data['additive'].length > 0) { - _ref1 = data.chrnames; - for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { - chr = _ref1[_j]; + if ('additive' in data) { + _ref = data.chrnames; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + chr = _ref[_i]; curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); } } @@ -431,152 +430,3 @@ lodchart = function() { }; return chart; }; - -reorgLodData = function(data, lodvarname) { - var additiveval, chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2; - if (lodvarname == null) { - lodvarname = null; - } - data.posByChr = {}; - data.lodByChr = {}; - data.additiveByChr = {}; - _ref = data.chrnames; - for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) { - chr = _ref[i]; - data.posByChr[chr[0]] = []; - data.lodByChr[chr[0]] = []; - data.additiveByChr[chr[0]] = []; - _ref1 = data.pos; - for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) { - pos = _ref1[j]; - if (data.chr[j] === chr[0]) { - data.posByChr[chr[0]].push(pos); - if (!Array.isArray(data.lodnames)) { - data.lodnames = [data.lodnames]; - } - if (data['additive'].length > 0) { - additiveval = (function() { - var _k, _len2, _ref2, _results; - _ref2 = data.lodnames; - _results = []; - for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { - lodcolumn = _ref2[_k]; - _results.push(data['additive'][j]); - } - return _results; - })(); - } - lodval = (function() { - var _k, _len2, _ref2, _results; - _ref2 = data.lodnames; - _results = []; - for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { - lodcolumn = _ref2[_k]; - _results.push(data[lodcolumn][j]); - } - return _results; - })(); - data.additiveByChr[chr[0]].push(additiveval); - data.lodByChr[chr[0]].push(lodval); - } - } - } - if (lodvarname != null) { - data.markers = []; - _ref2 = data.markernames; - for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) { - marker = _ref2[i]; - if (marker !== "") { - data.markers.push({ - name: marker, - chr: data.chr[i], - pos: data.pos[i], - lod: data[lodvarname][i] - }); - } - } - } - return data; -}; - -chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) { - var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1; - chrStart = []; - chrEnd = []; - chrLength = []; - totalChrLength = 0; - maxd = 0; - _ref = data.chrnames; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - chr = _ref[_i]; - d = maxdiff(data.posByChr[chr[0]]); - if (d > maxd) { - maxd = d; - } - 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; - } - if (pad4heatmap) { - data.recwidth = maxd; - chrStart = chrStart.map(function(x) { - return x - maxd / 2; - }); - chrEnd = chrEnd.map(function(x) { - return x + maxd / 2; - }); - chrLength = chrLength.map(function(x) { - return x + maxd; - }); - totalChrLength += chrLength.length * maxd; - } - data.chrStart = []; - data.chrEnd = []; - cur = leftMargin; - if (!pad4heatmap) { - cur += chrGap / 2; - } - data.xscale = {}; - _ref1 = data.chrnames; - for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) { - chr = _ref1[i]; - 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; - data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]); - } - return data; -}; - -maxdiff = function(x) { - var d, i, result, _i, _ref; - if (x.length < 2) { - return null; - } - result = x[1] - x[0]; - if (x.length < 3) { - return result; - } - for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) { - d = x[i] - x[i - 1]; - if (d > result) { - result = d; - } - } - return result; -}; - -formatAxis = function(d) { - var ndig; - d = d[1] - d[0]; - ndig = Math.floor(Math.log(d % 10) / Math.log(10)); - if (ndig > 0) { - ndig = 0; - } - ndig = Math.abs(ndig); - return d3.format("." + ndig + "f"); -}; diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.coffee b/wqflask/wqflask/static/new/javascript/lodheatmap.coffee index 6cb8bfc7..6ffaefeb 100644 --- a/wqflask/wqflask/static/new/javascript/lodheatmap.coffee +++ b/wqflask/wqflask/static/new/javascript/lodheatmap.coffee @@ -8,7 +8,7 @@ lodheatmap = () -> chrGap = 8 titlepos = 20 rectcolor = d3.rgb(230, 230, 230) - colors = ["slateblue", "white", "crimson"] + colors = ["slateblue", "black", "yellow"] title = "" xlab = "Chromosome" ylab = "" @@ -33,7 +33,9 @@ lodheatmap = () -> rectHeight = yscale(0)-yscale(1) xLR = {} + console.log("data.chrnames:", data.chrnames) for chr in data.chrnames + console.log("chr is:", chr) xLR[chr] = getLeftRight(data.posByChr[chr]) # z-axis (color) limits; if not provided, make symmetric about 0 diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.js b/wqflask/wqflask/static/new/javascript/lodheatmap.js index 447287da..b009b4cd 100644 --- a/wqflask/wqflask/static/new/javascript/lodheatmap.js +++ b/wqflask/wqflask/static/new/javascript/lodheatmap.js @@ -20,7 +20,7 @@ lodheatmap = function() { chrGap = 8; titlepos = 20; rectcolor = d3.rgb(230, 230, 230); - colors = ["slateblue", "white", "crimson"]; + colors = ["slateblue", "black", "yellow"]; title = ""; xlab = "Chromosome"; ylab = ""; @@ -41,9 +41,11 @@ lodheatmap = function() { yscale.domain([-0.5, nlod - 0.5]).range([margin.top + height, margin.top]); rectHeight = yscale(0) - yscale(1); xLR = {}; + console.log("data.chrnames:", data.chrnames); _ref = data.chrnames; for (_i = 0, _len = _ref.length; _i < _len; _i++) { chr = _ref[_i]; + console.log("chr is:", chr); xLR[chr] = getLeftRight(data.posByChr[chr]); } zmin = 0; diff --git a/wqflask/wqflask/static/new/javascript/show_corr.js b/wqflask/wqflask/static/new/javascript/show_corr.js index 0a866548..97b1a7db 100644 --- a/wqflask/wqflask/static/new/javascript/show_corr.js +++ b/wqflask/wqflask/static/new/javascript/show_corr.js @@ -1,11 +1,8 @@ -// Generated by CoffeeScript 1.6.1 -(function() { - var root; +// Generated by CoffeeScript 1.7.1 +var root; - root = typeof exports !== "undefined" && exports !== null ? exports : this; +root = typeof exports !== "undefined" && exports !== null ? exports : this; - $(function() { - return root.scatter_plot = new Scatter_Plot(); - }); - -}).call(this); +$(function() { + return root.scatter_plot = new Scatter_Plot(); +}); diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html index 1ffbd5d8..81c4a9d9 100644 --- a/wqflask/wqflask/templates/heatmap.html +++ b/wqflask/wqflask/templates/heatmap.html @@ -1,5 +1,5 @@ {% extends "base.html" %} -{% block title %}Interval Mapping{% endblock %} +{% block title %}Heatmap{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> @@ -35,7 +35,10 @@ <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/lodheatmap.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/create_heatmap.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/curvechart.js"></script> +<!-- <script language="javascript" type="text/javascript" src="/static/new/javascript/create_heatmap.js"></script>--> + <script language="javascript" type="text/javascript" src="/static/new/javascript/iplotMScanone_noeff.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> {% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index b55189eb..3c448988 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -209,7 +209,7 @@ def heatmap_page(): start_vars = request.form temp_uuid = uuid.uuid4() - version = "v1" + version = "v4" key = "heatmap:{}:".format(version) + json.dumps(start_vars, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): |