diff options
Diffstat (limited to 'wqflask')
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"): |