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diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 00000000..dba13ed2 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +<http://www.gnu.org/licenses/>. diff --git a/README.md b/README.md index ffb476dc..3d95d05f 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,8 @@ genenetwork on github (May 7, 2012 by Lei Yan and Rob Williams) www.genenetwork.org -Released under Affero General Public License 3 (AGPLv3) +Released under Affero General Public License 3 (AGPLv3). See also +LICENSE.txt For background see: http://en.wikipedia.org/wiki/Genenetwork @@ -24,4 +25,4 @@ Funded by the National Institutes of Health and University of Tennessee Center for Integrative and Translational Genomics -=========== \ No newline at end of file +=========== diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index b17396e5..d46e4363 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -811,11 +811,11 @@ class PhenotypeDataSet(DataSet): WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND - PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id + PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id Order BY Strain.Name - """ % (trait, self.id) - results = g.db.execute(query).fetchall() + """ + results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -898,15 +898,17 @@ class GenotypeDataSet(DataSet): left join GenoSE on (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) WHERE - Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND + Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.Name = '%s' AND + GenoFreeze.Name = %s AND GenoXRef.DataId = GenoData.Id AND GenoData.StrainId = Strain.Id Order BY Strain.Name - """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name) - results = g.db.execute(query).fetchall() + """ + results = g.db.execute(query, + (webqtlDatabaseFunction.retrieve_species_id(self.group.name), + trait, self.name)).fetchall() return results diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 2e0e86fb..4a088bc8 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -292,6 +292,7 @@ class GeneralTrait(object): """ % (self.name, self.dataset.id) print("query is:", query) + assert self.name.isdigit() trait_info = g.db.execute(query).fetchone() #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name @@ -330,10 +331,10 @@ class GeneralTrait(object): trait_info = g.db.execute(query).fetchone() #print("trait_info is: ", pf(trait_info)) else: #Temp type - query = """SELECT %s FROM %s WHERE Name = %s - """ % (string.join(self.dataset.display_fields,','), - self.dataset.type, self.name) - trait_info = g.db.execute(query).fetchone() + query = """SELECT %s FROM %s WHERE Name = %s""" + trait_info = g.db.execute(query, + (string.join(self.dataset.display_fields,','), + self.dataset.type, self.name)).fetchone() if trait_info: self.haveinfo = True diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 1a5c19d9..6e35f00a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -49,3 +49,21 @@ def pylmm_command(default=None): path = get_setting('PYLMM_PATH',default,guess,get_valid_path) pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py' return path,pylmm_command + +def plink_command(default=None): + """ + Return the path to the repository and the python command to call + """ + def get_valid_path(path): + """Test for a valid repository""" + if path: + sys.stderr.write("Trying PLINK_PATH in "+path+"\n") + if path and os.path.isfile(path+'/plink'): + return path + else: + None + + guess = os.environ.get('HOME')+'/plink' + path = get_setting('PLINK_PATH',default,guess,get_valid_path) + plink_command = path+'/plink' + return path,plink_command \ No newline at end of file diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index ab746228..f842dde0 100755 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -881,22 +881,6 @@ def cmpGenoPos(A,B): except: return 0 -#XZhou: Must use "BINARY" to enable case sensitive comparison. -def authUser(name,password,db, encrypt=None): - try: - if encrypt: - query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password) - else: - query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password) - db.execute(query) - records = db.fetchone() - if not records: - raise ValueError - return records#(privilege,id,name,password,grpName) - except: - return (None, None, None, None, None) - - def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users): access_to_confidential_phenotype_trait = 0 if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index a42503c1..cec71777 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -115,7 +115,7 @@ class MrnaAssaySearch(DoSearch): DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch" - base_query = """SELECT ProbeSet.Name as TNAME, + base_query = """SELECT distinct ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, @@ -394,7 +394,7 @@ class GenotypeSearch(DoSearch): # This adds a clause to the query that matches the search term # against each field in search_fields (above) - fields_clause = [] + where_clause = [] if "'" not in self.search_term[0]: self.search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]" diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 07b0b81a..a8363a1f 100755 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -8,9 +8,9 @@ class Docs(object): sql = """ SELECT Docs.title, Docs.content FROM Docs - WHERE Docs.entry LIKE '%s' + WHERE Docs.entry LIKE %s """ - result = g.db.execute(sql % (entry)).fetchone() + result = g.db.execute(sql, str(entry)).fetchone() self.entry = entry self.title = result[0] self.content = result[1] diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 4b4b7f73..672a9401 100755 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -74,6 +74,7 @@ class IntervalMapping(object): json.dumps(self.json_data, webqtlConfig.TMPDIR + json_filename) self.js_data = dict( + result_score_type = "LRS", manhattan_plot = self.manhattan_plot, additive = self.additive, chromosomes = chromosome_mb_lengths, @@ -85,7 +86,10 @@ class IntervalMapping(object): def set_options(self, start_vars): """Sets various options (physical/genetic mapping, # permutations, which chromosome""" - self.num_permutations = int(start_vars['num_perm']) + if start_vars['num_perm'] == "": + self.num_permutations = 0 + else: + self.num_permutations = int(start_vars['num_perm']) if start_vars['manhattan_plot'] == "true": self.manhattan_plot = True else: diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 2b0e89b3..c003f5e8 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -39,9 +39,10 @@ from utility import helper_functions from utility import Plot, Bunch from utility import temp_data from utility.benchmark import Bench -from utility.tools import pylmm_command +from utility.tools import pylmm_command, plink_command PYLMM_PATH,PYLMM_COMMAND = pylmm_command() +PLINK_PATH,PLINK_COMMAND = plink_command() class MarkerRegression(object): @@ -178,6 +179,7 @@ class MarkerRegression(object): self.js_data = dict( + result_score_type = "LOD", json_data = self.json_data, this_trait = self.this_trait.name, data_set = self.dataset.name, @@ -458,29 +460,16 @@ class MarkerRegression(object): def run_plink(self): - - os.chdir("/home/zas1024/plink") - plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name)) self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename) - plink_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) - + plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename) + print("plink_command:", plink_command) + os.system(plink_command) count, p_values = self.parse_plink_output(plink_output_filename) - #gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % ( - # self.dataset.group.name, - # self.dataset.group.name, - # self.dataset.group.name) - #print("gemma_command:" + gemma_command) - # - #os.system(gemma_command) - # - #included_markers, p_values = self.parse_gemma_output() - # - #self.dataset.group.get_specified_markers(markers = included_markers) #for marker in self.dataset.group.markers.markers: # if marker['name'] not in included_markers: @@ -567,10 +556,7 @@ class MarkerRegression(object): # get strain name from ped file in order def get_samples_from_ped_file(self): - - os.chdir("/home/zas1024/plink") - - ped_file= open("{}.ped".format(self.dataset.group.name),"r") + ped_file= open("{}/{}.ped".format(PLINK_PATH, self.dataset.group.name),"r") line = ped_file.readline() sample_list=[] diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee index 76be5490..df176f52 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee @@ -1,4 +1,4 @@ -create_manhattan_plot = -> +create_lod_chart = -> h = 500 w = 1200 margin = {left:60, top:40, right:40, bottom: 40, inner:5} @@ -18,7 +18,7 @@ create_manhattan_plot = -> .height(h) .width(w) .margin(margin) - .ylab("LOD score") + .ylab(js_data.result_score_type + " score") .manhattanPlot(js_data.manhattan_plot) #.additive(additive) @@ -44,8 +44,13 @@ create_manhattan_plot = -> d3.select(this) .transition().duration(500).attr("r", r*3) .transition().duration(500).attr("r", r) - -create_manhattan_plot() + +$ -> + #window.setTimeout ( -> + # console.log(js_data) + #), 1000 + #window.setTimeout(create_lod_chart(), 1000) + root.create_lod_chart = create_lod_chart $("#export").click => #Get d3 SVG element diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js index f61f05bd..a7cea8a5 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.js +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js @@ -1,73 +1,76 @@ // Generated by CoffeeScript 1.8.0 -var create_manhattan_plot; +(function() { + var create_lod_chart; -create_manhattan_plot = function() { - var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; - h = 500; - w = 1200; - margin = { - left: 60, - top: 40, - right: 40, - bottom: 40, - inner: 5 - }; - halfh = h + margin.top + margin.bottom; - totalh = halfh * 2; - totalw = w + margin.left + margin.right; - if ('additive' in js_data) { - additive = js_data.additive; - } else { - additive = false; - } - console.log("js_data:", js_data); - mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab("LOD score").manhattanPlot(js_data.manhattan_plot); - data = js_data.json_data; - d3.select("div#topchart").datum(data).call(mychart); - chrrect = mychart.chrSelect(); - chrrect.on("mouseover", function() { - return d3.select(this).attr("fill", "#E9CFEC"); - }).on("mouseout", function(d, i) { - return d3.select(this).attr("fill", function() { - if (i % 2) { - return "#F1F1F9"; - } - return "#FBFBFF"; + create_lod_chart = function() { + var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; + h = 500; + w = 1200; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * 2; + totalw = w + margin.left + margin.right; + if ('additive' in js_data) { + additive = js_data.additive; + } else { + additive = false; + } + console.log("js_data:", js_data); + mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot); + data = js_data.json_data; + d3.select("div#topchart").datum(data).call(mychart); + chrrect = mychart.chrSelect(); + chrrect.on("mouseover", function() { + return d3.select(this).attr("fill", "#E9CFEC"); + }).on("mouseout", function(d, i) { + return d3.select(this).attr("fill", function() { + if (i % 2) { + return "#F1F1F9"; + } + return "#FBFBFF"; + }); + }); + return mychart.markerSelect().on("click", function(d) { + var r; + r = d3.select(this).attr("r"); + return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); }); - }); - return mychart.markerSelect().on("click", function(d) { - var r; - r = d3.select(this).attr("r"); - return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); - }); -}; + }; -create_manhattan_plot(); + root.create_lod_chart = create_lod_chart; -$("#export").click((function(_this) { - return function() { - var filename, form, svg, svg_xml; - svg = $("#topchart").find("svg")[0]; - svg_xml = (new XMLSerializer).serializeToString(svg); - console.log("svg_xml:", svg_xml); - filename = "manhattan_plot_" + js_data.this_trait; - form = $("#exportform"); - form.find("#data").val(svg_xml); - form.find("#filename").val(filename); - return form.submit(); - }; -})(this)); + $("#export").click((function(_this) { + return function() { + var filename, form, svg, svg_xml; + svg = $("#topchart").find("svg")[0]; + svg_xml = (new XMLSerializer).serializeToString(svg); + console.log("svg_xml:", svg_xml); + filename = "manhattan_plot_" + js_data.this_trait; + form = $("#exportform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }; + })(this)); -$("#export_pdf").click((function(_this) { - return function() { - var filename, form, svg, svg_xml; - svg = $("#topchart").find("svg")[0]; - svg_xml = (new XMLSerializer).serializeToString(svg); - console.log("svg_xml:", svg_xml); - filename = "manhattan_plot_" + js_data.this_trait; - form = $("#exportpdfform"); - form.find("#data").val(svg_xml); - form.find("#filename").val(filename); - return form.submit(); - }; -})(this)); + $("#export_pdf").click((function(_this) { + return function() { + var filename, form, svg, svg_xml; + svg = $("#topchart").find("svg")[0]; + svg_xml = (new XMLSerializer).serializeToString(svg); + console.log("svg_xml:", svg_xml); + filename = "manhattan_plot_" + js_data.this_trait; + form = $("#exportpdfform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }; + })(this)); + +}).call(this); diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee index b0f4b2f5..55ffdce0 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee @@ -1,514 +1,517 @@ -lodchart = () -> - 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 - manhattanPlot = false - additive = false - ylim = null - additive_ylim = null - nyticks = 5 - yticks = null - additive_yticks = null - chrGap = 8 - darkrect = "#F1F1F9" - lightrect = "#FBFBFF" - lodlinecolor = "darkslateblue" - additivelinecolor = "red" - linewidth = 2 - suggestivecolor = "gainsboro" - significantcolor = "#EBC7C7" - pointcolor = "#E9CFEC" # pink - pointsize = 0 # default = no visible points at markers - pointstroke = "black" - title = "" - xlab = "Chromosome" - ylab = "LRS score" - additive_ylab = "Additive Effect" - rotate_ylab = null - yscale = d3.scale.linear() - additive_yscale = d3.scale.linear() - xscale = null - pad4heatmap = false - lodcurve = null - lodvarname = null - markerSelect = null - chrSelect = null - pointsAtMarkers = true - - - ## the main function - chart = (selection) -> - selection.each (data) -> - - #console.log("data:", data) - - if manhattanPlot == true - pointcolor = "darkslateblue" - pointsize = 2 - - lodvarname = lodvarname ? data.lodnames[0] - data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values - ylim = ylim ? [0, d3.max(data[lodvarname])] - if additive - data['additive'] = (Math.abs(x) for x in data['additive']) - additive_ylim = additive_ylim ? [0, d3.max(data['additive'])] - - lodvarnum = data.lodnames.indexOf(lodvarname) - - # 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) - - # Update the inner dimensions. - g = svg.select("g") - - # box - 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 yticks not provided, use nyticks to choose pretty ones - yticks = yticks ? yscale.ticks(nyticks) - - #if data['additive'].length > 0 - if additive - additive_yscale.domain(additive_ylim) - .range([height+margin.top, margin.top+margin.inner + height/2]) - - additive_yticks = additive_yticks ? additive_yscale.ticks(nyticks) - - # reorganize lod,pos by chromosomes - reorgLodData(data, lodvarname) - - # add chromosome scales (for x-axis) - data = chrscales(data, width, chrGap, margin.left, pad4heatmap) - xscale = data.xscale - - # chr rectangles - chrSelect = - g.append("g").attr("class", "chrRect") - .selectAll("empty") - .data(data.chrnames) - .enter() - .append("rect") - .attr("id", (d) -> "chrrect#{d[0]}") - .attr("x", (d,i) -> - return data.chrStart[i] if i==0 and pad4heatmap - data.chrStart[i]-chrGap/2) - .attr("width", (d,i) -> - return data.chrEnd[i] - data.chrStart[i]+chrGap/2 if (i==0 or i+1 == data.chrnames.length) and pad4heatmap - data.chrEnd[i] - data.chrStart[i]+chrGap) - .attr("y", margin.top) - .attr("height", height) - .attr("fill", (d,i) -> - return darkrect if i % 2 - lightrect) - .attr("stroke", "none") - .on("click", (d) -> - console.log("d is:", d) - redraw_plot(d) - ) - - # x-axis labels - xaxis = g.append("g").attr("class", "x axis") - xaxis.selectAll("empty") - .data(data.chrnames) - .enter() - .append("text") - .text((d) -> d[0]) - .attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2) - .attr("y", margin.top+height+axispos.xlabel) - .attr("dominant-baseline", "hanging") - .attr("text-anchor", "middle") - .attr("cursor", "pointer") - .on("click", (d) -> - redraw_plot(d) - ) - - xaxis.append("text").attr("class", "title") - .attr("y", margin.top+height+axispos.xtitle) - .attr("x", margin.left+width/2) - .attr("fill", "slateblue") - .text(xlab) - - - redraw_plot = (chr_ob) -> - #console.log("chr_name is:", chr_ob[0]) - #console.log("chr_length is:", chr_ob[1]) - $('#topchart').remove() - $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>') - chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot) - - # 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+7) - .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) - .attr("fill", "blue") - .attr("dominant-baseline", "middle") - .attr("text-anchor", "end") - .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 "") - .attr("text-anchor", "middle") - .attr("fill", "slateblue") - - #if data['additive'].length > 0 - if additive - rotate_additive_ylab = 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", (d) -> additive_yscale(d)) - .attr("y2", (d) -> additive_yscale(d)) - .attr("x1", margin.left + width) - .attr("x2", margin.left + width - 7) - .attr("fill", "none") - .attr("stroke", "white") - .attr("stroke-width", 1) - .style("pointer-events", "none") - - additive_yaxis.selectAll("empty") - .data(additive_yticks) - .enter() - .append("text") - .attr("y", (d) -> additive_yscale(d)) - .attr("x", (d) -> margin.left + width + axispos.ylabel + 20) - .attr("fill", "green") - .attr("dominant-baseline", "middle") - .attr("text-anchor", "end") - .text((d) -> formatAxis(additive_yticks)(d)) - - 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", if rotate_additive_ylab then "rotate(270,#{margin.left + width + axispos.ytitle}, #{margin.top+height*1.5})" else "") - .attr("text-anchor", "middle") - .attr("fill", "green") - - 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") - - if manhattanPlot == false - # lod curves by chr - lodcurve = (chr, lodcolumn) -> - d3.svg.line() - .x((d) -> xscale[chr](d)) - .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn])) - - if additive - additivecurve = (chr, lodcolumn) -> - d3.svg.line() - .x((d) -> xscale[chr](d)) - .y((d,i) -> additive_yscale(data.additiveByChr[chr][i][lodcolumn])) - - 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") - - if additive - for chr in data.chrnames - 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") - - # points at markers - console.log("before pointsize") - if pointsize > 0 - console.log("pointsize > 0 !!!") - markerpoints = g.append("g").attr("id", "markerpoints_visible") - markerpoints.selectAll("empty") - .data(data.markers) - .enter() - .append("circle") - .attr("cx", (d) -> xscale[d.chr](d.pos)) - .attr("cy", (d) -> yscale(d.lod)) - .attr("r", pointsize) - .attr("fill", pointcolor) - .attr("stroke", pointstroke) - .attr("pointer-events", "hidden") - - # title - titlegrp = g.append("g").attr("class", "title") - .append("text") - .attr("x", margin.left+width/2) - .attr("y", margin.top-titlepos) - .text(title) - - # another box around edge - g.append("rect") - .attr("x", margin.left) - .attr("y", margin.top) - .attr("height", height) - .attr("width", () -> - return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap - data.chrEnd[-1..][0]-margin.left+chrGap/2) - .attr("fill", "none") - .attr("stroke", "black") - .attr("stroke-width", "none") - - if pointsAtMarkers - # these hidden points are what gets selected...a bit larger - hiddenpoints = g.append("g").attr("id", "markerpoints_hidden") - - markertip = d3.tip() - .attr('class', 'd3-tip') - .html((d) -> - [d.name, " LRS = #{d3.format('.2f')(d.lod)}"]) - .direction("e") - .offset([0,10]) - svg.call(markertip) - - markerSelect = - hiddenpoints.selectAll("empty") - .data(data.markers) - .enter() - .append("circle") - .attr("cx", (d) -> xscale[d.chr](d.pos)) - .attr("cy", (d) -> yscale(d.lod)) - .attr("id", (d) -> d.name) - .attr("r", d3.max([pointsize*2, 3])) - .attr("opacity", 0) - .attr("fill", pointcolor) - .attr("stroke", pointstroke) - .attr("stroke-width", "1") - .on "mouseover.paneltip", (d) -> - d3.select(this).attr("opacity", 1) - markertip.show(d) - .on "mouseout.paneltip", -> - d3.select(this).attr("opacity", 0) - .call(markertip.hide) - - ## configuration parameters - chart.width = (value) -> - return width unless arguments.length - width = value - chart - - chart.height = (value) -> - return height unless arguments.length - height = value - chart - - chart.margin = (value) -> - return margin unless arguments.length - margin = value - chart - - chart.titlepos = (value) -> - return titlepos unless arguments.length - titlepos - chart - - chart.axispos = (value) -> - return axispos unless arguments.length - axispos = value - chart - - chart.manhattanPlot = (value) -> - return manhattanPlot unless arguments.length - manhattanPlot = value - chart - - chart.ylim = (value) -> - return ylim unless arguments.length - ylim = value - chart - - #if data['additive'].length > 0 - chart.additive_ylim = (value) -> - return additive_ylim unless arguments.length - additive_ylim = value - chart - - chart.nyticks = (value) -> - return nyticks unless arguments.length - nyticks = value - chart - - chart.yticks = (value) -> - return yticks unless arguments.length - yticks = value - chart - - chart.chrGap = (value) -> - return chrGap unless arguments.length - chrGap = value - chart - - chart.darkrect = (value) -> - return darkrect unless arguments.length - darkrect = value - chart - - chart.lightrect = (value) -> - return lightrect unless arguments.length - lightrect = value - chart - - chart.linecolor = (value) -> - return linecolor unless arguments.length - linecolor = value - chart - - chart.linewidth = (value) -> - return linewidth unless arguments.length - linewidth = value - chart - - chart.pointcolor = (value) -> - return pointcolor unless arguments.length - pointcolor = value - chart - - chart.pointsize = (value) -> - return pointsize unless arguments.length - pointsize = value - chart - - chart.pointstroke = (value) -> - return pointstroke unless arguments.length - pointstroke = value - chart - - chart.title = (value) -> - return title unless arguments.length - title = value - chart - - chart.xlab = (value) -> - return xlab unless arguments.length - xlab = value - chart - - chart.ylab = (value) -> - return ylab unless arguments.length - ylab = value - chart - - chart.rotate_ylab = (value) -> - return rotate_ylab if !arguments.length - rotate_ylab = value - chart - - chart.lodvarname = (value) -> - return lodvarname unless arguments.length - lodvarname = value - chart - - chart.pad4heatmap = (value) -> - return pad4heatmap unless arguments.length - pad4heatmap = value - chart - - chart.pointsAtMarkers = (value) -> - return pointsAtMarkers unless arguments.length - pointsAtMarkers = value - chart - - chart.yscale = () -> - return yscale - - chart.additive = () -> - return additive - - #if data['additive'].length > 0 - chart.additive_yscale = () -> - return additive_yscale - - chart.xscale = () -> - return xscale - - if manhattanPlot == false - chart.lodcurve = () -> - return lodcurve - - #if data['additive'].length > 0 - chart.additivecurve = () -> - return additivecurve - - chart.markerSelect = () -> - return markerSelect - - chart.chrSelect = () -> - return chrSelect - - # return the chart function - chart - +lodchart = () -> + 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 + manhattanPlot = false + additive = false + ylim = null + additive_ylim = null + nyticks = 5 + yticks = null + additive_yticks = null + chrGap = 8 + darkrect = "#F1F1F9" + lightrect = "#FBFBFF" + lodlinecolor = "darkslateblue" + additivelinecolor = "red" + linewidth = 2 + suggestivecolor = "gainsboro" + significantcolor = "#EBC7C7" + pointcolor = "#E9CFEC" # pink + pointsize = 0 # default = no visible points at markers + pointstroke = "black" + title = "" + xlab = "Chromosome" + ylab = "LRS score" + additive_ylab = "Additive Effect" + rotate_ylab = null + yscale = d3.scale.linear() + additive_yscale = d3.scale.linear() + xscale = null + pad4heatmap = false + lodcurve = null + lodvarname = null + markerSelect = null + chrSelect = null + pointsAtMarkers = true + + + ## the main function + chart = (selection) -> + selection.each (data) -> + + #console.log("data:", data) + + if manhattanPlot == true + pointcolor = "darkslateblue" + pointsize = 2 + + lodvarname = lodvarname ? data.lodnames[0] + data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values + ylim = ylim ? [0, d3.max(data[lodvarname])] + if additive + data['additive'] = (Math.abs(x) for x in data['additive']) + additive_ylim = additive_ylim ? [0, d3.max(data['additive'])] + + lodvarnum = data.lodnames.indexOf(lodvarname) + + # 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) + + # Update the inner dimensions. + g = svg.select("g") + + # box + 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 yticks not provided, use nyticks to choose pretty ones + yticks = yticks ? yscale.ticks(nyticks) + + #if data['additive'].length > 0 + if additive + additive_yscale.domain(additive_ylim) + .range([height+margin.top, margin.top+margin.inner + height/2]) + + additive_yticks = additive_yticks ? additive_yscale.ticks(nyticks) + + # reorganize lod,pos by chromosomes + reorgLodData(data, lodvarname) + + # add chromosome scales (for x-axis) + data = chrscales(data, width, chrGap, margin.left, pad4heatmap) + xscale = data.xscale + + # chr rectangles + chrSelect = + g.append("g").attr("class", "chrRect") + .selectAll("empty") + .data(data.chrnames) + .enter() + .append("rect") + .attr("id", (d) -> "chrrect#{d[0]}") + .attr("x", (d,i) -> + return data.chrStart[i] if i==0 and pad4heatmap + data.chrStart[i]-chrGap/2) + .attr("width", (d,i) -> + return data.chrEnd[i] - data.chrStart[i]+chrGap/2 if (i==0 or i+1 == data.chrnames.length) and pad4heatmap + data.chrEnd[i] - data.chrStart[i]+chrGap) + .attr("y", margin.top) + .attr("height", height) + .attr("fill", (d,i) -> + return darkrect if i % 2 + + lightrect) + .attr("stroke", "none") + .on("click", (d) -> + console.log("d is:", d) + redraw_plot(d) + ) + + # x-axis labels + xaxis = g.append("g").attr("class", "x axis") + xaxis.selectAll("empty") + .data(data.chrnames) + .enter() + .append("text") + .text((d) -> d[0]) + .attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2) + .attr("y", margin.top+height+axispos.xlabel) + .attr("dominant-baseline", "hanging") + .attr("text-anchor", "middle") + .attr("cursor", "pointer") + .on("click", (d) -> + redraw_plot(d) + ) + + xaxis.append("text").attr("class", "title") + .attr("y", margin.top+height+axispos.xtitle) + .attr("x", margin.left+width/2) + .attr("fill", "slateblue") + .text(xlab) + + + redraw_plot = (chr_ob) -> + #console.log("chr_name is:", chr_ob[0]) + #console.log("chr_length is:", chr_ob[1]) + $('#topchart').remove() + $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>') + chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot) + + # 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+7) + .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) + .attr("fill", "blue") + .attr("dominant-baseline", "middle") + .attr("text-anchor", "end") + .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 "") + .attr("text-anchor", "middle") + .attr("fill", "slateblue") + + #if data['additive'].length > 0 + if additive + rotate_additive_ylab = 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", (d) -> additive_yscale(d)) + .attr("y2", (d) -> additive_yscale(d)) + .attr("x1", margin.left + width) + .attr("x2", margin.left + width - 7) + .attr("fill", "none") + .attr("stroke", "white") + .attr("stroke-width", 1) + .style("pointer-events", "none") + + additive_yaxis.selectAll("empty") + .data(additive_yticks) + .enter() + .append("text") + .attr("y", (d) -> additive_yscale(d)) + .attr("x", (d) -> margin.left + width + axispos.ylabel + 20) + .attr("fill", "green") + .attr("dominant-baseline", "middle") + .attr("text-anchor", "end") + .text((d) -> formatAxis(additive_yticks)(d)) + + 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", if rotate_additive_ylab then "rotate(270,#{margin.left + width + axispos.ytitle}, #{margin.top+height*1.5})" else "") + .attr("text-anchor", "middle") + .attr("fill", "green") + + 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") + + if manhattanPlot == false + # lod curves by chr + lodcurve = (chr, lodcolumn) -> + d3.svg.line() + .x((d) -> xscale[chr](d)) + .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn])) + + if additive + additivecurve = (chr, lodcolumn) -> + d3.svg.line() + .x((d) -> xscale[chr](d)) + .y((d,i) -> additive_yscale(data.additiveByChr[chr][i][lodcolumn])) + + curves = g.append("g").attr("id", "curves") + + for chr in data.chrnames + if chr.indexOf(data['chr']) + 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 additive + for chr in data.chrnames + if chr.indexOf(data['chr']) + 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") + + # points at markers + console.log("before pointsize") + if pointsize > 0 + console.log("pointsize > 0 !!!") + markerpoints = g.append("g").attr("id", "markerpoints_visible") + markerpoints.selectAll("empty") + .data(data.markers) + .enter() + .append("circle") + .attr("cx", (d) -> xscale[d.chr](d.pos)) + .attr("cy", (d) -> yscale(d.lod)) + .attr("r", pointsize) + .attr("fill", pointcolor) + .attr("stroke", pointstroke) + .attr("pointer-events", "hidden") + + # title + titlegrp = g.append("g").attr("class", "title") + .append("text") + .attr("x", margin.left+width/2) + .attr("y", margin.top-titlepos) + .text(title) + + # another box around edge + g.append("rect") + .attr("x", margin.left) + .attr("y", margin.top) + .attr("height", height) + .attr("width", () -> + return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap + data.chrEnd[-1..][0]-margin.left+chrGap/2) + .attr("fill", "none") + .attr("stroke", "black") + .attr("stroke-width", "none") + + if pointsAtMarkers + # these hidden points are what gets selected...a bit larger + hiddenpoints = g.append("g").attr("id", "markerpoints_hidden") + + markertip = d3.tip() + .attr('class', 'd3-tip') + .html((d) -> + [d.name, " LRS = #{d3.format('.2f')(d.lod)}"]) + .direction("e") + .offset([0,10]) + svg.call(markertip) + + markerSelect = + hiddenpoints.selectAll("empty") + .data(data.markers) + .enter() + .append("circle") + .attr("cx", (d) -> xscale[d.chr](d.pos)) + .attr("cy", (d) -> yscale(d.lod)) + .attr("id", (d) -> d.name) + .attr("r", d3.max([pointsize*2, 3])) + .attr("opacity", 0) + .attr("fill", pointcolor) + .attr("stroke", pointstroke) + .attr("stroke-width", "1") + .on "mouseover.paneltip", (d) -> + d3.select(this).attr("opacity", 1) + markertip.show(d) + .on "mouseout.paneltip", -> + d3.select(this).attr("opacity", 0) + .call(markertip.hide) + + ## configuration parameters + chart.width = (value) -> + return width unless arguments.length + width = value + chart + + chart.height = (value) -> + return height unless arguments.length + height = value + chart + + chart.margin = (value) -> + return margin unless arguments.length + margin = value + chart + + chart.titlepos = (value) -> + return titlepos unless arguments.length + titlepos + chart + + chart.axispos = (value) -> + return axispos unless arguments.length + axispos = value + chart + + chart.manhattanPlot = (value) -> + return manhattanPlot unless arguments.length + manhattanPlot = value + chart + + chart.ylim = (value) -> + return ylim unless arguments.length + ylim = value + chart + + #if data['additive'].length > 0 + chart.additive_ylim = (value) -> + return additive_ylim unless arguments.length + additive_ylim = value + chart + + chart.nyticks = (value) -> + return nyticks unless arguments.length + nyticks = value + chart + + chart.yticks = (value) -> + return yticks unless arguments.length + yticks = value + chart + + chart.chrGap = (value) -> + return chrGap unless arguments.length + chrGap = value + chart + + chart.darkrect = (value) -> + return darkrect unless arguments.length + darkrect = value + chart + + chart.lightrect = (value) -> + return lightrect unless arguments.length + lightrect = value + chart + + chart.linecolor = (value) -> + return linecolor unless arguments.length + linecolor = value + chart + + chart.linewidth = (value) -> + return linewidth unless arguments.length + linewidth = value + chart + + chart.pointcolor = (value) -> + return pointcolor unless arguments.length + pointcolor = value + chart + + chart.pointsize = (value) -> + return pointsize unless arguments.length + pointsize = value + chart + + chart.pointstroke = (value) -> + return pointstroke unless arguments.length + pointstroke = value + chart + + chart.title = (value) -> + return title unless arguments.length + title = value + chart + + chart.xlab = (value) -> + return xlab unless arguments.length + xlab = value + chart + + chart.ylab = (value) -> + return ylab unless arguments.length + ylab = value + chart + + chart.rotate_ylab = (value) -> + return rotate_ylab if !arguments.length + rotate_ylab = value + chart + + chart.lodvarname = (value) -> + return lodvarname unless arguments.length + lodvarname = value + chart + + chart.pad4heatmap = (value) -> + return pad4heatmap unless arguments.length + pad4heatmap = value + chart + + chart.pointsAtMarkers = (value) -> + return pointsAtMarkers unless arguments.length + pointsAtMarkers = value + chart + + chart.yscale = () -> + return yscale + + chart.additive = () -> + return additive + + #if data['additive'].length > 0 + chart.additive_yscale = () -> + return additive_yscale + + chart.xscale = () -> + return xscale + + if manhattanPlot == false + chart.lodcurve = () -> + return lodcurve + + #if data['additive'].length > 0 + chart.additivecurve = () -> + return additivecurve + + chart.markerSelect = () -> + return markerSelect + + chart.chrSelect = () -> + return chrSelect + + # return the chart function + chart + diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js index 92289bfe..631d8632 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/lod_chart.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.8.0 +// Generated by CoffeeScript 1.9.2 var lodchart; lodchart = function() { @@ -53,33 +53,33 @@ 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, j, k, len, len1, lodvarnum, markerpoints, markertip, redraw_plot, ref, ref1, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis; if (manhattanPlot === true) { pointcolor = "darkslateblue"; pointsize = 2; } lodvarname = lodvarname != null ? lodvarname : data.lodnames[0]; data[lodvarname] = (function() { - var _i, _len, _ref, _results; - _ref = data[lodvarname]; - _results = []; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - x = _ref[_i]; - _results.push(Math.abs(x)); + var j, len, ref, results; + ref = data[lodvarname]; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + results.push(Math.abs(x)); } - return _results; + return results; })(); ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])]; if (additive) { 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)); + var j, len, ref, results; + ref = data['additive']; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + results.push(Math.abs(x)); } - return _results; + return results; })(); additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])]; } @@ -196,16 +196,20 @@ 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"); + ref = data.chrnames; + for (j = 0, len = ref.length; j < len; j++) { + chr = ref[j]; + if (chr.indexOf(data['chr'])) { + 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 (additive) { - _ref1 = data.chrnames; - for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { - chr = _ref1[_j]; - 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"); + ref1 = data.chrnames; + for (k = 0, len1 = ref1.length; k < len1; k++) { + chr = ref1[k]; + if (chr.indexOf(data['chr'])) { + 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"); + } } } } @@ -450,4 +454,4 @@ lodchart = function() { return chrSelect; }; return chart; -}; +}; \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee index a3bc0b44..f7b51457 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.coffee +++ b/wqflask/wqflask/static/new/javascript/panelutil.coffee @@ -30,16 +30,15 @@ reorgLodData = (data, lodvarname=null) -> data.lodByChr = {} for chr,i in data.chrnames - #console.log("chr:", chr) - data.posByChr[chr[0]] = [] - data.lodByChr[chr[0]] = [] - for pos, j in data.pos - if data.chr[j].toString() == chr[0] - #console.log(data.chr[j] + " AND " + chr[0]) - data.posByChr[chr[0]].push(pos) - data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames) - lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) - data.lodByChr[chr[0]].push(lodval) + if data.chr.indexOf(chr[0]) + data.posByChr[chr[0]] = [] + data.lodByChr[chr[0]] = [] + for pos, j in data.pos + if data.chr[j].toString() == chr[0] + data.posByChr[chr[0]].push(pos) + data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames) + lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) + data.lodByChr[chr[0]].push(lodval) #console.log("data.posByChr:", data.posByChr) diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js index 3a180e60..7c14f4de 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.js +++ b/wqflask/wqflask/static/new/javascript/panelutil.js @@ -106,10 +106,13 @@ chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) { 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]; + //rng = d3.extent(data.posByChr[chr[0]]); + //chrStart.push(rng[0]); + //chrEnd.push(rng[1]); + //L = rng[1] - rng[0]; + chrStart.push(0); + chrEnd.push(chr[1]); + L = chr[1] chrLength.push(L); totalChrLength += L; } @@ -436,4 +439,4 @@ abs = function(x) { return x; } return Math.abs(x); -}; +}; \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee index 881ea74d..211fedae 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -63,10 +63,12 @@ do_ajax_post = (url, form_data) -> console.log(xhr) clearInterval(this.my_timer) $('#progress_bar_container').modal('hide') + $('#static_progress_bar_container').modal('hide') $("body").html("We got an error.") success: (data) => clearInterval(this.my_timer) $('#progress_bar_container').modal('hide') + $('#static_progress_bar_container').modal('hide') open_mapping_results(data) #$("body").html(data) ) @@ -76,36 +78,22 @@ do_ajax_post = (url, form_data) -> return false open_mapping_results = (data) -> + #results_window = window.open("/mapping_results_container") + #results_window.onload = -> + # results_window.document.getElementById("mapping_results_container").innerHTML = data + $.colorbox( - html: data - href: "#mapping_results_holder" - height: "90%" - width: "90%" + html: data + href: "#mapping_results_holder" + height: "90%" + width: "90%" + onComplete: => root.create_lod_chart() ) showalert = (message,alerttype) -> $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">×</a><span>'+message+'</span></div>') -$("#interval_mapping_compute").click(() => - showalert("One or more outliers exist in this data set. Please review values before mapping. \ - Including outliers when mapping may lead to misleading results. \ - We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \ - or simply deleting them.", "alert-success") - console.log("In interval mapping") - $("#progress_bar_container").modal() - url = "/interval_mapping" - - $('input[name=method]').val("reaper") - $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()) - $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')) - $('input[name=suggestive]').val($('input[name=suggestive_reaper]')) - form_data = $('#trait_data_form').serialize() - console.log("form_data is:", form_data) - - do_ajax_post(url, form_data) -) - $('#suggestive').hide() $('input[name=display_all]').change(() => @@ -116,8 +104,8 @@ $('input[name=display_all]').change(() => $('#suggestive').hide() ) -$("#pylmm_compute").click(() => - $("#progress_bar_container").modal({show:true}) +$("#pylmm_compute").on("click", => + $("#progress_bar_container").modal() url = "/marker_regression" $('input[name=method]').val("pylmm") $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()) @@ -133,7 +121,7 @@ $("#pylmm_compute").click(() => -$("#rqtl_geno_compute").click(() => +$("#rqtl_geno_compute").on("click", => $("#progress_bar_container").modal() url = "/marker_regression" $('input[name=method]').val("rqtl_geno") @@ -150,7 +138,7 @@ $("#rqtl_geno_compute").click(() => ) -$("#plink_compute").click(() => +$("#plink_compute").on("click", => $("#static_progress_bar_container").modal() url = "/marker_regression" $('input[name=method]').val("plink") @@ -163,7 +151,7 @@ $("#plink_compute").click(() => do_ajax_post(url, form_data) ) -$("#gemma_compute").click(() => +$("#gemma_compute").on("click", => console.log("RUNNING GEMMA") $("#static_progress_bar_container").modal() url = "/marker_regression" @@ -177,6 +165,25 @@ $("#gemma_compute").click(() => do_ajax_post(url, form_data) ) +$("#interval_mapping_compute").on("click", => + showalert("One or more outliers exist in this data set. Please review values before mapping. \ + Including outliers when mapping may lead to misleading results. \ + We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \ + or simply deleting them.", "alert-success") + console.log("In interval mapping") + $("#progress_bar_container").modal() + url = "/interval_mapping" + + $('input[name=method]').val("reaper") + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()) + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')) + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')) + form_data = $('#trait_data_form').serialize() + console.log("form_data is:", form_data) + + do_ajax_post(url, form_data) +) + #$(".submit_special").click(submit_special) composite_mapping_fields = -> diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 1779df4b..259e4685 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -1,4 +1,4 @@ -// Generated by CoffeeScript 1.8.0 +// Generated by CoffeeScript 1.9.2 var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, showalert, submit_special, toggle_enable_disable, update_time_remaining; submit_special = function() { @@ -100,31 +100,19 @@ open_mapping_results = function(data) { html: data, href: "#mapping_results_holder", height: "90%", - width: "90%" + width: "90%", + onComplete: (function(_this) { + return function() { + return root.create_lod_chart(); + }; + })(this) }); }; showalert = function(message, alerttype) { - return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>'); + return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">×</a><span>' + message + '</span></div>'); }; -$("#interval_mapping_compute").click((function(_this) { - return function() { - var form_data, url; - showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success"); - console.log("In interval mapping"); - $("#progress_bar_container").modal(); - url = "/interval_mapping"; - $('input[name=method]').val("reaper"); - $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); - $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); - $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); - form_data = $('#trait_data_form').serialize(); - console.log("form_data is:", form_data); - return do_ajax_post(url, form_data); - }; -})(this)); - $('#suggestive').hide(); $('input[name=display_all]').change((function(_this) { @@ -138,12 +126,10 @@ $('input[name=display_all]').change((function(_this) { }; })(this)); -$("#pylmm_compute").click((function(_this) { +$("#pylmm_compute").on("click", (function(_this) { return function() { var form_data, url; - $("#progress_bar_container").modal({ - show: true - }); + $("#progress_bar_container").modal(); url = "/marker_regression"; $('input[name=method]').val("pylmm"); $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()); @@ -154,7 +140,7 @@ $("#pylmm_compute").click((function(_this) { }; })(this)); -$("#rqtl_geno_compute").click((function(_this) { +$("#rqtl_geno_compute").on("click", (function(_this) { return function() { var form_data, url; $("#progress_bar_container").modal(); @@ -169,14 +155,12 @@ $("#rqtl_geno_compute").click((function(_this) { }; })(this)); -$("#plink_compute").click((function(_this) { +$("#plink_compute").on("click", (function(_this) { return function() { var form_data, url; $("#static_progress_bar_container").modal(); url = "/marker_regression"; $('input[name=method]').val("plink"); - $('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val()); - $('input[name=suggestive]').val($('input[name=suggestive_plink]').val()); $('input[name=maf]').val($('input[name=maf_plink]').val()); form_data = $('#trait_data_form').serialize(); console.log("form_data is:", form_data); @@ -184,7 +168,7 @@ $("#plink_compute").click((function(_this) { }; })(this)); -$("#gemma_compute").click((function(_this) { +$("#gemma_compute").on("click", (function(_this) { return function() { var form_data, url; console.log("RUNNING GEMMA"); @@ -198,6 +182,23 @@ $("#gemma_compute").click((function(_this) { }; })(this)); +$("#interval_mapping_compute").on("click", (function(_this) { + return function() { + var form_data, url; + showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success"); + console.log("In interval mapping"); + $("#progress_bar_container").modal(); + url = "/interval_mapping"; + $('input[name=method]').val("reaper"); + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); + form_data = $('#trait_data_form').serialize(); + console.log("form_data is:", form_data); + return do_ajax_post(url, form_data); + }; +})(this)); + composite_mapping_fields = function() { return $(".composite_fields").toggle(); }; @@ -220,4 +221,4 @@ $("#choose_closet_control").change(function() { $("#display_all_lrs").change(function() { return toggle_enable_disable("#suggestive_lrs"); -}); +}); \ No newline at end of file diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 462a59a2..78682710 100755 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -1,3 +1,4 @@ +{% from "base_macro.html" import header, flash_me, timeago %} <!DOCTYPE HTML> <html lang="en"> <html xmlns="http://www.w3.org/1999/xhtml"> @@ -10,12 +11,6 @@ <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" /> <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" /> <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" /> - - <!-- HTML5 shim, for IE6-8 support of HTML5 elements --> - <!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> - <![endif]--> - <link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/main.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/parsley.css" /> @@ -25,37 +20,6 @@ </head> -{% macro header(main, second) %} - <header class="jumbotron subhead" id="overview" > - <div class="container"> - <h1>{{ main }}</h1> - <p class="lead"> - {{ second }} - </p> - </div> - </header> - - {{ flash_me() }} -{% endmacro %} - - -{% macro flash_me() -%} - {% with messages = get_flashed_messages(with_categories=true) %} - {% if messages %} - <div class="container"> - {% for category, message in messages %} - <div class="alert {{ category }}">{{ message }}</div> - {% endfor %} - </div> - {% endif %} - {% endwith %} -{% endmacro %} - -{% macro timeago(timestamp) %} -<time class="timeago" datetime="{{ timestamp }}">{{ timestamp }}</time> -{% endmacro %} - - <body style="width: 1500px !important;"> <!-- Navbar ================================================== --> diff --git a/wqflask/wqflask/templates/base_macro.html b/wqflask/wqflask/templates/base_macro.html new file mode 100644 index 00000000..c2905ebe --- /dev/null +++ b/wqflask/wqflask/templates/base_macro.html @@ -0,0 +1,28 @@ +{% macro flash_me() -%} + {% with messages = get_flashed_messages(with_categories=true) %} + {% if messages %} + <div class="container"> + {% for category, message in messages %} + <div class="alert {{ category }}">{{ message }}</div> + {% endfor %} + </div> + {% endif %} + {% endwith %} +{% endmacro %} + +{% macro header(main, second) %} + <header class="jumbotron subhead" id="overview" > + <div class="container"> + <h1>{{ main }}</h1> + <p class="lead"> + {{ second }} + </p> + </div> + </header> + + {{ flash_me() }} +{% endmacro %} + +{% macro timeago(timestamp) %} +<time class="timeago" datetime="{{ timestamp }}">{{ timestamp }}</time> +{% endmacro %} diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html deleted file mode 100755 index 82a96ba1..00000000 --- a/wqflask/wqflask/templates/interval_mapping.html +++ /dev/null @@ -1,116 +0,0 @@ -{% block css %} -<!-- <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />--> - <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.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" /> -{% endblock %} -{% block content %} <!-- Start of body --> - - - <div id="mapping_results" class="container"> - <div> - <h2> - Whole Genome Mapping - </h2> - <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post"> - <input type="hidden" id="data" name="data" value=""> - <input type="hidden" id="filename" name="filename" value=""> - <input type="submit" id="export" value="Download SVG"> - </form> - <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post"> - <input type="hidden" id="data" name="data" value=""> - <input type="hidden" id="filename" name="filename" value=""> - <input type="submit" id="export_pdf" value="Download PDF"> - </form> - </div> - <div id="chart_container"> - <div class="qtlcharts" id="topchart"> - - </div> - </div> - <div> - <h2> - Results - </h2> - </div> - <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered"> - <thead> - <tr> - <td>Index</td> - <td>LRS Score</td> - <td>Chr</td> - <td>Mb</td> - <td>Locus</td> - <td>Additive Effect</td> - </tr> - </thead> - <tbody> - {% for marker in qtl_results %} - <tr> - <td>{{ loop.index }}</td> - <td>{{ marker.lrs_value|float }}</td> - <td>{{ marker.chr|int }}</td> - <td>{{ marker.Mb|float }}</td> - <td>{{ marker.name }}</td> - <td>{{ marker.additive|float }}</td> - </tr> - {% endfor %} - </tbody> - </table> - - </div> - - <!-- End of body --> - -{% endblock %} - -{% block js %} - <script> - js_data = {{ js_data | safe }} - </script> - - <!--[if lt IE 9]> -<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>--> - <![endif]--> - <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> - <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/chr_interval_map.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/create_lodchart.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - - <script type="text/javascript" charset="utf-8"> - $(document).ready( function () { - console.time("Creating table"); - $('#qtl_results').dataTable( { - //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>", - "sDom": "lTftipr", - "oTableTools": { - "aButtons": [ - "copy", - "print", - { - "sExtends": "collection", - "sButtonText": 'Save <span class="caret" />', - "aButtons": [ "csv", "xls", "pdf" ] - } - ], - "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf" - }, - "iDisplayLength": 50, - "bLengthChange": true, - "bDeferRender": true, - "bSortClasses": false - } ); - console.timeEnd("Creating table"); - }); - </script> -{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html index 6aed69d5..0cd004cd 100755 --- a/wqflask/wqflask/templates/marker_regression.html +++ b/wqflask/wqflask/templates/marker_regression.html @@ -1,15 +1,5 @@ -{% extends "base.html" %} -{% block title %}Interval Mapping{% endblock %} -{% block css %} -<!-- <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />--> - <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.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" /> -{% endblock %} -{% block content %} <!-- Start of body --> - +{% from "base_macro.html" import header %} +{% block content %} {{ header("Mapping", '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }} @@ -75,28 +65,6 @@ js_data = {{ js_data | safe }} </script> - <!--[if lt IE 9]> -<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>--> - <![endif]--> - <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> - <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/packages/jsPDF/jspdf.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.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/chr_lod_chart.js"></script> -<!-- <script language="javascript" type="text/javascript" src="/static/new/javascript/manhattan_plot.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/create_lodchart.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); @@ -123,4 +91,4 @@ console.timeEnd("Creating table"); }); </script> -{% endblock %} \ No newline at end of file +{% endblock %} diff --git a/wqflask/wqflask/templates/old_index_page.html b/wqflask/wqflask/templates/old_index_page.html deleted file mode 100755 index db0b2d9e..00000000 --- a/wqflask/wqflask/templates/old_index_page.html +++ /dev/null @@ -1,320 +0,0 @@ -{% extends "base.html" %} -{% block title %}GeneNetwork{% endblock %} -{% block content %} - <!-- Start of body --> - <tr> - <td bgcolor="#EEEEEE" class="solidBorder"> - <table width="100%" cellspacing="0" cellpadding="5"> - <tr> - <td valign="top" width="40%" align="left" height="10" bgcolor="#EEEEEE"> - <p style="font-size:18px;font-family:verdana;color:black"><b>Select and - Search</b></p> - - <form method="get" action="/search" class="form-search" name="SEARCHFORM"> - <table width="100%"> - <!-- SPECIES SELECTION --> - - <tr> - <td align="right" height="35" style= - "font-size:14px;font-family:verdana;color:black" width="16%"> - <b>Species:</b></td> - - <td width="3%"></td> - - <td nowrap width="85%" align="left"> - <div id="menu0"> - <select name="species" size="1" id="species" onchange= - "fillOptions('species');"> - </select> - </div> - </td> - </tr><!-- GROUP SELECTION --> - - <tr> - <td align="right" height="35" style= - "font-size:14px;font-family:verdana;color:black"><b>Group:</b></td> - - <td width="3%"></td> - - <td nowrap width="85%" align="left"> - <div id="menu1"> - <select name="cross" size="1" id="cross" onchange="fillOptions('cross');"> - </select> <input type="button" class="btn" value="Info" onclick= - "javascript:crossinfo();"> - </div> - </td> - </tr><!-- TYPE SELECTION --> - - <tr> - <td align="right" height="35" style= - "font-size:14px;font-family:verdana;color:black"><b>Type:</b></td> - - <td width="3%"></td> - - <td nowrap width="85%" align="left"> - <div id="menu2"> - <select name="tissue" size="1" id="tissue" onchange= - "fillOptions('tissue');"> - </select> - </div> - </td> - </tr><!-- DATABASE SELECTION --> - - <tr> - <td align="right" height="35" style= - "font-size:14px;font-family:verdana;color:black"><b>Database:</b></td> - - <td width="3%"></td> - - <td nowrap width="85%" align="left"> - <div id="menu3"> - <select name="database" size="1" id="database"> - </select> <input type="submit" class="btn" value="Info" name= - "info_database"> - </div> - </td> - </tr><!-- USER HELP --> - - <tr> - <td align="right" height="20" width="10%"></td> - - <td width="3%"></td> - - <td align="left" width="85%"> - <p class="fs12"> Databases marked with <b>**</b> - suffix are not public yet.<br> - Access requires <a href="/account.html" target= - "_blank" class="fs14"><small>user login</small></a>.</p> - </td> - </tr><!-- GET ANY SEARCH --> - - <tr> - <td align="right" height="35" nowrap="on" style= - "font-size:14px;font-family:verdana;color:black" width="10%"> - <b>Search:</b></td> - - <td width="3%"></td> - - <td nowrap width="85%" align="left"><input class="input-medium search-query" - id="tfor" name="search_terms" style= - "width:420px; background-color:white; font-family:verdana; font-size:14px" - type="text" maxlength="500"></td> - </tr><!-- GET ANY HELP --> - - <tr> - <td align="right" height="20" width="10%"></td> - - <td width="3%"></td> - - <td width="85%" align="left"> - <p class="fs12"> Enter terms, genes, ID numbers in the - <b>Search</b> field.<br> - Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, - synap*).<br> - Use <b>quotes</b> for terms such as <i>"tyrosine - kinase"</i>.</p> - </td> - </tr><!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH --> - - <tr align="center"> - <td width="3%"></td> - - <td width="3%"></td> - - <td align="left" height="40" colspan="3"><input id="btsearch" type="submit" - class="btn btn-primary" value="Search"> <input type= - "button" class="btn" value="Make Default" onclick= - "setDefault(this.form);"> <input type="button" class= - "btn" value="Advanced Search" onclick= - "javascript:window.open('/index3.html', '_self');"></td> - </tr> - </table><input type="hidden" name="FormID" value="searchResult"> <input type= - "hidden" name="RISet" value="BXD"> <script src="/javascript/selectDatasetMenu.js" - type="text/javascript"> -</script> - </form><!-- QUICK HELP --> - - <p> ______________________________________________________</p> - - <p style="font-size:13px;font-family:verdana;color:black"><b> Quick HELP - Examples and</b> <a href="http://www.genenetwork.org/index4.html" target="_blank" - class="fs14"><b>User's Guide</b></a></p> You can also use advanced - commands. Copy these simple examples<br> - into the <b>Get Any</b> or <b>Combined</b> search fields: - - <ul style="font-size:12px;font-family:verdana;color:black"> - <li><b><i>POSITION=(chr1 25 30)</i></b> finds genes, markers, or transcripts on - chromosome 1 between 25 and 30 Mb.</li> - - <li><b><i>MEAN=(15 16) LRS=(23 46)</i></b> in the <b>Combined</b> field finds - highly expressed genes (15 to 16 log2 units) AND with peak <a href= - "http://www.genenetwork.org/glossary.html#L" target="_blank" class= - "fs14"><small>LRS</small></a> linkage between 23 and 46.</li> - - <li><b><i>RIF=mitochondrial</i></b> searches RNA databases for <a href= - "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank" - class="fs14"><small>GeneRIF</small></a> links.</li> - - <li><b><i>WIKI=nicotine</i></b> searches <a href= - "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class= - "fs14"><small>GeneWiki</small></a> for genes that you or other users have annotated - with the word <i>nicotine</i>.</li> - - <li><b><i>GO:0045202</i></b> searches for synapse-associated genes listed in the - <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class= - "fs14"><small>Gene Ontology</small></a>.</li> - - <li><b><i>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</i></b><br> - in <b>Combined</b> finds synapse-associated genes with <a href= - "http://www.genenetwork.org/glossary.html#E" target="_blank" class= - "fs14"><small>cis eQTL</small></a> on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.</li> - - <li><b><i>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</i></b><br> - in <b>Combined</b> finds diabetes-associated transcripts with peak <a href= - "http://www.genenetwork.org/glossary.html#E" target="_blank" class= - "fs14"><small>trans eQTLs</small></a> on Chr 2 between 100 and 105 Mb with LRS - scores between 9 and 999.</li> - </ul> - </td><!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE) --> - <!-- START OF TOP RIGHT PANEL --> - - <td valign="top" width="40%" bgcolor="#FFFFFF"> - <p style="font-size:15px;font-family:verdana;color:black"><b>Websites Affiliated with - GeneNetwork</b></p> - - <p style="font-size:12px;font-family:verdana;color:black"></p> - - <ul> - <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome - Browser</a> at UTHSC</li> - - <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at - UTHSC</li> - - <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon - Cloud (EC2)</a></li> - - <li>GeneNetwork Source Codes at <a href= - "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li> - - <li>GeneNetwork Source Codes at <a href= - "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li> - </ul> - - <p>____________________________</p> - - <p style="font-size:15px;font-family:verdana;color:black"><b>Getting Started</b> - </p> - - <ol style="font-size:12px;font-family:verdana;color:black"> - <li>Select <b>Species</b> (or select All)</li> - - <li>Select <b>Group</b> (a specific sample)</li> - - <li>Select <b>Type</b> of data: - - <ul> - <li>Phenotype (traits)</li> - - <li>Genotype (markers)</li> - - <li>Expression (mRNAs)</li> - </ul> - </li> - - <li>Select a <b>Database</b></li> - - <li>Enter search terms in the <b>Get Any</b> or <b>Combined</b> field: words, - genes, ID numbers, probes, advanced search commands</li> - - <li>Click on the <b>Search</b> button</li> - - <li>Optional: Use the <b>Make Default</b> button to save your preferences</li> - </ol> - - <p>____________________________</p> - - <p style="font-size:14px;font-family:verdana;color:black"><b>How to Use - GeneNetwork</b></p> - - <blockquote> - <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute - GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target= - "_blank" class="fs14"><small>Tour</small></a> that includes screen shots and - typical steps in the analysis.</p> - </blockquote> - - <blockquote> - <p style="font-size:12px;font-family:verdana;color:black">For information about - resources and methods, select the <img src= - "http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border="0" valign= - "middle"> buttons.</p> - - <p style="font-size:12px;font-family:verdana;color:black">Try the <a href= - "http://alexandria.uthsc.edu/" target="_blank" class= - "fs14"><small>Workstation</small></a> site to explore data and features that are - being implemented.</p> - - <p style="font-size:12px;font-family:verdana;color:black">Review the <a href= - "/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></a> - and <a href="/statusandContact.html" target="_blank" class= - "fs14"><small>Contacts</small></a> pages for information on the status of data sets - and advice on their use and citation.</p> - </blockquote> - - <p style="font-size:14px;font-family:verdana;color:black"><b>Mirror and Development - Sites</b></p> - - <ul> - <li><a href="http://www.genenetwork.org/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</a> (main - site)</li> - - <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li> - - <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li> - - <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li> - - <li><a href="https://genenetwork.hubrecht.eu/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</a> - (Development)</li> - - <li><a href="http://genenetwork.memphis.edu/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li> - - <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li> - - <li><a href="http://genenetwork.epfl.ch/" target="_blank" style= - "font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li> - </ul> - - <p style="font-size:14px;font-family:verdana;color:black"><b>History and - Archive</b></p> - - <blockquote> - <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <a href= - "http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time - Machine</small></a> links to earlier versions that correspond to specific - publication dates.</p> - </blockquote> - </td> - </tr> - </table> - </td> - </tr> - <!-- End of body --> - <script src="/javascript/searchtip.js" type="text/javascript"> - </script> - <script type="text/javascript"> - $(document).ready(function () { - initialDatasetSelection(); - }); - </script> -{% endblock %} - diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 1f53e089..cdde5d9d 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -12,6 +12,8 @@ <link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> + <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> + {% endblock %} {% block content %} <!-- Start of body --> @@ -133,13 +135,19 @@ <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script> <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script> <script type="text/javascript" src="/static/new/javascript/validation.js"></script> - - <script language="javascript" type="text/javascript" src="/static/packages/bootstrap/js/bootstrap.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.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/packages/DataTables/js/jquery.dataTables.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> -"></script> <script type="text/javascript" charset="utf-8"> function getValue(x) { diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index bd1e6f1e..1550647a 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -66,7 +66,7 @@ </div> <div class="form-group"> <div style="padding-left:15px;" class="controls"> - <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression"> + <button id="pylmm_compute" class="btn submit_special btn-primary" title="Compute Marker Regression"> <i class="icon-ok-circle icon-white"></i> Open Mapping Tool </button> </div> diff --git a/wqflask/wqflask/templates/show_trait_progress_bar.html b/wqflask/wqflask/templates/show_trait_progress_bar.html index 99906338..f9a34070 100755 --- a/wqflask/wqflask/templates/show_trait_progress_bar.html +++ b/wqflask/wqflask/templates/show_trait_progress_bar.html @@ -32,17 +32,4 @@ </div> </div> </div> -</div> - -<!--<div id="static_progress_bar_container" class="modal hide fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true"> - <div class="modal-header"> - <h3 id="progress_bar">Loading... (Estimated time ~10-15m)</h3> - </div> - <div class="modal-body"> - <div class="progress progress-striped active"> - <div id="marker_regression_progress" class="bar" style="width: 100%"></div> - </div> - <div id="time_remaining"> - </div> - </div> -</div>--> \ No newline at end of file +</div> \ No newline at end of file diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 79c1c967..f9b27207 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -288,6 +288,10 @@ def heatmap_page(): return rendered_template +@app.route("/mapping_results_container") +def mapping_results_container_page(): + return render_template("mapping_results_container.html") + @app.route("/marker_regression", methods=('POST',)) def marker_regression_page(): initial_start_vars = request.form @@ -312,7 +316,7 @@ def marker_regression_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value - version = "v4" + version = "v3" key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): @@ -439,7 +443,7 @@ def interval_mapping_page(): Redis.expire(key, 60*60) with Bench("Rendering template"): - rendered_template = render_template("interval_mapping.html", **result) + rendered_template = render_template("marker_regression.html", **result) return rendered_template |