diff options
Diffstat (limited to 'wqflask')
12 files changed, 271 insertions, 125 deletions
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index 58a44b2a..f2ea22c0 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -114,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase): create_trait.side_effect = create_trait_side_effect group = MockGroup({"name": "group_X", "samplelist": samplelist}) - this_dataset = AttributeSetter({"group": group, "name": "A"}) + this_dataset = AttributeSetter({"group": group, "name": "dataset1_name"}) flat_files.return_value = "Home/Genenetwork" with mock.patch("builtins.open", mock.mock_open())as mock_open: @@ -134,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase): flat_files.assert_called_once_with('mapping') mock_open.assert_called_once_with( - 'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w') + 'Home/Genenetwork/COVAR_npKxIOnq3azWdgYixtd9IQ.txt', 'w') filehandler = mock_open() filehandler.write.assert_has_calls([mock.call( '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index 9d13e943..b4423d8f 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -32,7 +32,7 @@ class TestRqtlMapping(unittest.TestCase): "results" : []} results = run_rqtl(trait_name="the_trait", vals=[], samples=[], - dataset=dataset, mapping_scale="cM", model="normal", method="hk", + dataset=dataset, pair_scan=False, mapping_scale="cM", model="normal", method="hk", num_perm=5, perm_strata_list=[], do_control="false", control_marker="", manhattan_plot=True, cofactors="") diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index e6421fe2..3bf06ea6 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -20,7 +20,8 @@ from utility.tools import locate, GN3_LOCAL_URL import utility.logger logger = utility.logger.getLogger(__name__) -def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors): + +def run_rqtl(trait_name, vals, samples, dataset, pair_scan, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors): """Run R/qtl by making a request to the GN3 endpoint and reading in the output file(s)""" pheno_file = write_phenotype_file(trait_name, samples, vals, dataset, cofactors, perm_strata_list) @@ -38,6 +39,9 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n "scale": mapping_scale } + if pair_scan: + post_data["pairscan"] = True + if cofactors: covarstruct_file = write_covarstruct_file(cofactors) post_data["covarstruct"] = covarstruct_file @@ -45,7 +49,7 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n if do_control == "true" and control_marker: post_data["control"] = control_marker - if not manhattan_plot: + if not manhattan_plot and not pair_scan: post_data["interval"] = True if cofactors: post_data["addcovar"] = True diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 9d70bb15..35678df9 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -108,6 +108,7 @@ class RunMapping: self.mapping_results_path = "{}{}.csv".format( webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) + self.pair_scan = False self.manhattan_plot = False if 'manhattan_plot' in start_vars: if start_vars['manhattan_plot'].lower() != "false": @@ -125,8 +126,6 @@ class RunMapping: self.use_loco = None self.suggestive = "" self.significant = "" - # Initializing this since it is checked in views to determine which template to use - self.pair_scan = False if 'transform' in start_vars: self.transform = start_vars['transform'] else: @@ -233,18 +232,19 @@ class RunMapping: self.score_type = "-logP" self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] - if 'mapmethod_rqtl_geno' in start_vars: - self.method = start_vars['mapmethod_rqtl_geno'] + if 'mapmethod_rqtl' in start_vars: + self.method = start_vars['mapmethod_rqtl'] else: self.method = "em" - self.model = start_vars['mapmodel_rqtl_geno'] - # if start_vars['pair_scan'] == "true": - # self.pair_scan = True + self.model = start_vars['mapmodel_rqtl'] + self.pair_scan = False + if start_vars['pair_scan'] == "true": + self.pair_scan = True if self.permCheck and self.num_perm > 0: self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl( - self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) + self.this_trait.name, self.vals, self.samples, self.dataset, self.pair_scan, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) else: - results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, + results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.pair_scan, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) elif self.mapping_method == "reaper": if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON @@ -311,33 +311,8 @@ class RunMapping: self.no_results = True else: if self.pair_scan == True: - self.qtl_results = [] - highest_chr = 1 # This is needed in order to convert the highest chr to X/Y - for marker in results: - if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y": - if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y": - highest_chr = marker['chr1'] - if 'lod_score' in list(marker.keys()): - self.qtl_results.append(marker) - - self.trimmed_markers = results - - for qtl in enumerate(self.qtl_results): - self.json_data['chr1'].append(str(qtl['chr1'])) - self.json_data['chr2'].append(str(qtl['chr2'])) - self.json_data['Mb'].append(qtl['Mb']) - self.json_data['markernames'].append(qtl['name']) - - self.js_data = dict( - json_data=self.json_data, - this_trait=self.this_trait.name, - data_set=self.dataset.name, - maf=self.maf, - manhattan_plot=self.manhattan_plot, - mapping_scale=self.mapping_scale, - qtl_results=self.qtl_results - ) - + self.figure_data = results[0] + self.table_data = results[1] else: self.qtl_results = [] self.results_for_browser = [] diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 93f95852..d9821d9c 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -280,6 +280,9 @@ class ShowTrait: hddn['species'] = self.dataset.group.species hddn['use_outliers'] = False hddn['method'] = "gemma" + hddn['mapmethod_rqtl'] = "hk" + hddn['mapmodel_rqtl'] = "normal" + hddn['pair_scan'] = "" hddn['selected_chr'] = -1 hddn['mapping_display_all'] = True hddn['suggestive'] = 0 diff --git a/wqflask/wqflask/static/new/css/d3panels.min.css b/wqflask/wqflask/static/new/css/d3panels.min.css new file mode 100644 index 00000000..7db7b91f --- /dev/null +++ b/wqflask/wqflask/static/new/css/d3panels.min.css @@ -0,0 +1 @@ +svg.qtlcharts,svg.d3panels{font-family:sans-serif;font-size:11pt}svg.qtlcharts .title text,svg.d3panels .title text{dominant-baseline:middle;fill:#0074d9;text-anchor:middle}svg.qtlcharts .y.axis text,svg.d3panels .y.axis text{dominant-baseline:middle;text-anchor:end}svg.qtlcharts .y.axis text.title,svg.d3panels .y.axis text.title{text-anchor:middle;fill:slateblue}svg.qtlcharts .x.axis text,svg.d3panels .x.axis text{dominant-baseline:hanging;text-anchor:middle}svg.qtlcharts .x.axis text.title,svg.d3panels .x.axis text.title{fill:slateblue}svg.qtlcharts line.axis.grid,svg.d3panels line.axis.grid{fill:none;stroke-width:1;pointer-events:none}svg.qtlcharts line.x.axis.grid,svg.d3panels line.x.axis.grid{stroke:#c8c8c8;stroke-width:3}svg.qtlcharts line.y.axis.grid,svg.d3panels line.y.axis.grid{stroke:white}svg.qtlcharts .extent,svg.d3panels .extent{fill:#cac;opacity:.3}svg.qtlcharts circle.selected,svg.d3panels circle.selected{fill:hotpink;opacity:1}svg.qtlcharts a,svg.d3panels a{color:#08c;text-decoration:none}svg.qtlcharts a:hover,svg.d3panels a:hover{color:#333;text-decoration:underline}svg.qtlcharts text.crosstab,svg.d3panels text.crosstab{dominant-baseline:middle;text-anchor:end}svg.qtlcharts text.crosstabtitle,svg.d3panels text.crosstabtitle{dominant-baseline:middle;text-anchor:center}.caption{font-family:Sans-serif;font-size:11pt;margin-left:60px;width:600px}div.d3panels-tooltip{position:absolute;text-align:center;width:max-content;height:min-content;padding:5px;font-size:16px;font-family:sans-serif;font-weight:bold;background:darkslateblue;color:white;text-align:center;border:0;border-radius:3px;pointer-events:none;z-index:999}div.d3panels-tooltip-tri{position:absolute;text-align:center;width:32px;height:32px;padding:0;font-size:16px;font-family:sans-serif;font-weight:bold;background:#ffffff00;color:darkslateblue;text-align:center;border:0;pointer-events:none;z-index:998}div.error p{font-family:sans-serif;font-size:16pt;font-weight:bold;padding:5px}div.qtlcharts{font-family:sans-serif;font-size:12pt}div.searchbox{font-family:Sans-serif;font-size:12pt;margin-left:60px}div.searchbox.inactive input{color:#888} diff --git a/wqflask/wqflask/static/new/css/pair_scan.css b/wqflask/wqflask/static/new/css/pair_scan.css new file mode 100644 index 00000000..90cec529 --- /dev/null +++ b/wqflask/wqflask/static/new/css/pair_scan.css @@ -0,0 +1,6 @@ +/* Unset CSS for tooltip since it will inherit from the bootstrap tooltip class CSS otherwise */
+.tooltip{all:unset;}
+
+.pairscan-container {
+ width: 1000px;
+}
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l,ref1,results1;results1=[];for(i=l=0,ref1=mat.length;0<=ref1?l<ref1:l>ref1;i=0<=ref1?++l:--l){results1.push(mat[i][j])}return results1}())}return results};d3panels.colSums=function(mat){return d3panels.rowSums(d3panels.transpose(mat))};d3panels.log2=function(x){if(x==null){return x}return Math.log(x)/Math.log(2)};d3panels.log10=function(x){if(x==null){return x}return Math.log(x)/Math.log(10)};d3panels.abs=function(x){if(x==null){return x}return Math.abs(x)};d3panels.mean_by_group=function(g,y){var i,means,n;means={};n={};for(i in g){if(n[g[i]]!=null){if(y[i]!=null){means[g[i]]+=y[i]}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){means[g[i]]=y[i]}if(y[i]!=null){n[g[i]]=1}}}for(i in means){means[i]/=n[i]}return means};d3panels.sd_by_group=function(g,y){var dev,i,means,n,sds;means=d3panels.mean_by_group(g,y);sds={};n={};for(i in g){dev=y[i]-means[g[i]];if(n[g[i]]!=null){if(y[i]!=null){sds[g[i]]+=dev*dev}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){sds[g[i]]=dev*dev}if(y[i]!=null){n[g[i]]=1}}}for(i in sds){sds[i]=n[i]<2?null:Math.sqrt(sds[i]/(n[i]-1))}return sds};d3panels.count_groups=function(g,y){var i,n;n={};for(i in g){if(n[g[i]]!=null){if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){n[g[i]]=1}}}return n};d3panels.ci_by_group=function(g,y){var m=arguments.length>2&&arguments[2]!==undefined?arguments[2]:2;var ci,dev,i,means,n,sds;means=d3panels.mean_by_group(g,y);sds={};n={};for(i in g){dev=y[i]-means[g[i]];if(n[g[i]]!=null){if(y[i]!=null){sds[g[i]]+=dev*dev}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){sds[g[i]]=dev*dev}if(y[i]!=null){n[g[i]]=1}}}for(i in sds){sds[i]=n[i]<2?null:Math.sqrt(sds[i]/(n[i]-1))}ci={};for(i in means){ci[i]={mean:means[i],low:n[i]>0?means[i]-m*sds[i]/Math.sqrt(n[i]):means[i],high:n[i]>0?means[i]+m*sds[i]/Math.sqrt(n[i]):means[i]}}return ci};d3panels.pad_ylim=function(ylim){var p=arguments.length>1&&arguments[1]!==undefined?arguments[1]:.025;var d;d=ylim[1]-ylim[0];return[ylim[0]-d*p,ylim[1]+d*p]};d3panels.add_chrname_start_end=function(data){var c,i,k,l,len,len1,ref,ref1,these_pos;if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(data.chrstart==null){data.chrstart=[];ref=data.chrname;for(k=0,len=ref.length;k<len;k++){c=ref[k];these_pos=function(){var results;results=[];for(i in data.chr){if(data.chr[i]===c){results.push(data.pos[i])}}return results}();data.chrstart.push(d3.min(these_pos))}}if(data.chrend==null){data.chrend=[];ref1=data.chrname;for(l=0,len1=ref1.length;l<len1;l++){c=ref1[l];these_pos=function(){var results;results=[];for(i in data.chr){if(data.chr[i]===c){results.push(data.pos[i])}}return results}();data.chrend.push(d3.max(these_pos))}}data.start=d3panels.forceAsArray(data.start);data.end=d3panels.forceAsArray(data.end);return data};d3panels.calc_breaks=function(number,low,high){var d,i,results;if(low>=high){d3panels.displayError("calc_breaks: should have low < high");if(low>high){var _ref=[high,low];low=_ref[0];high=_ref[1]}if(low===high){low-=.5;high+=.5}}if(number<2){d3panels.displayError("calc_breaks: number should be >= 2");number=2}d=(high-low)/(number-1);results=[];for(i in d3.range(number)){results.push(low+d*i)}return results};d3panels.calc_freq=function(values,breaks){var return_counts=arguments.length>2&&arguments[2]!==undefined?arguments[2]:false;var br,i,k,len,n,ref,result,v,z;v=values.slice(0);v.sort(function(a,b){return+a-b});br=breaks.slice(0);br.sort(function(a,b){return+a-b});br[0]-=1e-6;br[br.length-1]+=1e-6;result=function(){var k,len,ref,results;ref=d3.range(br.length-1);results=[];for(k=0,len=ref.length;k<len;k++){i=ref[k];results.push(0)}return results}();n=v.length;v=function(){var k,len,results;results=[];for(k=0,len=v.length;k<len;k++){z=v[k];if(z>br[0]&&z<br[br.length-1]){results.push(z)}}return results}();if(v.length<n){d3panels.displayError("calc_freq: values out of range of breaks")}n=v.length;ref=d3.range(br.length-1);for(k=0,len=ref.length;k<len;k++){i=ref[k];result[i]=function(){var l,len1,results;results=[];for(l=0,len1=v.length;l<len1;l++){z=v[l];if(z>=br[i]&&z<br[i+1]){results.push(z)}}return results}().length;if(!return_counts){result[i]/=n*(br[i+1]-br[i])}}return result};d3panels.calc_hist_path=function(freq,breaks){var i,result;if(freq.length!==breaks.length-1){d3panels.displayError("freq.length ("+freq.length+") should be breaks.length - 1 ("+(breaks.length-1)+")")}result=[{x:breaks[0],y:0}];for(i in freq){result.push({x:breaks[i],y:freq[i]});result.push({x:breaks[+i+1],y:freq[i]})}result.push({x:breaks[breaks.length-1],y:0});return result};d3panels.index_of_nearest=function(d,vec){var abs_diff;abs_diff=vec.map(function(val){return Math.abs(val-d)});return abs_diff.indexOf(d3.min(abs_diff))};d3panels.check_listarg_v_default=function(arg,defaults){var key;for(key in defaults){if(arg[key]==null){arg[key]=defaults[key]}}return arg};d3panels.object_position=function(object){var obj,x,y;obj=object.node().getBoundingClientRect();x=obj.left/2+obj.right/2;y=obj.top/2+obj.bottom/2;return{x:x,y:y}};"use strict";d3panels.lod2dheatmap=function(chartOpts){var cellSelect,cells,celltip,chart,chrGap,colors,equalCells,height,hilitcolor,margin,nullcolor,oneAtTop,ref,ref1,ref10,ref11,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,width,xscale,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:800;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:60};chrGap=(ref3=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref3:6;equalCells=(ref4=chartOpts!=null?chartOpts.equalCells:void 0)!=null?ref4:false;oneAtTop=(ref5=chartOpts!=null?chartOpts.oneAtTop:void 0)!=null?ref5:false;colors=(ref6=chartOpts!=null?chartOpts.colors:void 0)!=null?ref6:["slateblue","white","crimson"];nullcolor=(ref7=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref7:"#e6e6e6";zlim=(ref8=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref8:null;zthresh=(ref9=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref9:null;hilitcolor=(ref10=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref10:"black";tipclass=(ref11=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref11:"tooltip";xscale=null;yscale=null;zscale=null;celltip=null;cells=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cellg,chr,i,indexWithinChr,j,k,l,len,len1,len2,m,myframe,n_pos,posByChr,ref12,ref13,ref14,tooltipfunc,x,xmid_scaled,y,ymid_scaled,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});if(data.chr==null){d3panels.displayError("lod2dheatmap: data.chr is missing")}if(data.pos==null){d3panels.displayError("lod2dheatmap: data.pos is missing")}if(data.lod==null){d3panels.displayError("lod2dheatmap: data.lod is missing")}n_pos=data.chr.length;if(data.pos.length!==n_pos){d3panels.displayError("lod2dheatmap: data.pos.length ("+data.pos.length+") != data.chr.length ("+n_pos+")")}if(data.lod.length!==n_pos){d3panels.displayError("lod2dheatmap: data.lod.length ("+data.lod.length+") != data.chr.length ("+n_pos+")")}for(i in data.lod){if(data.lod[i].length!==n_pos){d3panels.displayError("lod2dheatmap: data.lod["+i+"].length ("+data.lod[i].length+") != data.chr.length ("+n_pos+")")}}if(data.poslabel!=null){if(data.poslabel.length!==n_pos){d3panels.displayError("lod2dheatmap: data.poslabel.length ("+data.poslabel.length+") != data.chr.length ("+n_pos+")")}}else{data.poslabel=function(){var results;results=[];for(i in data.chr){results.push(data.chr[i]+"@"+d3panels.formatAxis(data.pos)(data.pos[i]))}return results}()}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(equalCells){data.pos=[];ref12=data.chrname;for(k=0,len=ref12.length;k<len;k++){chr=ref12[k];data.pos=data.pos.concat(function(){var results;results=[];for(i in data.chr){if(data.chr[i]===chr){results.push(+i)}}return results}())}}data=d3panels.add_chrname_start_end(data);if(equalCells){chrGap=(width-margin.left-margin.right-2*data.chrname.length)/data.chr.length+2}chartOpts.chrGap=chrGap;chartOpts.width=width;chartOpts.height=height;chartOpts.margin=margin;myframe=d3panels.chr2dpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();posByChr=d3panels.reorgByChr(data.chrname,data.chr,data.pos);xmid_scaled={};ymid_scaled={};ref13=data.chrname;for(l=0,len1=ref13.length;l<len1;l++){chr=ref13[l];xmid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref14,results;ref14=posByChr[chr];results=[];for(m=0,len2=ref14.length;m<len2;m++){x=ref14[m];results.push(xscale[chr](x))}return results}(),chrGap-2));ymid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref14,results;ref14=posByChr[chr];results=[];for(m=0,len2=ref14.length;m<len2;m++){y=ref14[m];results.push(yscale[chr](y))}return results}(),oneAtTop?chrGap-2:2-chrGap))}zmin=d3panels.matrixMin(data.lod);zmax=d3panels.matrixMaxAbs(data.lod);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("lod2dheatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;indexWithinChr=[];ref14=data.chrname;for(m=0,len2=ref14.length;m<len2;m++){chr=ref14[m];indexWithinChr=indexWithinChr.concat(function(){var results;results=[];for(i in posByChr[chr]){results.push(+i)}return results}())}cells=[];for(i in data.chr){for(j in data.chr){if(Math.abs(data.lod[i][j])>=zthresh){cells.push({lod:data.lod[i][j],chrx:data.chr[i],chry:data.chr[j],poslabelx:data.poslabel[i],poslabely:data.poslabel[j],xindex:i,yindex:j,xindexByChr:indexWithinChr[i],yindexByChr:indexWithinChr[j]})}}}d3panels.calc_2dchrcell_rect(cells,xmid_scaled,ymid_scaled);cellg=svg.append("g").attr("id","cells");cellSelect=cellg.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return d.left}).attr("y",function(d){return d.top}).attr("width",function(d){return d.width}).attr("height",function(d){return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.lod!=null){return zscale(d.lod)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").on("mouseover",function(d){return d3.select(this).attr("stroke",hilitcolor).raise()}).on("mouseout",function(){return d3.select(this).attr("stroke","none")});tooltipfunc=function tooltipfunc(d){var z;z=d3.format(".2f")(Math.abs(d.lod));return"("+d.poslabelx+","+d.poslabely+") → "+z};return celltip=d3panels.tooltip_create(d3.select("body"),cellg.selectAll("rect"),{tipclass:tipclass},tooltipfunc)};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return zscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.panelframe=function(chartOpts){var axispos,box,boxcolor,boxwidth,chart,height,margin,nxticks,nyticks,plot_height,plot_width,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,ref18,ref19,ref2,ref20,ref21,ref22,ref23,ref24,ref25,ref26,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,v_over_h,width,xNA,xNA_size,xlab,xlabels,xlim,xlineOpts,xlines,xscale,xscale_wnull,xticklab,xticks,yNA,yNA_size,ylab,ylabels,ylim,ylineOpts,ylines,yscale,yscale_wnull,yticklab,yticks;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40,inner:3};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:"X";ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"Y";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;xNA=(ref9=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref9:false;yNA=(ref10=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref10:false;xNA_size=(ref11=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref11:{width:20,gap:10};yNA_size=(ref12=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref12:{width:20,gap:10};xlim=(ref13=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref13:[0,1];ylim=(ref14=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref14:[0,1];nxticks=(ref15=chartOpts!=null?chartOpts.nxticks:void 0)!=null?ref15:5;xticks=(ref16=chartOpts!=null?chartOpts.xticks:void 0)!=null?ref16:null;xticklab=(ref17=chartOpts!=null?chartOpts.xticklab:void 0)!=null?ref17:null;nyticks=(ref18=chartOpts!=null?chartOpts.nyticks:void 0)!=null?ref18:5;yticks=(ref19=chartOpts!=null?chartOpts.yticks:void 0)!=null?ref19:null;yticklab=(ref20=chartOpts!=null?chartOpts.yticklab:void 0)!=null?ref20:null;rectcolor=(ref21=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref21:"#e6e6e6";boxcolor=(ref22=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref22:"black";boxwidth=(ref23=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref23:2;xlineOpts=(ref24=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref24:{color:"white",width:2};ylineOpts=(ref25=chartOpts!=null?chartOpts.ylineOpts:void 0)!=null?ref25:{color:"white",width:2};v_over_h=(ref26=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref26:false;xscale=null;yscale=null;xNA=xNA;yNA=yNA;xlines=null;ylines=null;xlabels=null;ylabels=null;plot_width=null;plot_height=null;box=null;svg=null;xscale_wnull=null;yscale_wnull=null;chart=function chart(selection){var boxes,boxes2include,d,g,i,inner_height,inner_width,xNA_xpos,xaxis,xrange,yNA_ypos,yaxis,ylabpos_x,ylabpos_y,yrange;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40,inner:3});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});xNA_size=d3panels.check_listarg_v_default(xNA_size,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA_size,{width:20,gap:10});xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"white",width:2});ylineOpts=d3panels.check_listarg_v_default(ylineOpts,{color:"white",width:2});svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");if(!xNA){xNA_size={width:0,gap:0}}if(!yNA){yNA_size={width:0,gap:0}}plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);inner_width=width-(margin.right+margin.left+xNA_size.width+xNA_size.gap);inner_height=height-(margin.top+margin.bottom+yNA_size.width+yNA_size.gap);boxes={left:[margin.left+xNA_size.width+xNA_size.gap,margin.left,margin.left,margin.left+xNA_size.width+xNA_size.gap],width:[inner_width,xNA_size.width,xNA_size.width,inner_width],top:[margin.top,margin.top,height-(margin.bottom+yNA_size.width),height-(margin.bottom+yNA_size.width)],height:[inner_height,inner_height,yNA_size.width,yNA_size.width]};xNA_xpos=xNA?margin.left+xNA_size.width/2:-5e4;yNA_ypos=yNA?height-margin.bottom-yNA_size.width/2:-5e4;xrange=[boxes.left[0],boxes.left[0]+boxes.width[0]];yrange=[boxes.top[0]+boxes.height[0],boxes.top[0]];for(i in boxes.left){if(boxes.width[i]>0&&boxes.height[i]>0){g.append("rect").attr("x",boxes.left[i]).attr("y",boxes.top[i]).attr("height",boxes.height[i]).attr("width",boxes.width[i]).attr("fill",rectcolor).attr("stroke","none").attr("shape-rendering","crispEdges")}}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1;if(v_over_h){yaxis=g.append("g").attr("class","y axis");xaxis=g.append("g").attr("class","x axis")}else{xaxis=g.append("g").attr("class","x axis");yaxis=g.append("g").attr("class","y axis")}xaxis.append("text").attr("class","title").text(xlab).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(ylab).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");xscale=d3.scaleLinear().domain(xlim).range([xrange[0]+margin.inner,xrange[1]-margin.inner]);yscale=d3.scaleLinear().domain(ylim).range([yrange[0]-margin.inner,yrange[1]+margin.inner]);xscale_wnull=function xscale_wnull(val){if(val==null){return xNA_xpos}return xscale(val)};yscale_wnull=function yscale_wnull(val){if(val==null){return yNA_ypos}return yscale(val)};xticks=xticks!=null?xticks:xscale.ticks(nxticks);if(xticklab!=null&&xticklab.length!==xticks.length){d3panels.displayError("panelframe: xticklab.length ("+xticklab.length+") != xticks.length ("+xticks.length+")")}if(!(xticklab!=null&&xticklab.length===xticks.length)){xticklab=function(){var j,len,results;results=[];for(j=0,len=xticks.length;j<len;j++){d=xticks[j];results.push(d3panels.formatAxis(xticks)(d))}return results}()}if(xNA){xticks=[null].concat(xticks)}if(xNA){xticklab=["NA"].concat(xticklab)}yticks=yticks!=null?yticks:yscale.ticks(nyticks);if(yticklab!=null&&yticklab.length!==yticks.length){d3panels.displayError("panelframe: yticklab.length ("+yticklab.length+") != yticks.length ("+yticks.length+")")}if(!(yticklab!=null&&yticklab.length===yticks.length)){yticklab=function(){var j,len,results;results=[];for(j=0,len=yticks.length;j<len;j++){d=yticks[j];results.push(d3panels.formatAxis(yticks)(d))}return results}()}if(yNA){yticks=[null].concat(yticks)}if(yNA){yticklab=["NA"].concat(yticklab)}ylines=yaxis.append("g").attr("id","ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1",function(d){return yscale_wnull(d)}).attr("y2",function(d){return yscale_wnull(d)}).attr("x1",function(d,i){if(i<yticks.length){return xrange[0]}return margin.left}).attr("x2",function(d,i){if(i<yticks.length){return xrange[1]}return margin.left+xNA_size.width}).attr("fill","none").attr("stroke",ylineOpts.color).attr("stroke-width",ylineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");xlines=xaxis.append("g").attr("id","xlines").selectAll("empty").data(xticks.concat(xticks)).enter().append("line").attr("x1",function(d){return xscale_wnull(d)}).attr("x2",function(d){return xscale_wnull(d)}).attr("y1",function(d,i){if(i<xticks.length){return yrange[0]}return height-margin.bottom}).attr("y2",function(d,i){if(i<xticks.length){return yrange[1]}return height-margin.bottom-yNA_size.width}).attr("fill","none").attr("stroke",xlineOpts.color).attr("stroke-width",xlineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(xticklab).enter().append("text").attr("x",function(d,i){return xscale_wnull(xticks[i])}).attr("y",height-margin.bottom+axispos.xlabel).text(function(d){return d});ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y",function(d,i){return yscale_wnull(yticks[i])}).attr("x",margin.left-axispos.ylabel).text(function(d){return d});boxes2include=function(){var results;results=[];for(i in boxes.left){if(boxes.width[i]>0&&boxes.height[i]>0){results.push(i)}}return results}();box=svg.append("g").attr("id","box");return box.selectAll("empty").data(boxes2include).enter().append("rect").attr("x",function(i){return boxes.left[i]}).attr("y",function(i){return boxes.top[i]}).attr("height",function(i){return boxes.height[i]}).attr("width",function(i){return boxes.width[i]}).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale_wnull};chart.yscale=function(){return yscale_wnull};chart.xNA=function(){return xNA};chart.yNA=function(){return yNA};chart.xlines=function(){return xlines};chart.ylines=function(){return ylines};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.chrpanelframe=function(chartOpts){var altrectcolor,axispos,box,boxcolor,boxwidth,chart,chrGap,chrSelect,chrlinecolor,chrlines,chrlinewidth,height,horizontal,margin,nyticks,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,ref18,ref19,ref2,ref20,ref21,ref22,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,width,xlab,xlabels,xlineOpts,xscale,ylab,ylabels,ylim,ylineOpts,yscale,yticklab,yticks;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:null;ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"LOD score";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;ylim=(ref9=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref9:[0,1];nyticks=(ref10=chartOpts!=null?chartOpts.nyticks:void 0)!=null?ref10:5;yticks=(ref11=chartOpts!=null?chartOpts.yticks:void 0)!=null?ref11:null;yticklab=(ref12=chartOpts!=null?chartOpts.yticklab:void 0)!=null?ref12:null;rectcolor=(ref13=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref13:"#e6e6e6";altrectcolor=(ref14=chartOpts!=null?chartOpts.altrectcolor:void 0)!=null?ref14:"#d4d4d4";chrlinecolor=(ref15=chartOpts!=null?chartOpts.chrlinecolor:void 0)!=null?ref15:"";chrlinewidth=(ref16=chartOpts!=null?chartOpts.chrlinewidth:void 0)!=null?ref16:2;boxcolor=(ref17=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref17:"black";boxwidth=(ref18=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref18:2;xlineOpts=(ref19=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref19:{color:"#d4d4d4",width:2};ylineOpts=(ref20=chartOpts!=null?chartOpts.ylineOpts:void 0)!=null?ref20:{color:"white",width:2};chrGap=(ref21=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref21:6;horizontal=(ref22=chartOpts.horizontal)!=null?ref22:false;xscale=null;yscale=null;xlabels=null;ylabels=null;chrSelect=null;chrlines=null;box=null;svg=null;chart=function chart(selection,data){var c,d,g,plot_height,plot_width,thechr,xaxis,xlines,xticks,yaxis,ylabpos_x,ylabpos_y,ylines;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"white",width:2});ylineOpts=d3panels.check_listarg_v_default(ylineOpts,{color:"white",width:2});if(data.chr==null){d3panels.displayError("chrpanelframe: data.chr is missing")}if(data.end==null){d3panels.displayError("chrpanelframe: data.end is missing")}if(xlab==null){xlab=data.chr.length===1?"Position":"Chromosome"}svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);if(!(data!=null?data.start:void 0)){data.start=function(){var j,len,ref23,results;ref23=data.chr;results=[];for(j=0,len=ref23.length;j<len;j++){c=ref23[j];results.push(0)}return results}()}if(data.chr.length!==data.start.length){d3panels.displayError("chrpanelframe: data.start.length ("+data.start.length+") != data.chr.length ("+data.chr.length+")")}if(data.chr.length!==data.end.length){d3panels.displayError("chrpanelframe: data.end.length ("+data.end.length+") != data.chr.length ("+data.chr.length+")")}if(horizontal){xscale=d3panels.calc_chrscales(plot_height,margin.top,chrGap,data.chr,data.start,data.end);yscale=d3.scaleLinear().domain(ylim.reverse()).range([plot_width+margin.left,margin.left])}else{xscale=d3panels.calc_chrscales(plot_width,margin.left,chrGap,data.chr,data.start,data.end);yscale=d3.scaleLinear().domain(ylim).range([plot_height+margin.top,margin.top])}g.append("rect").attr("x",margin.left).attr("width",plot_width).attr("y",margin.top).attr("height",plot_height).attr("fill",rectcolor).attr("shape-rendering","crispEdges");if(altrectcolor!==""){chrSelect=g.append("g").selectAll("empty").data(data.chr).enter().append("rect").attr("x",function(d,i){if(horizontal){return margin.left}return xscale[d](data.start[i])-chrGap/2}).attr("width",function(d,i){if(horizontal){return plot_width}return xscale[d](data.end[i])-xscale[d](data.start[i])+chrGap}).attr("y",function(d,i){if(horizontal){return xscale[d](data.start[i])-chrGap/2}return margin.top}).attr("height",function(d,i){if(horizontal){return xscale[d](data.end[i])-xscale[d](data.start[i])+chrGap}return plot_height}).attr("fill",function(d,i){if(i%2===0){return rectcolor}return altrectcolor}).attr("shape-rendering","crispEdges")}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);if(horizontal){rotate_ylab=rotate_ylab!=null?rotate_ylab:xlab.length>1}else{rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1}xaxis=g.append("g").attr("class",function(){if(horizontal){return"y axis"}return"x axis"});yaxis=g.append("g").attr("class",function(){if(horizontal){return"x axis"}return"y axis"});xaxis.append("text").attr("class","title").text(function(){if(horizontal){return ylab}return xlab}).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(function(){if(horizontal){return xlab}return ylab}).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");if(data.chr.length>1){xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x",function(d,i){if(horizontal){return margin.left-axispos.ylabel}return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}).attr("y",function(d,i){if(horizontal){return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}return height-margin.bottom+axispos.xlabel}).text(function(d){return d})}else{thechr=data.chr[0];xticks=xscale[thechr].ticks(5);xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(xticks).enter().append("text").attr("x",function(d){if(horizontal){return margin.left-axispos.ylabel}return xscale[thechr](d)}).attr("y",function(d,i){if(horizontal){return xscale[thechr](d)}return height-margin.bottom+axispos.xlabel}).text(function(d){return d});xlines=xaxis.append("g").attr("id","xlines").selectAll("empty").data(xticks).enter().append("line").attr("x1",function(d){if(horizontal){return margin.left}return xscale[thechr](d)}).attr("x2",function(d){if(horizontal){return margin.left+plot_width}return xscale[thechr](d)}).attr("y1",function(d,i){if(horizontal){return xscale[thechr](d)}return margin.top}).attr("y2",function(d,i){if(horizontal){return xscale[thechr](d)}return plot_height+margin.top}).attr("fill","none").attr("stroke",xlineOpts.color).attr("stroke-width",xlineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none")}yticks=yticks!=null?yticks:yscale.ticks(nyticks);if(yticklab!=null&&yticklab.length!==yticks.length){displayError("chrpanelframe: yticklab.length ("+yticklab.length+") != yticks.length ("+yticks.length+")")}if(!(yticklab!=null&&yticklab.length===yticks.length)){yticklab=function(){var j,len,results;results=[];for(j=0,len=yticks.length;j<len;j++){d=yticks[j];results.push(d3panels.formatAxis(yticks)(d))}return results}()}ylines=yaxis.append("g").attr("id","ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1",function(d){if(horizontal){return margin.top}return yscale(d)}).attr("y2",function(d){if(horizontal){return margin.top+plot_height}return yscale(d)}).attr("x1",function(d,i){if(horizontal){return yscale(d)}return margin.left}).attr("x2",function(d,i){if(horizontal){return yscale(d)}return plot_width+margin.left}).attr("fill","none").attr("stroke",ylineOpts.color).attr("stroke-width",ylineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y",function(d,i){if(horizontal){return height-margin.bottom+axispos.xlabel}return yscale(yticks[i])}).attr("x",function(d,i){if(horizontal){return yscale(yticks[i])}return margin.left-axispos.ylabel}).text(function(d){return d});if(chrlinecolor!==""&&data.chr.length>1){chrlines=svg.append("g").attr("id","chrlines");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("x1",function(d,i){if(horizontal){return margin.left}return xscale[d](data.end[i])+chrGap/2}).attr("x2",function(d,i){if(horizontal){return margin.left+plot_width}return xscale[d](data.end[i])+chrGap/2}).attr("y1",function(d,i){if(horizontal){return xscale[d](data.end[i])+chrGap/2}return margin.top}).attr("y2",function(d,i){if(horizontal){return xscale[d](data.end[i])+chrGap/2}return margin.top+plot_height}).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges")}return box=svg.append("rect").attr("class","box").attr("x",margin.left).attr("y",margin.top).attr("height",plot_height).attr("width",plot_width).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.chrSelect=function(){return chrSelect};chart.chrlines=function(){return chrlines};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.chr2dpanelframe=function(chartOpts){var altrectcolor,axispos,box,boxcolor,boxwidth,chart,chrGap,chrSelect,chrlinecolor,chrlines,chrlinewidth,height,margin,oneAtTop,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,width,xlab,xlabels,xscale,ylab,ylabels,yscale;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:800;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:60};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:"Chromosome";ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"Chromosome";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;rectcolor=(ref9=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref9:"#e6e6e6";altrectcolor=(ref10=chartOpts!=null?chartOpts.altrectcolor:void 0)!=null?ref10:"#d4d4d4";chrlinecolor=(ref11=chartOpts!=null?chartOpts.chrlinecolor:void 0)!=null?ref11:"";chrlinewidth=(ref12=chartOpts!=null?chartOpts.chrlinewidth:void 0)!=null?ref12:2;boxcolor=(ref13=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref13:"black";boxwidth=(ref14=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref14:2;chrGap=(ref15=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref15:6;oneAtTop=(ref16=chartOpts!=null?chartOpts.oneAtTop:void 0)!=null?ref16:false;xscale=null;yscale=null;xlabels=null;ylabels=null;chrSelect=null;chrlines=null;box=null;svg=null;chart=function chart(selection,data){var c,chrRect,chrx,chry,g,j,k,len,len1,plot_height,plot_width,ref17,ref18,x,xaxis,y,yaxis,ylabpos_x,ylabpos_y;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});if(data.chr==null){d3panels.displayError("chr2dpanelframe: data.chr is missing")}if(data.end==null){d3panels.displayError("chr2dpanelframe: data.end is missing")}svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);if(!(data!=null?data.start:void 0)){data.start=function(){var j,len,ref17,results;ref17=data.chr;results=[];for(j=0,len=ref17.length;j<len;j++){c=ref17[j];results.push(0)}return results}()}if(data.chr.length!==data.start.length){d3panels.displayError("chr2dpanelframe: data.start.length ("+data.start.length+") != data.chr.length ("+data.chr.length+")")}if(data.chr.length!==data.end.length){d3panels.displayError("chr2dpanelframe: data.end.length ("+data.end.length+") != data.chr.length ("+data.chr.length+")")}xscale=d3panels.calc_chrscales(plot_width,margin.left,chrGap,data.chr,data.start,data.end);yscale=d3panels.calc_chrscales(plot_height,margin.top,chrGap,data.chr,data.start,data.end,!oneAtTop);g.append("rect").attr("x",margin.left).attr("width",plot_width).attr("y",margin.top).attr("height",plot_height).attr("fill",rectcolor).attr("shape-rendering","crispEdges");chrRect=[];ref17=data.chr;for(x=j=0,len=ref17.length;j<len;x=++j){chrx=ref17[x];ref18=data.chr;for(y=k=0,len1=ref18.length;k<len1;y=++k){chry=ref18[y];chrRect.push({chrx:chrx,xi:x,chry:chry,yi:y,odd:(x+y)%2})}}if(altrectcolor!==""){chrSelect=g.append("g").selectAll("empty").data(chrRect).enter().append("rect").attr("x",function(d){return xscale[d.chrx](data.start[d.xi])-chrGap/2}).attr("width",function(d){return xscale[d.chrx](data.end[d.xi])-xscale[d.chrx](data.start[d.xi])+chrGap}).attr("y",function(d){if(oneAtTop){return yscale[d.chry](data.start[d.yi])-chrGap/2}return yscale[d.chry](data.end[d.yi])-chrGap/2}).attr("height",function(d){if(oneAtTop){return yscale[d.chry](data.end[d.yi])-yscale[d.chry](data.start[d.yi])+chrGap}return yscale[d.chry](data.start[d.yi])-yscale[d.chry](data.end[d.yi])+chrGap}).attr("fill",function(d,i){if(!d.odd){return rectcolor}return altrectcolor}).attr("shape-rendering","crispEdges")}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1;xaxis=g.append("g").attr("class","x axis");yaxis=g.append("g").attr("class","y axis");xaxis.append("text").attr("class","title").text(function(){return xlab}).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(function(){return ylab}).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x",function(d,i){return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}).attr("y",height-margin.bottom+axispos.xlabel).text(function(d){return d});ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(data.chr).enter().append("text").attr("y",function(d,i){return(yscale[d](data.start[i])+yscale[d](data.end[i]))/2}).attr("x",margin.left-axispos.ylabel).text(function(d){return d});if(chrlinecolor!==""&&data.chr.length>1){chrlines=svg.append("g").attr("id","chrlines");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("x1",function(d,i){return xscale[d](data.end[i])+chrGap/2}).attr("x2",function(d,i){return xscale[d](data.end[i])+chrGap/2}).attr("y1",margin.top).attr("y2",margin.top+plot_height).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("y1",function(d,i){if(oneAtTop){return yscale[d](data.end[i])+chrGap/2}return yscale[d](data.end[i])-chrGap/2}).attr("y2",function(d,i){if(oneAtTop){return yscale[d](data.end[i])+chrGap/2}return yscale[d](data.end[i])-chrGap/2}).attr("x1",margin.left).attr("x2",margin.left+plot_width).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges")}return box=svg.append("rect").attr("class","box").attr("x",margin.left).attr("y",margin.top).attr("height",plot_height).attr("width",plot_width).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.chrSelect=function(){return chrSelect};chart.chrlines=function(){return chrlines};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.cichart=function(chartOpts){var chart,horizontal,ref,ref1,ref10,ref11,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,segcolor,segments,segstrokewidth,segwidth,svg,tip,tipclass,v_over_h,vertsegcolor,xcatlabels,xlab,xlineOpts,xscale,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xcatlabels=(ref=chartOpts!=null?chartOpts.xcatlabels:void 0)!=null?ref:null;segwidth=(ref1=chartOpts!=null?chartOpts.segwidth:void 0)!=null?ref1:.4;segcolor=(ref2=chartOpts!=null?chartOpts.segcolor:void 0)!=null?ref2:"slateblue";segstrokewidth=(ref3=chartOpts!=null?chartOpts.segstrokewidth:void 0)!=null?ref3:"3";vertsegcolor=(ref4=chartOpts!=null?chartOpts.vertsegcolor:void 0)!=null?ref4:"slateblue";xlab=(ref5=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref5:"Group";ylab=(ref6=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref6:"Response";ylim=(ref7=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref7:null;xlineOpts=(ref8=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref8:{color:"#CDCDCD",width:5};horizontal=(ref9=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref9:false;v_over_h=(ref10=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref10:horizontal;tipclass=(ref11=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref11:"tooltip";xscale=null;yscale=null;segments=null;tip=null;svg=null;chart=function chart(selection,data){var direction,high,i,low,mean,myframe,ncat,segmentGroup,tipfunc,xlim,xticks,xval,yval;xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"#CDCDCD",width:5});if(data.mean==null){d3panels.displayError("cichart: data.mean is missing")}if(data.low==null){d3panels.displayError("cichart: data.low is missing")}if(data.high==null){d3panels.displayError("cichart: data.high is missing")}mean=data.mean;low=data.low;high=data.high;ncat=mean.length;if(ncat!==low.length){d3panels.displayError("cichart: low.length ["+low.length+"] != mean.length ["+ncat+"]")}if(ncat!==high.length){d3panels.displayError("cichart: high.length ["+high.length+"] != mean.length ["+ncat+"]")}xticks=function(){var results;results=[];for(i in mean){results.push(+i+1)}return results}();xcatlabels=xcatlabels!=null?xcatlabels:xticks;if(xcatlabels.length!==mean.length){d3panels.displayError("cichart: xcatlabels.length ["+xcatlabels.length+"] != mean.length ["+ncat+"]")}ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(low.concat(high)));xlim=[.5,mean.length+.5];segcolor=d3panels.expand2vector(d3panels.forceAsArray(segcolor),mean.length);vertsegcolor=d3panels.expand2vector(d3panels.forceAsArray(vertsegcolor),mean.length);if(horizontal){chartOpts.ylim=xlim.reverse();chartOpts.xlim=ylim;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.yNA=chartOpts.xNA;chartOpts.xNA=chartOpts.yNA;chartOpts.yticks=xticks;chartOpts.yticklab=xcatlabels;chartOpts.v_over_h=v_over_h}else{chartOpts.ylim=ylim;chartOpts.xlim=xlim;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.ylineOpts=chartOpts.ylineOpts;chartOpts.xlineOpts=xlineOpts;chartOpts.xticks=xticks;chartOpts.xticklab=xcatlabels;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();segmentGroup=svg.append("g").attr("id","segments");segments=segmentGroup.selectAll("empty").data(low).enter().append("line").attr("x1",function(d,i){if(!horizontal){return xscale(i+1)}return xscale(d)}).attr("x2",function(d,i){if(!horizontal){return xscale(i+1)}return xscale(high[i])}).attr("y1",function(d,i){if(!horizontal){return yscale(d)}return yscale(i+1)}).attr("y2",function(d,i){if(!horizontal){return yscale(high[i])}return yscale(i+1)}).attr("fill","none").attr("stroke",function(d,i){return vertsegcolor[i]}).attr("stroke-width",segstrokewidth).attr("shape-rendering","crispEdges");yval=mean.concat(low,high);xval=function(){var results;results=[];for(i in yval){results.push(+(i%ncat)+1)}return results}();segments=segmentGroup.selectAll("empty").data(yval).enter().append("line").attr("x1",function(d,i){if(horizontal){return xscale(d)}else{if(i<ncat){return xscale(xval[i]-segwidth/2)}return xscale(xval[i]-segwidth/3)}}).attr("x2",function(d,i){if(horizontal){return xscale(d)}else{if(i<ncat){return xscale(xval[i]+segwidth/2)}return xscale(xval[i]+segwidth/3)}}).attr("y1",function(d,i){if(horizontal){if(i<ncat){return yscale(xval[i]-segwidth/2)}return yscale(xval[i]-segwidth/3)}else{return yscale(d)}}).attr("y2",function(d,i){if(horizontal){if(i<ncat){return yscale(xval[i]+segwidth/2)}return yscale(xval[i]+segwidth/3)}else{return yscale(d)}}).attr("fill","none").attr("stroke",function(d,i){return segcolor[i%mean.length]}).attr("stroke-width",segstrokewidth).attr("shape-rendering","crispEdges");direction=horizontal?"north":"east";tipfunc=function tipfunc(d,i){var f,index;index=i%mean.length;f=d3panels.formatAxis([low[index],mean[index]],1);return f(mean[index])+" ("+f(low[index])+" - "+f(high[index])+")"};tip=d3panels.tooltip_create(d3.select("body"),segments,{direction:direction,tipclass:tipclass},tipfunc);return myframe.box().raise()};chart.yscale=function(){return yscale};chart.xscale=function(){return xscale};chart.segments=function(){return segments};chart.tip=function(){return tip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(tip);return null};return chart};"use strict";d3panels.crosstab=function(chartOpts){var bordercolor,cellPad,chart,colrect,fontsize,height,hilitcolor,margin,rectcolor,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rowrect,svg,title,titlepos,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:600;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:300;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:80,right:40,bottom:20};cellPad=(ref3=chartOpts!=null?chartOpts.cellPad:void 0)!=null?ref3:null;titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:50;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";fontsize=(ref6=chartOpts!=null?chartOpts.fontsize:void 0)!=null?ref6:null;rectcolor=(ref7=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref7:"#e6e6e6";hilitcolor=(ref8=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref8:"#e9cfec";bordercolor=(ref9=chartOpts!=null?chartOpts.bordercolor:void 0)!=null?ref9:"black";rowrect=null;colrect=null;svg=null;chart=function chart(selection,data){var borders,cell,cellHeight,cellWidth,cells,collab,denom,i,j,k,l,n,ncol,nrow,plot_height,plot_width,rect,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,rowlab,tab,titles,values,xscale,xv,yscale,yv;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});if(data.x==null){d3panels.displayError("crosstab: data.x is missing")}if(data.y==null){d3panels.displayError("crosstab: data.y is missing")}n=data.x.length;if(data.y.length!==n){d3panels.displayError("crosstab: data.x.length ["+data.x.length+"] != data.y.length ["+data.y.length+"]")}data.xcat=(ref10=data!=null?data.xcat:void 0)!=null?ref10:function(){var k,len,ref11,results;ref11=d3.range(d3.max(data.x));results=[];for(k=0,len=ref11.length;k<len;k++){xv=ref11[k];results.push(xv+1)}return results}();data.ycat=(ref11=data!=null?data.ycat:void 0)!=null?ref11:function(){var k,len,ref12,results;ref12=d3.range(d3.max(data.y));results=[];for(k=0,len=ref12.length;k<len;k++){yv=ref12[k];results.push(yv+1)}return results}();ncol=data.xcat.length;if(d3.max(data.x)>ncol||d3.min(data.x)<=0){d3panels.displayError("crosstab: data.x should be in range 1-"+ncol+" [was "+d3.min(data.x)+" - "+d3.max(data.x)+"]")}nrow=data.ycat.length;if(d3.max(data.y)>nrow||d3.min(data.y)<=0){d3panels.displayError("crosstab: data.y should be in range 1-"+nrow+" [was "+d3.min(data.y)+" - "+d3.max(data.y)+"]")}data.x=function(){var k,len,ref12,results;ref12=data.x;results=[];for(k=0,len=ref12.length;k<len;k++){xv=ref12[k];results.push(xv-1)}return results}();data.y=function(){var k,len,ref12,results;ref12=data.y;results=[];for(k=0,len=ref12.length;k<len;k++){yv=ref12[k];results.push(yv-1)}return results}();tab=d3panels.calc_crosstab(data);data.xlabel=(ref12=data!=null?data.xlabel:void 0)!=null?ref12:"";data.ylabel=(ref13=data!=null?data.ylabel:void 0)!=null?ref13:"";cells=[];for(i=k=0,ref14=nrow;0<=ref14?k<=ref14:k>=ref14;i=0<=ref14?++k:--k){for(j=l=0,ref15=ncol;0<=ref15?l<=ref15:l>=ref15;j=0<=ref15?++l:--l){cell={value:tab[i][j],row:i,col:j,shaded:false,rowpercent:"",colpercent:""};if(i<nrow-1&&(j<ncol-1||j===ncol)){cell.shaded=true}if(j<ncol-1&&(i<nrow-1||i===nrow)){cell.shaded=true}if(i<nrow-1){denom=tab[nrow][j]-tab[nrow-1][j];cell.colpercent=denom>0?Math.round(100*tab[i][j]/denom)+"%":"—"}else if(i===nrow-1){denom=tab[nrow][j];cell.colpercent=denom>0?"("+Math.round(100*tab[i][j]/denom)+"%)":"—"}else{cell.colpercent=cell.value}if(j<ncol-1){denom=tab[i][ncol]-tab[i][ncol-1];cell.rowpercent=denom>0?Math.round(100*tab[i][j]/denom)+"%":"—"}else if(j===ncol-1){denom=tab[i][ncol];cell.rowpercent=denom>0?"("+Math.round(100*tab[i][j]/denom)+"%)":"—"}else{cell.rowpercent=cell.value}cells.push(cell)}}plot_width=width-margin.left-margin.right;plot_height=height-margin.top-margin.bottom;cellWidth=plot_width/(ncol+2);cellHeight=plot_height/(nrow+2);fontsize=fontsize!=null?fontsize:cellHeight*.5;cellPad=cellPad!=null?cellPad:cellWidth*.1;xscale=d3.scaleBand().domain(function(){var results=[];for(var m=0,ref16=ncol+1;0<=ref16?m<=ref16:m>=ref16;0<=ref16?m++:m--){results.push(m)}return results}.apply(this)).range([margin.left,width-margin.right]);yscale=d3.scaleBand().domain(function(){var results=[];for(var m=0,ref17=nrow+1;0<=ref17?m<=ref17:m>=ref17;0<=ref17?m++:m--){results.push(m)}return results}.apply(this)).range([margin.top,height-margin.bottom]);svg=selection.append("svg").attr("width",width).attr("height",height).attr("class","d3panels");rect=svg.append("g").attr("id","value_rect");rect.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return xscale(d.col+1)}).attr("y",function(d){return yscale(d.row+1)}).attr("width",cellWidth).attr("height",cellHeight).attr("fill",function(d){if(d.shaded){return rectcolor}else{return"none"}}).attr("stroke",function(d){if(d.shaded){return rectcolor}else{return"none"}}).attr("stroke-width",0).style("pointer-events","none").attr("shape-rendering","crispEdges");values=svg.append("g").attr("id","values");values.selectAll("empty").data(cells).enter().append("text").attr("x",function(d){return xscale(d.col+1)+cellWidth-cellPad}).attr("y",function(d){return yscale(d.row+1)+cellHeight/2}).text(function(d){return d.value}).attr("class",function(d){return"crosstab row"+d.row+" col"+d.col}).style("font-size",fontsize).style("pointer-events","none");colrect=svg.append("g").attr("id","colrect");colrect.selectAll("empty").data(data.xcat.concat("Total")).enter().append("rect").attr("x",function(d,i){return xscale(i+1)}).attr("y",yscale(0)).attr("width",cellWidth).attr("height",cellHeight).attr("fill","white").attr("stroke","white").attr("shape-rendering","crispEdges").on("mouseover",function(d,i){d3.select(this).attr("fill",hilitcolor).attr("stroke",hilitcolor);return values.selectAll(".col"+i).text(function(d){return d.colpercent})}).on("mouseout",function(d,i){d3.select(this).attr("fill","white").attr("stroke","white");return values.selectAll("text.col"+i).text(function(d){return d.value})});collab=svg.append("g").attr("id","collab");collab.selectAll("empty").data(data.xcat.concat("Total")).enter().append("text").attr("x",function(d,i){return xscale(i+1)+cellWidth-cellPad}).attr("y",yscale(0)+cellHeight/2).text(function(d){return d}).attr("class","crosstab").style("font-size",fontsize).style("pointer-events","none");rowrect=svg.append("g").attr("id","rowrect");rowrect.selectAll("empty").data(data.ycat.concat("Total")).enter().append("rect").attr("x",xscale(0)).attr("y",function(d,i){return yscale(i+1)}).attr("width",cellWidth).attr("height",cellHeight).attr("fill","white").attr("stroke","white").attr("shape-rendering","crispEdges").on("mouseover",function(d,i){d3.select(this).attr("fill",hilitcolor).attr("stroke",hilitcolor);return values.selectAll(".row"+i).text(function(d){return d.rowpercent})}).on("mouseout",function(d,i){d3.select(this).attr("fill","white").attr("stroke","white");return values.selectAll(".row"+i).text(function(d){return d.value})});rowlab=svg.append("g").attr("id","rowlab");rowlab.selectAll("empty").data(data.ycat.concat("Total")).enter().append("text").attr("x",xscale(0)+cellWidth-cellPad).attr("y",function(d,i){return yscale(i+1)+cellHeight/2}).text(function(d){return d}).attr("class","crosstab").style("font-size",fontsize).style("pointer-events","none");borders=svg.append("g").attr("id","borders");borders.append("rect").attr("x",xscale(1)).attr("y",yscale(1)).attr("width",cellWidth*ncol).attr("height",cellHeight*nrow).attr("fill","none").attr("stroke",bordercolor).attr("stroke-width",2).style("pointer-events","none").attr("shape-rendering","crispEdges");borders.append("rect").attr("x",xscale(ncol+1)).attr("y",yscale(nrow+1)).attr("width",cellWidth).attr("height",cellHeight).attr("fill","none").attr("stroke",bordercolor).attr("stroke-width",2).style("pointer-events","none").attr("shape-rendering","crispEdges");titles=svg.append("g").attr("id","titles");titles.append("text").attr("class","crosstabtitle").attr("x",margin.left+(ncol+1)*cellWidth/2).attr("y",margin.top-cellHeight/2).text(data.xlabel).style("font-size",fontsize).style("font-weight","bold");titles.append("text").attr("class","crosstab").attr("x",xscale(0)+cellWidth-cellPad).attr("y",yscale(0)+cellHeight/2).text(data.ylabel).style("font-size",fontsize).style("font-weight","bold");return titles.append("text").attr("class","crosstabtitle").attr("x",margin.left+(width-margin.left-margin.right)/2).attr("y",margin.top-titlepos).text(title).style("font-size",fontsize)};chart.rowrect=function(){return rowrect};chart.colrect=function(){return colrect};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.curvechart=function(chartOpts){var chart,curves,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref2,ref3,ref4,ref5,ref6,svg,tipclass,xlim,xscale,ylim,yscale;if(chartOpts==null){chartOpts={}}xlim=(ref=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref:null;ylim=(ref1=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref1:null;linecolor=(ref2=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref2:null;linecolorhilit=(ref3=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref3:null;linewidth=(ref4=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref4:2;linewidthhilit=(ref5=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref5:2;tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";xscale=null;yscale=null;curves=null;indtip=null;svg=null;chart=function chart(selection,data){var add_curves,i,j,myframe,n_ind,ref7,x,y;if(data.x==null){d3panels.displayError("curvechart: data.x is missing")}if(data.y==null){d3panels.displayError("curvechart: data.y is missing")}x=data.x;y=data.y;n_ind=y.length;if(x.length===1&&y.length>1){for(j=i=2,ref7=n_ind;2<=ref7?i<=ref7:i>=ref7;j=2<=ref7?++i:--i){x.push(x[0])}}if(x.length!==n_ind){d3panels.displayError("curvechart: data.x.length ("+x.length+") != data.y.length ("+n_ind+")")}xlim=xlim!=null?xlim:d3panels.matrixExtent(x);ylim=ylim!=null?ylim:d3panels.matrixExtent(y);chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();add_curves=d3panels.add_curves({linecolor:linecolor,linecolorhilit:linecolorhilit,linewidth:linewidth,linewidthhilit:linewidthhilit,tipclass:tipclass});add_curves(myframe,data);curves=add_curves.curves();indtip=add_curves.indtip();return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";var indexOf=[].indexOf;d3panels.dotchart=function(chartOpts){var chart,horizontal,indtip,jitter,pointcolor,points,pointsize,pointstroke,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,v_over_h,xNA,xNA_size,xcategories,xcatlabels,xlab,xlineOpts,xscale,yNA,yNA_size,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xcategories=(ref=chartOpts!=null?chartOpts.xcategories:void 0)!=null?ref:null;xcatlabels=(ref1=chartOpts!=null?chartOpts.xcatlabels:void 0)!=null?ref1:null;xNA=(ref2=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref2:{handle:true,force:false};yNA=(ref3=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref3:{handle:true,force:false};xNA_size=(ref4=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref4:{width:20,gap:10};yNA_size=(ref5=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref5:{width:20,gap:10};ylim=(ref6=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref6:null;xlab=(ref7=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref7:"Group";ylab=(ref8=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref8:"Response";xlineOpts=(ref9=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref9:{color:"#cdcdcd",width:5};pointcolor=(ref10=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref10:null;pointstroke=(ref11=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref11:"black";pointsize=(ref12=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref12:3;jitter=(ref13=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref13:"beeswarm";tipclass=(ref14=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref14:"tooltip";horizontal=(ref15=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref15:false;v_over_h=(ref16=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref16:horizontal;xscale=null;yscale=null;xNA=xNA;yNA=yNA;points=null;indtip=null;svg=null;chart=function chart(selection,data){var force,g,group,i,indID,jitter_width,myframe,ngroup,pointGroup,ref17,ref18,ref19,ref20,scaledPoints,u,x,xlim,xv,y;xNA=d3panels.check_listarg_v_default(xNA,{handle:true,force:false});yNA=d3panels.check_listarg_v_default(yNA,{handle:true,force:false});xNA_size=d3panels.check_listarg_v_default(xNA,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA,{width:20,gap:10});if(data.x==null){d3panels.displayError("dotchart: data.x is missing")}if(data.y==null){d3panels.displayError("dotchart: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);indID=(ref17=data!=null?data.indID:void 0)!=null?ref17:function(){var results=[];for(var j=1,ref18=x.length;1<=ref18?j<=ref18:j>=ref18;1<=ref18?j++:j--){results.push(j)}return results}.apply(this);if(x.length!==y.length){d3panels.displayError("dotchart: length(x) ["+x.length+"] != length(y) ["+y.length+"]")}if(indID.length!==x.length){d3panels.displayError("dotchart: length(indID) ["+indID.length+"] != length(x) ["+x.length+"]")}group=(ref19=data!=null?data.group:void 0)!=null?ref19:function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){i=x[j];results.push(1)}return results}();group=d3panels.expand2vector(group,x.length);ngroup=d3.max(group);group=function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("dotchart: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==x.length){d3panels.displayError("dotchart: group.length ("+group.length+") != x.length ("+x.length+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}xcategories=xcategories!=null?xcategories:d3panels.unique(x);xcategories=d3panels.forceAsArray(xcategories);xcatlabels=xcatlabels!=null?xcatlabels:xcategories;xcatlabels=d3panels.forceAsArray(xcatlabels);if(xcatlabels.length!==xcategories.length){d3panels.displayError("dotchart: xcatlabels.length ["+xcatlabels.length+"] != xcategories.length ["+xcategories.length+"]")}if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){xv=x[j];results.push(xv!=null&&!(indexOf.call(xcategories,xv)>=0))}return results}())>0){d3panels.displayError("dotchart: Some x values not in xcategories");console.log("xcategories:");console.log(xcategories);console.log("x:");console.log(x);for(i in x){if(x[i]!=null&&!(ref20=x[i],indexOf.call(xcategories,ref20)>=0)){x[i]=null}}}ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(y));xlim=[d3.min(xcategories)-.5,d3.max(xcategories)+.5];xNA.handle=xNA.force||xNA.handle&&!x.every(function(v){return v!=null});yNA.handle=yNA.force||yNA.handle&&!y.every(function(v){return v!=null});if(horizontal){chartOpts.ylim=xlim.reverse();chartOpts.xlim=ylim;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.yNA=xNA.handle;chartOpts.xNA=yNA.handle;chartOpts.xNA_size=yNA_size;chartOpts.yNA_size=xNA_size;chartOpts.yticks=xcategories;chartOpts.yticklab=xcatlabels;chartOpts.v_over_h=v_over_h}else{chartOpts.ylim=ylim;chartOpts.xlim=xlim;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.ylineOpts=chartOpts.ylineOpts;chartOpts.xlineOpts=xlineOpts;chartOpts.xNA=xNA.handle;chartOpts.yNA=yNA.handle;chartOpts.xNA_size=xNA_size;chartOpts.yNA_size=yNA_size;chartOpts.xticks=xcategories;chartOpts.xticklab=xcatlabels;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();if(horizontal){scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(y[i]),y:yscale(x[i])})}return results}()}else{scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(x[i]),y:yscale(y[i])})}return results}()}pointGroup=svg.append("g").attr("id","points");points=pointGroup.selectAll("empty").data(scaledPoints).enter().append("circle").attr("class",function(d,i){return"pt"+i}).attr("r",pointsize).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width","1").attr("cx",function(d){return d.x}).attr("cy",function(d){return d.y});indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]});if(jitter==="random"){jitter_width=.2;u=function(){var results;results=[];for(i in scaledPoints){results.push((Math.random()-.5)*jitter_width)}return results}();if(horizontal){points.attr("cy",function(d,i){if(x[i]!=null){return yscale(x[i]+u[i])}return yscale(x[i])+u[i]/jitter_width*xNA_size.width/2})}else{points.attr("cx",function(d,i){if(x[i]!=null){return xscale(x[i]+u[i])}return xscale(x[i])+u[i]/jitter_width*xNA_size.width/2})}}else if(jitter==="beeswarm"){if(horizontal){d3.range(scaledPoints.length).map(function(i){return scaledPoints[i].fx=scaledPoints[i].x});force=d3.forceSimulation(scaledPoints).force("y",d3.forceY(function(d){return d.y})).force("collide",d3.forceCollide(pointsize*1.1)).stop()}else{d3.range(scaledPoints.length).map(function(i){return scaledPoints[i].fy=scaledPoints[i].y});force=d3.forceSimulation(scaledPoints).force("x",d3.forceX(function(d){return d.x})).force("collide",d3.forceCollide(pointsize*1.1)).stop()}(function(){var results=[];for(var j=0;j<=30;j++){results.push(j)}return results}).apply(this).map(function(d){force.tick();return points.attr("cx",function(d){return d.x}).attr("cy",function(d){return d.y})})}else if(jitter!=="none"){d3panels.displayError('dotchart: jitter should be "beeswarm", "random", or "none"')}return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xNA=function(){return xNA.handle};chart.yNA=function(){return yNA.handle};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.heatmap=function(chartOpts){var cellSelect,cells,celltip,chart,colors,hilitcolor,margin,nullcolor,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,ref8,svg,tipclass,xlim,xscale,ylim,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}margin=(ref=chartOpts!=null?chartOpts.margin:void 0)!=null?ref:{left:60,top:40,right:40,bottom:40,inner:0};xlim=(ref1=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref1:null;ylim=(ref2=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref2:null;nullcolor=(ref3=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref3:"#e6e6e6";colors=(ref4=chartOpts!=null?chartOpts.colors:void 0)!=null?ref4:["slateblue","white","crimson"];zlim=(ref5=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref5:null;zthresh=(ref6=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref6:null;hilitcolor=(ref7=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref7:"black";tipclass=(ref8=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref8:"tooltip";xscale=null;yscale=null;zscale=null;cells=null;celltip=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cell,cellrect,i,j,myframe,nx,ny,ref10,ref9,tooltipfunc,xlabels,xmid,xmid_scaled,xv,ylabels,ymid,ymid_scaled,yv,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40,inner:0});if(!(data.x!=null||data.xcat!=null)){d3panels.displayError("heatmap: data.x is missing")}if(!(data.y!=null||data.ycat!=null)){d3panels.displayError("heatmap: data.y is missing")}if(data.z==null){d3panels.displayError("heatmap: data.z is missing")}if(data.xcat!=null){data.x=function(){var results;results=[];for(i in data.xcat){results.push(+i)}return results}();xlim=xlim!=null?xlim:[-.5,data.x.length-.5];chartOpts.xticks=data.x;chartOpts.xlineOpts={color:"none",width:0};chartOpts.xlab=(ref9=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref9:""}if(data.ycat!=null){data.y=function(){var results;results=[];for(i in data.ycat){results.push(+i)}return results}();ylim=ylim!=null?ylim:[-.5,data.x.length-.5];chartOpts.yticks=data.y;chartOpts.ylineOpts={color:"none",width:0};chartOpts.ylab=(ref10=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref10:""}nx=data.x.length;ny=data.y.length;if(data.z.length!==nx){d3panels.displayError("heatmap: data.x.length ("+nx+") != data.z.length ("+data.z.length+")")}for(i in data.z){if(data.z[i].length!==ny){d3panels.displayError("heatmap: data.y.length ("+ny+") != data.z["+i+"].length ("+data.z[i].length+")")}}cells=[];for(i in data.z){for(j in data.z[i]){cells.push({x:data.x[i],y:data.y[j],z:data.z[i][j],xindex:+i,yindex:+j})}}xmid=d3panels.calc_midpoints(d3panels.pad_vector(data.x));ymid=d3panels.calc_midpoints(d3panels.pad_vector(data.y));xlim=xlim!=null?xlim:d3.extent(xmid);ylim=ylim!=null?ylim:d3.extent(ymid);zmin=d3panels.matrixMin(data.z);zmax=d3panels.matrixMaxAbs(data.z);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("heatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;cells=function(){var k,len,results;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];if(Math.abs(cell.z)>=zthresh){results.push(cell)}}return results}();chartOpts.margin=margin;chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();xlabels=myframe.xlabels();ylabels=myframe.ylabels();xmid_scaled=function(){var k,len,results;results=[];for(k=0,len=xmid.length;k<len;k++){xv=xmid[k];results.push(xscale(xv))}return results}();ymid_scaled=function(){var k,len,results;results=[];for(k=0,len=ymid.length;k<len;k++){yv=ymid[k];results.push(yscale(yv))}return results}();d3panels.calc_cell_rect(cells,xmid_scaled,ymid_scaled);cellrect=svg.append("g").attr("id","cells");cellSelect=cellrect.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return d.left}).attr("y",function(d){return d.top}).attr("width",function(d){return d.width}).attr("height",function(d){return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.z!=null){return zscale(d.z)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").attr("shape-rendering","crispEdges").on("mouseover",function(d){d3.select(this).attr("stroke",hilitcolor).raise();if(data.xcat!=null){svg.select("text#xlab"+d.x).attr("opacity",1)}if(data.ycat!=null){return svg.select("text#ylab"+d.y).attr("opacity",1)}}).on("mouseout",function(d){d3.select(this).attr("stroke","none");if(data.xcat!=null){svg.select("text#xlab"+d.x).attr("opacity",0)}if(data.ycat!=null){return svg.select("text#ylab"+d.y).attr("opacity",0)}});tooltipfunc=function tooltipfunc(d,i){var x,y,z;x=d3panels.formatAxis(data.x)(d.x);y=d3panels.formatAxis(data.y)(d.y);z=d3panels.formatAxis([0,zmax/100])(d.z);if(data.xcat!=null&&data.ycat!=null){return""+z}if(data.xcat!=null){return"("+y+") → "+z}if(data.ycat!=null){return"("+x+") → "+z}return"("+x+", "+y+") → "+z};celltip=d3panels.tooltip_create(d3.select("body"),cellrect.selectAll("rect"),{tipclass:tipclass},tooltipfunc);if(data.xcat!=null){xlabels.text(function(d,i){return data.xcat[i]}).attr("opacity",0).attr("id",function(d,i){return"xlab"+data.x[i]})}if(data.ycat!=null){ylabels.text(function(d,i){return data.ycat[i]}).attr("opacity",0).attr("id",function(d,i){return"ylab"+data.y[i]})}return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return zscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.lodchart=function(chartOpts){var chart,chrSelect,linecolor,linewidth,markerSelect,markertip,pointcolor,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,ref5,ref6,_svg,tipclass,_xscale,ylim,_yscale;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:"darkslateblue";linewidth=(ref1=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref1:2;pointcolor=(ref2=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref2:"#e9cfec";pointsize=(ref3=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref3:0;pointstroke=(ref4=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref4:"black";ylim=(ref5=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref5:null;tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";_xscale=null;_yscale=null;chrSelect=null;markerSelect=null;markertip=null;_svg=null;chart=function chart(selection,data){var add2chart,i,myframe,self_chart;if(data.chr==null){d3panels.displayError("lodchart: data.chr is missing")}if(data.pos==null){d3panels.displayError("lodchart: data.pos is missing")}if(data.lod==null){d3panels.displayError("lodchart: data.lod is missing")}if(data.marker==null){d3panels.displayError("lodchart: data.marker is missing")}if(data.pos.length!==data.chr.length){d3panels.displayError("lodchart: data.pos.length ("+data.pos.length+") != data.chr.length ("+data.chr.length+")")}if(data.lod.length!==data.chr.length){d3panels.displayError("lodchart: data.lod.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}if(data.marker==null){data.marker=[function(){var results;results=[];for(i in data.chr){results.push("")}return results}()]}if(data.marker.length!==data.chr.length){d3panels.displayError("lodchart: data.marker.length ("+data.marker.length+") != data.chr.length ("+data.chr.length+")")}data=d3panels.add_chrname_start_end(data);data=d3panels.reorgLodData(data);chartOpts.ylim=ylim!=null?ylim:[0,d3.max(data.lod)*1.05];myframe=d3panels.chrpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});_svg=myframe.svg();_xscale=myframe.xscale();_yscale=myframe.yscale();chrSelect=myframe.chrSelect();self_chart={svg:function svg(){return _svg},xscale:function xscale(){return _xscale},yscale:function yscale(){return _yscale}};add2chart=d3panels.add_lodcurve(chartOpts);add2chart(self_chart,data);markerSelect=add2chart.markerSelect();markertip=add2chart.markertip();return myframe.box().raise()};chart.xscale=function(){return _xscale};chart.yscale=function(){return _yscale};chart.chrSelect=function(){return chrSelect};chart.markerSelect=function(){return markerSelect};chart.markertip=function(){return markertip};chart.svg=function(){return _svg};chart.remove=function(){_svg.remove();d3panels.tooltip_destroy(markertip);return null};return chart};"use strict";d3panels.add_lodcurve=function(chartOpts){var chart,g,horizontal,linecolor,linedash,linewidth,markerSelect,markertip,pointcolor,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,tipclass;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:"darkslateblue";linewidth=(ref1=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref1:2;linedash=(ref2=chartOpts!=null?chartOpts.linedash:void 0)!=null?ref2:"";pointcolor=(ref3=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref3:"#e9cfec";pointsize=(ref4=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref4:0;pointstroke=(ref5=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref5:"black";tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";horizontal=(ref7=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref7:false;markerSelect=null;markertip=null;g=null;chart=function chart(prevchart,data){var bigpointsize,chr,curves,hiddenpoints,i,j,len,lodcurve,markerpoints,ref8,svg,xscale,yscale;if(data.chr==null){d3panels.displayError("add_lodcurve: data.chr is missing")}if(data.pos==null){d3panels.displayError("add_lodcurve: data.pos is missing")}if(data.lod==null){d3panels.displayError("add_lodcurve: data.lod is missing")}if(data.marker==null){d3panels.displayError("add_lodcurve: data.marker is missing")}if(data.pos.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.pos.length ("+data.pos.length+") != data.chr.length ("+data.chr.length+")")}if(data.lod.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.lod.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}if(data.marker==null){data.marker=[function(){var results;results=[];for(i in data.chr){results.push("")}return results}()]}if(data.marker.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.marker.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}data=d3panels.add_chrname_start_end(data);if(!(data.posByChr!=null&&data.lodByChr!=null&&data.markerinfo!=null)){data=d3panels.reorgLodData(data)}svg=prevchart.svg();g=svg.append("g").attr("id","lod_curve");xscale=prevchart.xscale();yscale=prevchart.yscale();lodcurve=function lodcurve(chr){return d3.line().x(function(d,i){if(horizontal){return yscale(data.lodByChr[chr][i])}return xscale[chr](d)}).y(function(d,i){if(horizontal){return xscale[chr](d)}return yscale(data.lodByChr[chr][i])})};if(linewidth>0){curves=g.append("g").attr("id","curves");ref8=data.chrname;for(j=0,len=ref8.length;j<len;j++){chr=ref8[j];curves.append("path").datum(data.posByChr[chr]).attr("d",lodcurve(chr)).attr("stroke",linecolor).attr("fill","none").attr("stroke-width",linewidth).attr("stroke-dasharray",linedash).style("pointer-events","none")}}if(pointsize>0){markerpoints=g.append("g").attr("id","markerpoints_visible");markerpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx",function(d){if(horizontal){return yscale(d.lod)}return xscale[d.chr](d.pos)}).attr("cy",function(d){if(horizontal){return xscale[d.chr](d.pos)}return yscale(d.lod)}).attr("r",function(d){if(d.lod!=null){return pointsize}else{return null}}).attr("fill",pointcolor).attr("stroke",pointstroke).attr("pointer-events","hidden")}hiddenpoints=g.append("g").attr("id","markerpoints_hidden");bigpointsize=d3.max([2*pointsize,3]);markerSelect=hiddenpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx",function(d){if(horizontal){return yscale(d.lod)}return xscale[d.chr](d.pos)}).attr("cy",function(d){if(horizontal){return xscale[d.chr](d.pos)}return yscale(d.lod)}).attr("id",function(d){return d.name}).attr("r",function(d){if(d.lod!=null){return bigpointsize}else{return null}}).attr("opacity",0).attr("fill",pointcolor).attr("stroke",pointstroke).attr("stroke-width","1").on("mouseover",function(d){return d3.select(this).attr("opacity",1)}).on("mouseout",function(){return d3.select(this).attr("opacity",0)});return markertip=d3panels.tooltip_create(d3.select("body"),markerSelect,{tipclass:tipclass},function(d,i){return[d.name," LOD = "+d3.format(".2f")(d.lod)]})};chart.markerSelect=function(){return markerSelect};chart.markertip=function(){return markertip};chart.remove=function(){g.remove();d3panels.tooltip_destroy(markertip);return null};return chart};"use strict";d3panels.add_curves=function(chartOpts){var chart,curveGroup,curves,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref2,ref3,ref4,tipclass;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:null;linecolorhilit=(ref1=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref1:null;linewidth=(ref2=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref2:2;linewidthhilit=(ref3=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref3:2;tipclass=(ref4=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref4:"tooltip";curves=null;indtip=null;curveGroup=null;chart=function chart(prevchart,data){var curvefunc,dataByPoint,g,group,i,indID,j,k,n_ind,ngroup,ref5,ref6,ref7,svg,x,xscale,y,yscale;if(data.x==null){d3panels.displayError("add_curves: data.x is missing")}if(data.y==null){d3panels.displayError("add_curves: data.y is missing")}x=function(){var k,len,ref5,results;ref5=data.x;results=[];for(k=0,len=ref5.length;k<len;k++){x=ref5[k];results.push(d3panels.missing2null(x))}return results}();y=function(){var k,len,ref5,results;ref5=data.y;results=[];for(k=0,len=ref5.length;k<len;k++){y=ref5[k];results.push(d3panels.missing2null(y))}return results}();n_ind=y.length;if(x.length===1&&y.length>1){for(j=k=2,ref5=n_ind;2<=ref5?k<=ref5:k>=ref5;j=2<=ref5?++k:--k){x.push(x[0])}}if(x.length!==n_ind){d3panels.displayError("add_curves: data.x.length ("+x.length+") != data.y.length ("+n_ind+")")}indID=(ref6=data!=null?data.indID:void 0)!=null?ref6:function(){var results=[];for(var l=1;1<=n_ind?l<=n_ind:l>=n_ind;1<=n_ind?l++:l--){results.push(l)}return results}.apply(this);if(indID.length!==n_ind){d3panels.displayError("add_curves: data.indID.length ("+indID.length+") != data.y.length ("+n_ind+")")}group=(ref7=data!=null?data.group:void 0)!=null?ref7:function(){var results;results=[];for(i in y){results.push(1)}return results}();group=d3panels.expand2vector(group,n_ind);ngroup=d3.max(group);group=function(){var l,len,results;results=[];for(l=0,len=group.length;l<len;l++){g=group[l];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var l,len,results;results=[];for(l=0,len=group.length;l<len;l++){g=group[l];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_curves: group values out of range");console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==n_ind){d3panels.displayError("add_curves: data.group.length ("+group.length+") != data.y.length ("+n_ind+")")}for(i in y){if(x[i].length!==y[i].length){d3panels.displayError("add_curves: length(x) ("+x[i].length+") != length(y) ("+y[i].length+") for individual "+indID[i]+" (index "+(i+1)+")")}}linecolor=linecolor!=null?linecolor:d3panels.selectGroupColors(ngroup,"pastel");linecolor=d3panels.expand2vector(linecolor,ngroup);linecolorhilit=linecolorhilit!=null?linecolorhilit:d3panels.selectGroupColors(ngroup,"dark");linecolorhilit=d3panels.expand2vector(linecolorhilit,ngroup);svg=prevchart.svg();xscale=prevchart.xscale();yscale=prevchart.yscale();dataByPoint=[];for(i in y){dataByPoint.push(function(){var results;results=[];for(j in y[i]){if(x[i][j]!=null&&y[i][j]!=null){results.push({x:x[i][j],y:y[i][j]})}}return results}())}curvefunc=d3.line().x(function(d){return xscale(d.x)}).y(function(d){return yscale(d.y)});curveGroup=svg.append("g").attr("id","curves");curves=curveGroup.selectAll("empty").data(d3.range(n_ind)).enter().append("path").datum(function(d){return dataByPoint[d]}).attr("d",curvefunc).attr("class",function(d,i){return"path"+i}).attr("fill","none").attr("stroke",function(d,i){return linecolor[group[i]]}).attr("stroke-width",linewidth).on("mouseover.panel",function(d,i){return d3.select(this).attr("stroke",linecolorhilit[group[i]]).attr("stroke-width",linewidthhilit).raise()}).on("mouseout.panel",function(d,i){return d3.select(this).attr("stroke",linecolor[group[i]]).attr("stroke-width",linewidth)});indtip=d3panels.tooltip_create(d3.select("body"),curves,{tipclass:tipclass},function(d,i){return indID[i]});return prevchart.box().raise()};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.remove=function(){curveGroup.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.add_points=function(chartOpts){var chart,indtip,jitter,pointGroup,pointcolor,points,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,tipclass;if(chartOpts==null){chartOpts={}}pointcolor=(ref=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref:null;pointsize=(ref1=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref1:3;pointstroke=(ref2=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref2:"black";jitter=(ref3=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref3:"beeswarm";tipclass=(ref4=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref4:"tooltip";points=null;indtip=null;pointGroup=null;chart=function chart(prevchart,data){var force,g,group,i,indID,ngroup,ref5,ref6,ref7,scaledPoints,svg,ux,uy,x,xscale,xwid,y,yscale,ywid;if(data.x==null){d3panels.displayError("add_points: data.x is missing")}if(data.y==null){d3panels.displayError("add_points: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);if(x.length!==y.length){d3panels.displayError("add_points: x.length ("+x.length+") != y.length ("+y.length+")")}indID=(ref5=data!=null?data.indID:void 0)!=null?ref5:null;indID=indID!=null?indID:function(){var results=[];for(var j=1,ref6=x.length;1<=ref6?j<=ref6:j>=ref6;1<=ref6?j++:j--){results.push(j)}return results}.apply(this);if(indID.length!==x.length){d3panels.displayError("add_points: indID.length ("+indID.length+") != x.length ("+x.length+")")}group=(ref7=data!=null?data.group:void 0)!=null?ref7:function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){i=x[j];results.push(1)}return results}();group=d3panels.expand2vector(group,x.length);ngroup=d3.max(group);group=function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_points: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==x.length){d3panels.displayError("add_points: group.length ("+group.length+") != x.length ("+x.length+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}svg=prevchart.svg();xscale=prevchart.xscale();yscale=prevchart.yscale();pointGroup=svg.append("g").attr("id","points");points=pointGroup.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx",function(d,i){return xscale(x[i])}).attr("cy",function(d,i){return yscale(y[i])}).attr("class",function(d,i){return"pt"+i}).attr("r",pointsize).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width","1");indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]});if(prevchart.xNA()||prevchart.yNA()){if(jitter==="random"){xwid=20-pointsize-2;xwid=xwid<=2?2:xwid;ywid=20-pointsize-2;ywid=ywid<=2?2:ywid;ux=function(){var results;results=[];for(i in x){results.push((Math.random()-.5)*xwid)}return results}();uy=function(){var results;results=[];for(i in x){results.push((Math.random()-.5)*ywid)}return results}();points.attr("cx",function(d,i){if(x[i]!=null){return xscale(x[i])}return xscale(x[i])+ux[i]}).attr("cy",function(d,i){if(y[i]!=null){return yscale(y[i])}return yscale(y[i])+uy[i]})}else if(jitter==="beeswarm"){scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(x[i]),y:yscale(y[i]),xnull:x[i]==null,ynull:y[i]==null})}return results}();d3.range(scaledPoints.length).map(function(i){if(!scaledPoints[i].xnull){scaledPoints[i].fx=scaledPoints[i].x}if(!scaledPoints[i].ynull){return scaledPoints[i].fy=scaledPoints[i].y}});force=d3.forceSimulation(scaledPoints).force("x",d3.forceX(function(d){return d.x})).force("y",d3.forceY(function(d){return d.y})).force("collide",d3.forceCollide(pointsize*1.1)).stop();(function(){var results=[];for(var j=0;j<=30;j++){results.push(j)}return results}).apply(this).map(function(d){force.tick();return points.attr("cx",function(d,i){return scaledPoints[i].x}).attr("cy",function(d,i){return scaledPoints[i].y})})}else if(jitter!=="none"){d3panels.displayError('add_points: jitter should be "beeswarm", "random", or "none"')}}return prevchart.box().raise()};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.remove=function(){pointGroup.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.lodheatmap=function(chartOpts){var cellSelect,cells,celltip,chart,chrGap,colors,equalCells,height,hilitcolor,horizontal,margin,nullcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,width,xlab,xscale,ylab,ylim,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40};colors=(ref3=chartOpts!=null?chartOpts.colors:void 0)!=null?ref3:["slateblue","white","crimson"];nullcolor=(ref4=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref4:"#e6e6e6";xlab=(ref5=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref5:null;ylab=(ref6=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref6:"";ylim=(ref7=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref7:null;zlim=(ref8=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref8:null;zthresh=(ref9=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref9:null;horizontal=(ref10=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref10:false;hilitcolor=(ref11=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref11:"black";chrGap=(ref12=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref12:6;equalCells=(ref13=chartOpts!=null?chartOpts.equalCells:void 0)!=null?ref13:false;tipclass=(ref14=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref14:"tooltip";xscale=null;yscale=null;zscale=null;cells=null;celltip=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cellg,celltipfunc,chr,direction,i,j,k,l,len,len1,len2,len3,len4,lod,m,myframe,n,n_lod,n_pos,o,pos,ref15,ref16,ref17,ref18,ref19,x,xmid_scaled,y,ylabels,ymid,ymid_scaled,yv,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40});if(data.chr==null){d3panels.displayError("lodheatmap: data.chr is missing")}if(data.pos==null){d3panels.displayError("lodheatmap: data.pos is missing")}if(data.lod==null){d3panels.displayError("lodheatmap: data.lod is missing")}if(data.ycat!=null){data.y=function(){var results;results=[];for(i in data.ycat){results.push(i+1)}return results}()}if(data.y==null){data.ycat=function(){var results;results=[];for(i in data.lod[0]){results.push(i+1)}return results}();data.y=function(){var results;results=[];for(i in data.lod[0]){results.push(i+1)}return results}()}data.y=function(){var k,len,ref15,results;ref15=data.y;results=[];for(k=0,len=ref15.length;k<len;k++){yv=ref15[k];results.push(+yv)}return results}();n_pos=data.chr.length;n_lod=data.y.length;if(n_pos!==data.pos.length){d3panels.displayError("lodheatmap: data.pos.length ("+data.pos.length+") != data.chr.length ("+n_pos+")")}if(n_pos!==data.lod.length){d3panels.displayError("lodheatmap: data.lod.length ("+data.lod.length+") != data.chr.length ("+n_pos+")")}for(i in data.lod){if(data.lod[i].length!==data.y.length){d3panels.displayError("lodheatmap: data.lod["+i+"].length ("+data.lod[i].length+") != data.y.length ("+n_lod+")")}}if(data.poslabel!=null){if(data.poslabel.length!==n_pos){d3panels.displayError("lodheatmap: data.poslabel.length ("+data.poslabel.length+") != data.chr.length ("+n_pos+")")}}else{data.poslabel=function(){var results;results=[];for(i in data.chr){results.push(data.chr[i]+"@"+d3panels.formatAxis(data.pos)(data.pos[i]))}return results}()}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(equalCells){data.pos=[];ref15=data.chrname;for(k=0,len=ref15.length;k<len;k++){chr=ref15[k];data.pos=data.pos.concat(function(){var results;results=[];for(i in data.chr){if(data.chr[i]===chr){results.push(+i)}}return results}())}}data=d3panels.add_chrname_start_end(data);if(equalCells){chrGap=(width-margin.left-margin.right-2*data.chrname.length)/data.chr.length+2}data=d3panels.reorgLodData(data);ymid=d3panels.calc_midpoints(d3panels.pad_vector(data.y));chartOpts.ylim=ylim!=null?ylim:d3.extent(ymid);chartOpts.horizontal=horizontal;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.chrGap=chrGap;chartOpts.width=width;chartOpts.height=height;chartOpts.margin=margin;if(data.ycat!=null){chartOpts.yticks=data.y;chartOpts.yticklab=data.ycat}myframe=d3panels.chrpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();ylabels=myframe.ylabels();ymid_scaled=function(){var l,len1,results;results=[];for(l=0,len1=ymid.length;l<len1;l++){y=ymid[l];results.push(yscale(y))}return results}();xmid_scaled={};ref16=data.chrname;for(l=0,len1=ref16.length;l<len1;l++){chr=ref16[l];xmid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref17,results;ref17=data.posByChr[chr];results=[];for(m=0,len2=ref17.length;m<len2;m++){x=ref17[m];results.push(xscale[chr](x))}return results}(),(chrGap-2)/2))}zmin=d3panels.matrixMin(data.lod);zmax=d3panels.matrixMaxAbs(data.lod);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("lodheatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;cells=[];ref17=data.chrname;for(m=0,len2=ref17.length;m<len2;m++){chr=ref17[m];ref18=data.posByChr[chr];for(i=n=0,len3=ref18.length;n<len3;i=++n){pos=ref18[i];ref19=data.lodByChr[chr][i];for(j=o=0,len4=ref19.length;o<len4;j=++o){lod=ref19[j];if(Math.abs(lod)>=zthresh){cells.push({lod:lod,chr:chr,pos:pos,poslabel:data.poslabelByChr[chr][i],posindex:+i,lodindex:+j})}}}}d3panels.calc_chrcell_rect(cells,xmid_scaled,ymid_scaled);cellg=svg.append("g").attr("id","cells");cellSelect=cellg.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){if(horizontal){return d.top}return d.left}).attr("y",function(d){if(horizontal){return d.left}return d.top}).attr("width",function(d){if(horizontal){return d.height}return d.width}).attr("height",function(d){if(horizontal){return d.width}return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.lod!=null){return zscale(d.lod)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").attr("shape-rendering","crispEdges").on("mouseover",function(d){d3.select(this).attr("stroke",hilitcolor).raise();if(data.ycat!=null){return svg.select("text#ylab"+d.lodindex).attr("opacity",1)}}).on("mouseout",function(d){d3.select(this).attr("stroke","none");if(data.ycat!=null){return svg.select("text#ylab"+d.lodindex).attr("opacity",0)}});if(data.ycat!=null){svg.selectAll("g#ylines").remove();ylabels.attr("opacity",0).attr("id",function(d,i){return"ylab"+i})}celltipfunc=function celltipfunc(d){var lodlabel,z;z=d3.format(".2f")(Math.abs(d.lod));lodlabel=data.ycat!=null?data.ycat[d.lodindex]:d3panels.formatAxis(data.y)(data.y[d.lodindex]);if(horizontal){return lodlabel+", "+d.poslabel+" → "+z}return d.poslabel+", "+lodlabel+" → "+z};direction=horizontal?"north":"east";celltip=d3panels.tooltip_create(d3.select("body"),cellg.selectAll("rect"),{direction:direction,tipclass:tipclass},celltipfunc);return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return yscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.mapchart=function(chartOpts){var chart,horizontal,linecolor,linecolorhilit,linewidth,markerSelect,martip,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,shiftStart,svg,tickwidth,tipclass,v_over_h,xlab,xlineOpts,xscale,ylab,yscale;if(chartOpts==null){chartOpts={}}tickwidth=(ref=chartOpts!=null?chartOpts.tickwidth:void 0)!=null?ref:10;linecolor=(ref1=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref1:"slateblue";linecolorhilit=(ref2=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref2:"Orchid";linewidth=(ref3=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref3:3;xlab=(ref4=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref4:"Chromosome";ylab=(ref5=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref5:"Position (cM)";xlineOpts=(ref6=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref6:{color:"#cdcdcd",width:5};horizontal=(ref7=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref7:false;v_over_h=(ref8=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref8:horizontal;shiftStart=(ref9=chartOpts!=null?chartOpts.shiftStart:void 0)!=null?ref9:false;tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;markerSelect=null;martip=null;svg=null;chart=function chart(selection,data){var chr,chrscale,direction,extentByChr,i,j,k,l,len,len1,markerpos,markers,minpos,myframe,n_chr,n_pos,pos,ref11,ref12,these_index,these_pos,tipfunc,x,xlim,xticklab,xticks,ylim;xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"#cdcdcd",width:5});if(data.chr==null){d3panels.displayError("mapchart: data.chr is missing")}if(data.pos==null){d3panels.displayError("mapchart: data.pos is missing")}if(data.marker==null){d3panels.displayError("mapchart: data.marker is missing")}n_pos=data.pos.length;if(data.chr.length!==n_pos){d3panels.displayError("mapchart: data.chr.length ("+data.chr.length+") != data.pos.length ("+n_pos+")")}if(data.marker.length!==n_pos){d3panels.displayError("mapchart: data.marker.length ("+data.marker.length+") != data.pos.length ("+n_pos+")")}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);data.adjpos=data.pos.slice(0);if(shiftStart){ref11=data.chrname;for(k=0,len=ref11.length;k<len;k++){chr=ref11[k];these_pos=function(){var results;results=[];for(i in data.pos){if(data.chr[i]===chr){results.push(data.pos[i])}}return results}();these_index=function(){var results;results=[];for(i in data.pos){if(data.chr[i]===chr){results.push(i)}}return results}();minpos=d3.min(these_pos);these_pos=function(){var l,len1,results;results=[];for(l=0,len1=these_pos.length;l<len1;l++){x=these_pos[l];results.push(x-minpos)}return results}();for(j in these_pos){data.adjpos[these_index[j]]=these_pos[j]}}}extentByChr={};ref12=data.chrname;for(l=0,len1=ref12.length;l<len1;l++){chr=ref12[l];pos=function(){var results;results=[];for(i in data.adjpos){if(data.chr[i]===chr){results.push(data.adjpos[i])}}return results}();extentByChr[chr]=d3.extent(pos)}ylim=ylim!=null?ylim:d3.extent(data.adjpos);n_chr=data.chrname.length;xlim=[.5,n_chr+.5];xticks=function(){var len2,m,ref13,results;ref13=d3.range(n_chr);results=[];for(m=0,len2=ref13.length;m<len2;m++){i=ref13[m];results.push(i+1)}return results}();xticklab=data.chrname;chartOpts.xNA=false;chartOpts.yNA=false;if(horizontal){chartOpts.xlim=ylim;chartOpts.ylim=xlim.reverse();chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xticks=chartOpts.yticks;chartOpts.yticks=xticks;chartOpts.nxticks=chartOpts.nyticks;chartOpts.xticklab=chartOpts.yticklab;chartOpts.yticklab=xticklab;chartOpts.v_over_h=v_over_h}else{chartOpts.xlim=xlim;chartOpts.ylim=ylim.reverse();chartOpts.xlineOpts=xlineOpts;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.xticks=xticks;chartOpts.xticklab=xticklab;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();chrscale=function chrscale(chr){var chrpos;chrpos=data.chrname.indexOf(chr)+1;if(!horizontal){return xscale(chrpos)}return yscale(chrpos)};svg.append("g").attr("id","chromosomes").selectAll("empty").data(data.chrname).enter().append("line").attr("x1",function(d){if(horizontal){return xscale(extentByChr[d][0])}return chrscale(d)}).attr("x2",function(d){if(horizontal){return xscale(extentByChr[d][1])}return chrscale(d)}).attr("y1",function(d){if(horizontal){return chrscale(d)}return yscale(extentByChr[d][0])}).attr("y2",function(d){if(horizontal){return chrscale(d)}return yscale(extentByChr[d][1])}).attr("fill","none").attr("stroke",linecolor).attr("stroke-width",linewidth).attr("shape-rendering","crispEdges").style("pointer-events","none");markerpos={};for(i in data.marker){markerpos[data.marker[i]]=d3.format(".1f")(data.pos[i])}markers=svg.append("g").attr("id","points");markerSelect=markers.selectAll("empty").data(data.marker).enter().append("line").attr("x1",function(d,i){if(horizontal){return xscale(data.adjpos[i])}return chrscale(data.chr[i])-tickwidth}).attr("x2",function(d,i){if(horizontal){return xscale(data.adjpos[i])}return chrscale(data.chr[i])+tickwidth}).attr("y1",function(d,i){if(horizontal){return chrscale(data.chr[i])-tickwidth}return yscale(data.adjpos[i])}).attr("y2",function(d,i){if(horizontal){return chrscale(data.chr[i])+tickwidth}return yscale(data.adjpos[i])}).attr("id",function(d){return d}).attr("fill","none").attr("stroke",linecolor).attr("stroke-width",linewidth).attr("shape-rendering","crispEdges").on("mouseover.paneltip",function(d){return d3.select(this).attr("stroke",linecolorhilit)}).on("mouseout.paneltip",function(){return d3.select(this).attr("stroke",linecolor)});tipfunc=function tipfunc(d,i){return d+" ("+markerpos[d]+")"};direction=horizontal?"north":"east";martip=d3panels.tooltip_create(d3.select("body"),markers.selectAll("line"),{direction:direction,tipclass:tipclass},tipfunc);return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.markerSelect=function(){return markerSelect};chart.martip=function(){return martip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(martip);return null};return chart};"use strict";d3panels.scatterplot=function(chartOpts){var chart,indtip,jitter,pointcolor,points,pointsize,pointstroke,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,xNA,xNA_size,xlim,xscale,yNA,yNA_size,ylim,yscale;if(chartOpts==null){chartOpts={}}xNA=(ref=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref:{handle:true,force:false};yNA=(ref1=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref1:{handle:true,force:false};xNA_size=(ref2=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref2:{width:20,gap:10};yNA_size=(ref3=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref3:{width:20,gap:10};xlim=(ref4=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref4:null;ylim=(ref5=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref5:null;pointcolor=(ref6=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref6:null;pointstroke=(ref7=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref7:"black";pointsize=(ref8=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref8:3;jitter=(ref9=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref9:"beeswarm";tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;xNA=xNA;yNA=yNA;points=null;indtip=null;svg=null;chart=function chart(selection,data){var addpts,myframe,x,y;xNA=d3panels.check_listarg_v_default(xNA,{handle:true,force:false});yNA=d3panels.check_listarg_v_default(yNA,{handle:true,force:false});xNA_size=d3panels.check_listarg_v_default(xNA,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA,{width:20,gap:10});if(data.x==null){d3panels.displayError("scatterplot: data.x is missing")}if(data.y==null){d3panels.displayError("scatterplot: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);if(x.length!==y.length){d3panels.displayError("scatterplot: x.length ("+x.length+") != y.length ("+y.length+")")}xNA.handle=xNA.force||xNA.handle&&!x.every(function(v){return v!=null});yNA.handle=yNA.force||yNA.handle&&!y.every(function(v){return v!=null});xlim=xlim!=null?xlim:d3panels.pad_ylim(d3.extent(x));ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(y));chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=xNA.handle;chartOpts.yNA=yNA.handle;chartOpts.xNA_size=xNA_size;chartOpts.yNA_size=yNA_size;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();addpts=d3panels.add_points({pointcolor:pointcolor,pointstroke:pointstroke,pointsize:pointsize,jitter:jitter,tipclass:tipclass});addpts(myframe,{x:x,y:y,indID:data.indID,group:data.group});points=addpts.points();return indtip=addpts.indtip()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xNA=function(){return xNA.handle};chart.yNA=function(){return yNA.handle};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.trichart=function(chartOpts){var boxcolor,boxwidth,chart,gridcolor,gridlines,gridwidth,height,indtip,labelpos,labels,margin,pointcolor,points,pointsize,pointstroke,pscale,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,title,titlepos,width,xscale,yscale;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:600;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:520;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:60,bottom:10};labelpos=(ref3=chartOpts!=null?chartOpts.labelpos:void 0)!=null?ref3:10;titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";labels=(ref6=chartOpts!=null?chartOpts.labels:void 0)!=null?ref6:["(1,0,0)","(0,1,0)","(0,0,1)"];rectcolor=(ref7=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref7:"#e6e6e6";boxcolor=(ref8=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref8:"black";boxwidth=(ref9=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref9:2;pointcolor=(ref10=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref10:null;pointstroke=(ref11=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref11:"black";pointsize=(ref12=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref12:3;gridlines=(ref13=chartOpts!=null?chartOpts.gridlines:void 0)!=null?ref13:0;gridcolor=(ref14=chartOpts!=null?chartOpts.gridcolor:void 0)!=null?ref14:"white";gridwidth=(ref15=chartOpts!=null?chartOpts.gridwidth:void 0)!=null?ref15:1;tipclass=(ref16=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref16:"tooltip";xscale=null;yscale=null;pscale=null;points=null;indtip=null;svg=null;chart=function chart(selection,data){var d,first,flag_length_not_3,flag_out_of_range,flag_sum_not_1,frame,framefunc,g,gr,group,i,indID,indices,j,len,n,ngroup,p,p1,p2,p3,p4,plot_height,plot_width,ref17,ref18,second,sum,v,vertices,vv,xlim,xy,ylim;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:60,bottom:10});if(data.p==null){d3panels.displayError("trichart: data.p is missing")}p=function(){var j,len,ref17,results;ref17=data.p;results=[];for(j=0,len=ref17.length;j<len;j++){v=ref17[j];results.push(d3panels.missing2null(v))}return results}();flag_length_not_3=false;flag_sum_not_1=false;flag_out_of_range=false;for(j=0,len=p.length;j<len;j++){v=p[j];if(v.length!==3){flag_length_not_3=true}sum=d3panels.sumArray(v);if(d3panels.abs(sum-1)>1e-6){flag_sum_not_1}if(d3panels.sumArray(function(){var k,len1,results;results=[];for(k=0,len1=v.length;k<len1;k++){vv=v[k];results.push(vv<0||vv>1)}return results}())>0){flag_out_of_range=true}}if(flag_length_not_3){d3panels.displayError("trichart: points not all of length 3")}if(flag_sum_not_1){d3panels.displayError("trichart: points not all summing to 1")}if(flag_out_of_range){d3panels.displayError("trichart: points not all in [0,1]")}n=p.length;indID=(ref17=data!=null?data.indID:void 0)!=null?ref17:function(){var results;results=[];for(i in p){results.push(+i+1)}return results}();if(indID.length!==n){d3panels.displayError("trichart: data.indID.length ("+indID.length+") != data.p.length ("+n+")")}group=(ref18=data!=null?data.group:void 0)!=null?ref18:function(){var results;results=[];for(i in p){results.push(1)}return results}();group=d3panels.expand2vector(group,n);ngroup=d3.max(group);group=function(){var k,len1,results;results=[];for(k=0,len1=group.length;k<len1;k++){g=group[k];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var k,len1,results;results=[];for(k=0,len1=group.length;k<len1;k++){g=group[k];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_points: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==n){d3panels.displayError("trichart: data.group.length ("+group.length+") != data.p.length ("+n+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}xlim=[0,2/Math.sqrt(3)];ylim=[0,1];plot_height=height-margin.top-margin.bottom;plot_width=width-margin.left-margin.right;if(plot_height>plot_width/xlim[1]){d=plot_height-plot_width/xlim[1];margin.top+=d/2;margin.bottom+=d/2;plot_height-=d}else{d=plot_width-plot_height*xlim[1];margin.left+=d/2;margin.right+=d/2;plot_width-=d}xscale=d3.scaleLinear().domain(xlim).range([margin.left,margin.left+plot_width]);yscale=d3.scaleLinear().domain(ylim).range([plot_height+margin.top,margin.top]);pscale=function pscale(p){sum=d3panels.sumArray(p);return{x:xscale((p[0]*2+p[1])/Math.sqrt(3)/sum),y:yscale(p[1]/sum)}};xy=function(){var k,len1,results;results=[];for(k=0,len1=p.length;k<len1;k++){v=p[k];results.push({x:(v[0]*2+v[1])/Math.sqrt(3),y:v[1]})}return results}();svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");frame=svg.append("g").attr("id","frame");vertices=[{x:xlim[0],y:ylim[0]},{x:xlim[1]/2,y:ylim[1]},{x:xlim[1],y:ylim[0]}];framefunc=d3.line().x(function(d){return xscale(vertices[d].x)}).y(function(d){return yscale(vertices[d].y)});indices=function(){var results;results=[];for(i in vertices){results.push(+i)}return results}().concat(0);frame.append("path").datum(indices).attr("d",framefunc).attr("fill",rectcolor).attr("stroke",boxcolor).attr("stroke-width",boxwidth);if(gridlines>0){gr=function(){var results=[];for(var k=1;1<=gridlines?k<=gridlines:k>=gridlines;1<=gridlines?k++:k--){results.push(k)}return results}.apply(this).map(function(i){return i/(gridlines+1)});p1=gr.map(function(x){return[x,0,1-x]});p2=gr.map(function(x){return[x,1-x,0]});p3=gr.map(function(x){return[0,1-x,x]});p4=gr.map(function(x){return[1-x,0,x]});first=p1.concat(p2).concat(p3);second=p2.concat(p3).concat(p4);g=frame.append("g").attr("class","gridlines").selectAll("empty").data(first).enter().append("line").attr("x1",function(d){return pscale(d).x}).attr("y1",function(d){return pscale(d).y}).attr("x2",function(d,i){return pscale(second[i]).x}).attr("y2",function(d,i){return pscale(second[i]).y}).attr("stroke",gridcolor).attr("stroke-width",gridwidth).attr("shape-rendering","crispEdges").style("pointer-events","none").attr("fill","none");frame.append("path").datum(indices).attr("d",framefunc).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth)}frame.append("g").attr("class","title").append("text").text(title).attr("x",plot_width/2+margin.left).attr("y",margin.top-titlepos);frame.append("g").attr("id","labels").selectAll("empty").data(vertices).enter().append("text").attr("x",function(d,i){return xscale(d.x)+[-1,+1,+1][i]*labelpos}).attr("y",function(d){return yscale(d.y)}).style("dominant-baseline","middle").style("text-anchor",function(d,i){return["end","start","start"][i]}).text(function(d,i){return labels[i]});points=svg.append("g").attr("id","points").selectAll("empty").data(p).enter().append("circle").attr("r",pointsize).attr("cx",function(d){return pscale(d).x}).attr("cy",function(d){return pscale(d).y}).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width",1);return indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]})};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.pscale=function(){return pscale};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.histchart=function(chartOpts){var chart,curves,density,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,tipclass,xlab,xlim,xscale,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xlim=(ref=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref:null;ylim=(ref1=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref1:null;xlab=(ref2=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref2:"";ylab=(ref3=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref3:"";rotate_ylab=(ref4=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref4:null;linecolor=(ref5=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref5:null;linecolorhilit=(ref6=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref6:null;linewidth=(ref7=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref7:2;linewidthhilit=(ref8=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref8:2;density=(ref9=chartOpts!=null?chartOpts.density:void 0)!=null?ref9:true;tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;curves=null;indtip=null;svg=null;chart=function chart(selection,data){var add_curves,breaks,brlim,d,f,freq,i,j,k,l,len,len1,maxn,maxpos,myframe,n_ind,p,path_data,path_x,path_y,pt,ref11,x,xv,xx;if(data.x==null){d3panels.displayError("histchart: data.x is missing")}x=data.x;data.group=function(){var results;results=[];for(i in x){results.push(+i+1)}return results}();n_ind=x.length;if(data.breaks==null){maxn=d3.max(function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];results.push(xv.length)}return results}());data.breaks=[2*Math.ceil(Math.sqrt(maxn)+1)]}breaks=d3panels.forceAsArray(data.breaks);xlim=xlim!=null?xlim:d3panels.matrixExtent(x);if(breaks.length===1){breaks=d3panels.calc_breaks(breaks[0],xlim[0],xlim[1])}brlim=[d3.min(breaks)-1e-6,d3.max(breaks)+1e-6];x=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xx=x[k];results.push(function(){var l,len1,results1;results1=[];for(l=0,len1=xx.length;l<len1;l++){xv=xx[l];if(xv>=brlim[0]&xv<=brlim[1]){results1.push(xv)}}return results1}())}return results}();freq=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];results.push(d3panels.calc_freq(xv,breaks,!density))}return results}();maxpos=[];for(k=0,len=freq.length;k<len;k++){f=freq[k];pt={x:breaks[1],y:f[0]};ref11=d3.range(f.length);for(l=0,len1=ref11.length;l<len1;l++){j=ref11[l];if(f[j]>pt.y){pt.y=f[j];pt.x=breaks[j+1]}}maxpos.push(pt)}ylim=ylim!=null?ylim:[0,d3panels.matrixMax(freq)*1.05];chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.rotate_ylab=rotate_ylab;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();path_data=function(){var len2,m,results;results=[];for(m=0,len2=freq.length;m<len2;m++){f=freq[m];results.push(d3panels.calc_hist_path(f,breaks))}return results}();path_x=function(){var len2,m,results;results=[];for(m=0,len2=path_data.length;m<len2;m++){p=path_data[m];results.push(function(){var len3,n,results1;results1=[];for(n=0,len3=p.length;n<len3;n++){d=p[n];results1.push(d.x)}return results1}())}return results}();path_y=function(){var len2,m,results;results=[];for(m=0,len2=path_data.length;m<len2;m++){p=path_data[m];results.push(function(){var len3,n,results1;results1=[];for(n=0,len3=p.length;n<len3;n++){d=p[n];results1.push(d.y)}return results1}())}return results}();add_curves=d3panels.add_curves({linecolor:linecolor,linecolorhilit:linecolorhilit,linewidth:linewidth,linewidthhilit:linewidthhilit,tipclass:tipclass});add_curves(myframe,{x:path_x,y:path_y,indID:data.indID,group:data.group});curves=add_curves.curves();indtip=add_curves.indtip();return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_dstroy(indtip);return null};return chart};"use strict";d3panels.slider=function(chartOpts){var buttoncolor,buttondotcolor,buttondotsize,buttonround,buttonsize,buttonstroke,_chart,height,margin,nticks,rectcolor,rectheight,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,slider_svg,stopindex,textsize,tickgap,tickheight,ticks,ticks_at_stops,value,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:80;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:25,right:25,inner:0,top:40,bottom:40};rectheight=(ref3=chartOpts!=null?chartOpts.rectheight:void 0)!=null?ref3:10;rectcolor=(ref4=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref4:"#ccc";buttonsize=(ref5=chartOpts!=null?chartOpts.buttonsize:void 0)!=null?ref5:rectheight*2;buttoncolor=(ref6=chartOpts!=null?chartOpts.buttoncolor:void 0)!=null?ref6:"#eee";buttonstroke=(ref7=chartOpts!=null?chartOpts.buttonstroke:void 0)!=null?ref7:"black";buttonround=(ref8=chartOpts!=null?chartOpts.buttonround:void 0)!=null?ref8:buttonsize*.2;buttondotcolor=(ref9=chartOpts!=null?chartOpts.buttondotcolor:void 0)!=null?ref9:"slateblue";buttondotsize=(ref10=chartOpts!=null?chartOpts.buttondotsize:void 0)!=null?ref10:buttonsize/4;tickheight=(ref11=chartOpts!=null?chartOpts.tickheight:void 0)!=null?ref11:10;tickgap=(ref12=chartOpts!=null?chartOpts.tickgap:void 0)!=null?ref12:tickheight/2;textsize=(ref13=chartOpts!=null?chartOpts.textsize:void 0)!=null?ref13:14;nticks=(ref14=chartOpts!=null?chartOpts.nticks:void 0)!=null?ref14:5;ticks=(ref15=chartOpts!=null?chartOpts.ticks:void 0)!=null?ref15:null;ticks_at_stops=(ref16=chartOpts!=null?chartOpts.ticks_at_stops:void 0)!=null?ref16:true;value=0;stopindex=0;slider_svg=null;_chart=function chart(selection,callback,range,stops,initial_value){var button,clamp_pixels,dragged,end_drag,xcscale,xscale;margin=d3panels.check_listarg_v_default(margin,{left:25,right:25,inner:0,top:40,bottom:40});margin.left+=margin.inner;margin.right+=margin.inner;if(range==null){range=[margin.left,width-margin.right]}if(margin.top!=null&&margin.top+margin.bottom>0){margin.top=height*margin.top/(margin.top+margin.bottom)}else{margin.top=height/2}if(initial_value!=null){value=initial_value;if(value<range[0]){value=range[0]}if(value>range[1]){value=range[1]}if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops)}if(stops!=null){value=stops[stopindex]}}else{if(stops!=null){stopindex=Math.floor(Math.random()*stops.length);value=stops[stopindex]}else{value=(range[1]-range[0])*Math.random()+range[0]}}slider_svg=selection.insert("svg").attr("height",height).attr("width",width);xcscale=d3.scaleLinear().range([margin.left,width-margin.right]).domain(range).clamp(true);xscale=function xscale(d){if(stops!=null){return xcscale(stops[d3panels.index_of_nearest(d,stops)])}return xcscale(d)};clamp_pixels=function clamp_pixels(pixels,interval){if(pixels<interval[0]){return interval[0]}if(pixels>interval[1]){return interval[1]}return pixels};slider_svg.insert("rect").attr("x",margin.left).attr("y",margin.top-rectheight/2).attr("rx",rectheight*.3).attr("ry",rectheight*.3).attr("width",width-margin.left-margin.right).attr("height",rectheight).attr("fill",rectcolor);if(ticks==null){ticks=xcscale.ticks(nticks)}slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top+rectheight/2+tickgap).attr("y2",margin.top+rectheight/2+tickgap+tickheight).attr("stroke","black").attr("shape-rendering","crispEdges");slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x",function(d){return xcscale(d)}).attr("y",margin.top+rectheight/2+tickgap*2+tickheight).text(function(d){return d}).style("font-size",textsize).style("dominant-baseline","hanging").style("text-anchor","middle").style("pointer-events","none").style("-webkit-user-select","none").style("-moz-user-select","none").style("-ms-user-select","none");if(stops!=null&&ticks_at_stops){slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top-rectheight/2-tickgap).attr("y2",margin.top-rectheight/2-tickgap-tickheight).attr("stroke","black").attr("shape-rendering","crispEdges")}button=slider_svg.insert("g").attr("id","button").attr("transform","translate("+xscale(value)+",0)");button.insert("rect").attr("x",-buttonsize/2).attr("y",margin.top-buttonsize/2).attr("height",buttonsize).attr("width",buttonsize).attr("rx",buttonround).attr("ry",buttonround).attr("stroke",buttonstroke).attr("stroke-width",2).attr("fill",buttoncolor);button.insert("circle").attr("cx",0).attr("cy",margin.top).attr("r",buttondotsize).attr("fill",buttondotcolor);dragged=function dragged(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value=xcscale.invert(clamped_pixels);d3.select(this).attr("transform","translate("+xcscale(value)+",0)");if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops);value=stops[stopindex]}if(callback!=null){return callback(_chart)}};end_drag=function end_drag(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value=xcscale.invert(clamped_pixels);if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops);value=stops[stopindex]}if(callback!=null){callback(_chart)}return d3.select(this).attr("transform","translate("+xcscale(value)+",0)")};button.call(d3.drag().on("drag",dragged).on("end",end_drag));if(callback!=null){return callback(_chart)}};_chart.value=function(){return value};_chart.stopindex=function(){return stopindex};_chart.remove=function(){return slider_svg.remove()};return _chart};"use strict";d3panels.double_slider=function(chartOpts){var buttoncolor,buttondotcolor,buttondotsize,buttonround,buttonsize,buttonstroke,_chart,height,margin,nticks,rectcolor,rectheight,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,slider_svg,stopindex,textsize,tickgap,tickheight,ticks,ticks_at_stops,value,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:80;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:25,right:25,inner:0,top:40,bottom:40};rectheight=(ref3=chartOpts!=null?chartOpts.rectheight:void 0)!=null?ref3:10;rectcolor=(ref4=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref4:"#ccc";buttonsize=(ref5=chartOpts!=null?chartOpts.buttonsize:void 0)!=null?ref5:rectheight*2;buttoncolor=(ref6=chartOpts!=null?chartOpts.buttoncolor:void 0)!=null?ref6:"#eee";buttonstroke=(ref7=chartOpts!=null?chartOpts.buttonstroke:void 0)!=null?ref7:"black";buttonround=(ref8=chartOpts!=null?chartOpts.buttonround:void 0)!=null?ref8:buttonsize*.2;buttondotcolor=(ref9=chartOpts!=null?chartOpts.buttondotcolor:void 0)!=null?ref9:["slateblue","orchid"];buttondotsize=(ref10=chartOpts!=null?chartOpts.buttondotsize:void 0)!=null?ref10:buttonsize/4;tickheight=(ref11=chartOpts!=null?chartOpts.tickheight:void 0)!=null?ref11:10;tickgap=(ref12=chartOpts!=null?chartOpts.tickgap:void 0)!=null?ref12:tickheight/2;textsize=(ref13=chartOpts!=null?chartOpts.textsize:void 0)!=null?ref13:14;nticks=(ref14=chartOpts!=null?chartOpts.nticks:void 0)!=null?ref14:5;ticks=(ref15=chartOpts!=null?chartOpts.ticks:void 0)!=null?ref15:null;ticks_at_stops=(ref16=chartOpts!=null?chartOpts.ticks_at_stops:void 0)!=null?ref16:true;value=[0,0];stopindex=[0,0];slider_svg=null;if(!Array.isArray(buttoncolor)){buttoncolor=[buttoncolor,buttoncolor]}if(!Array.isArray(buttonstroke)){buttonstroke=[buttonstroke,buttonstroke]}if(!Array.isArray(buttondotcolor)){buttondotcolor=[buttondotcolor,buttondotcolor]}_chart=function chart(selection,callback1,callback2,range,stops,initial_value){var buttons,callbacks,clamp_pixels,dragged,end_drag,start_drag,xcscale,xscale;margin=d3panels.check_listarg_v_default(margin,{left:25,right:25,inner:0,top:40,bottom:40});callbacks=[callback1,callback2];margin.left+=margin.inner;margin.right+=margin.inner;if(range==null){range=[margin.left,width-margin.right]}if(margin.top!=null&&margin.top+margin.bottom>0){margin.top=height*margin.top/(margin.top+margin.bottom)}else{margin.top=height/2}if(initial_value!=null){value=initial_value.map(function(d){if(d<range[0]){return range[0]}if(d>range[1]){return range[1]}return d});if(stops!=null){stopindex=value.map(function(d){return d3panels.index_of_nearest(d,stops)})}if(stops!=null){value=stopindex.map(function(i){return stops[i]})}}else{if(stops!=null){stopindex=[0,1].map(function(i){return Math.floor(Math.random()*stops.length)});value=stopindex.map(function(i){return stops[i]})}else{value=[0,1].map(function(i){return(range[1]-range[0])*Math.random()+range[0]})}}slider_svg=selection.insert("svg").attr("height",height).attr("width",width);xcscale=d3.scaleLinear().range([margin.left,width-margin.right]).domain(range).clamp(true);xscale=function xscale(d){if(stops!=null){return xcscale(stops[d3panels.index_of_nearest(d,stops)])}return xcscale(d)};clamp_pixels=function clamp_pixels(pixels,interval){if(pixels<interval[0]){return interval[0]}if(pixels>interval[1]){return interval[1]}return pixels};slider_svg.insert("rect").attr("x",margin.left).attr("y",margin.top-rectheight/2).attr("rx",rectheight*.3).attr("ry",rectheight*.3).attr("width",width-margin.left-margin.right).attr("height",rectheight).attr("fill",rectcolor);if(ticks==null){ticks=xcscale.ticks(nticks)}slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top+rectheight/2+tickgap).attr("y2",margin.top+rectheight/2+tickgap+tickheight).attr("stroke","black").attr("shape-rendering","crispEdges");slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x",function(d){return xcscale(d)}).attr("y",margin.top+rectheight/2+tickgap*2+tickheight).text(function(d){return d}).style("font-size",textsize).style("dominant-baseline","hanging").style("text-anchor","middle").style("pointer-events","none").style("-webkit-user-select","none").style("-moz-user-select","none").style("-ms-user-select","none");if(stops!=null&&ticks_at_stops){slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top-rectheight/2-tickgap).attr("y2",margin.top-rectheight/2-tickgap-tickheight).attr("stroke","black").attr("shape-rendering","crispEdges")}buttons=[0,1].map(function(i){return slider_svg.insert("g").attr("id","button"+(i+1)).attr("transform",function(d){return"translate("+xscale(value[i])+",0)"})});[0,1].map(function(i){buttons[i].insert("rect").attr("x",-buttonsize/2).attr("y",margin.top-buttonsize/2).attr("height",buttonsize).attr("width",buttonsize).attr("rx",buttonround).attr("ry",buttonround).attr("stroke",buttonstroke[i]).attr("stroke-width",2).attr("fill",buttoncolor[i]);return buttons[i].insert("circle").attr("cx",0).attr("cy",margin.top).attr("r",buttondotsize).attr("fill",buttondotcolor[i])});start_drag=function start_drag(i){return function(d){return buttons[i].raise()}};dragged=function dragged(i){return function(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value[i]=xcscale.invert(clamped_pixels);d3.select(this).attr("transform","translate("+xcscale(value[i])+",0)");if(stops!=null){stopindex[i]=d3panels.index_of_nearest(value[i],stops);value[i]=stops[stopindex[i]]}if(callbacks[i]!=null){return callbacks[i](_chart)}}};end_drag=function end_drag(i){return function(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value[i]=xcscale.invert(clamped_pixels);if(stops!=null){stopindex[i]=d3panels.index_of_nearest(value[i],stops);value[i]=stops[stopindex[i]]}if(callbacks[i]!=null){callbacks[i](_chart)}return d3.select(this).attr("transform","translate("+xcscale(value[i])+",0)")}};return[0,1].map(function(i){buttons[i].call(d3.drag().on("start",start_drag(i)).on("drag",dragged(i)).on("end",end_drag(i)));if(callbacks[i]!=null){return callbacks[i](_chart)}})};_chart.value=function(){return value};_chart.stopindex=function(){return stopindex};_chart.remove=function(){return slider_svg.remove()};return _chart};"use strict";d3panels.tooltip_create=function(selection,objects,options,tooltip_func){var direction,fill,fontcolor,fontsize,in_duration,out_duration,pad,ref,ref1,ref2,ref3,ref4,tipclass,tipdiv,tipgroup,triChar,tridiv;tipclass=(ref=options!=null?options.tipclass:void 0)!=null?ref:"d3panels-tooltip";direction=(ref1=options!=null?options.direction:void 0)!=null?ref1:"east";out_duration=(ref2=options!=null?options.out_duration:void 0)!=null?ref2:1e3;in_duration=(ref3=options!=null?options.in_duration:void 0)!=null?ref3:0;pad=(ref4=options!=null?options.pad:void 0)!=null?ref4:8;fill=options!=null?options.fill:void 0;fontcolor=options!=null?options.fontcolor:void 0;fontsize=options!=null?options.fontsize:void 0;tipgroup=selection.append("g").attr("class","d3panels-tooltip "+tipclass).style("opacity",0).datum({direction:direction,pad:pad});tipdiv=tipgroup.append("div").attr("class","d3panels-tooltip "+tipclass);if(direction==="east"){triChar="◀"}else if(direction==="west"){triChar="▶"}else if(direction==="north"){triChar="▼"}else if(direction==="south"){triChar="▲"}else{d3panels.displayError("tooltip_create: invalid direction ("+direction+")")}tridiv=tipgroup.append("div").attr("class","d3panels-tooltip-tri "+tipclass).html(triChar);if(fill!=null){tipdiv.style("background",fill)}if(fontcolor!=null){tipdiv.style("color",fontcolor)}if(fontsize!=null){tipdiv.style("font-size",fontsize+"px")}if(fill!=null){tridiv.style("color",fill)}if(fontsize!=null){tridiv.style("font-size",fontsize+"px")}objects.on("mouseover."+tipclass,function(d,i){var mouseX,mouseY;mouseX=d3.event.pageX*1;mouseY=d3.event.pageY*1;tipdiv.html(tooltip_func(d,i));d3panels.tooltip_move(tipgroup,mouseX,mouseY);return d3panels.tooltip_show(tipgroup,in_duration)});objects.on("mouseout."+tipclass,function(d){return d3panels.tooltip_hide(tipgroup,out_duration)});return tipgroup};d3panels.tooltip_move=function(tipgroup,x,y){var direction,divpad,fontsize,pad,posX,posY,shiftX,shiftY,tipbox_height,tipbox_width,tipdiv,triX,triY,tridiv;tipdiv=tipgroup.select("div.d3panels-tooltip");tridiv=tipgroup.select("div.d3panels-tooltip-tri");tipbox_height=tipdiv.node().getBoundingClientRect().height*1;tipbox_width=tipdiv.node().getBoundingClientRect().width*1;fontsize=tridiv.style("font-size").replace("px","")*1;pad=tipgroup.datum().pad*1+fontsize;direction=tipgroup.datum().direction;shiftX=shiftY=0;if(direction==="east"){posX=x+pad;posY=y-tipbox_height/2;divpad=tipdiv.style("padding-left").replace("px","")*1;shiftX=-fontsize-divpad;shiftY=tipbox_height/2-fontsize/2}else if(direction==="west"){posX=x-tipbox_width*1-pad;posY=y-tipbox_height/2;divpad=tipdiv.style("padding-right").replace("px","")*1;shiftX=tipbox_width-fontsize+divpad;shiftY=tipbox_height/2-fontsize/2}else if(direction==="north"){posX=x-tipbox_width/2;posY=y-tipbox_height-pad;divpad=tipdiv.style("padding-bottom").replace("px","")*1;shiftX=tipbox_width/2-fontsize;shiftY=tipbox_height+divpad/2-fontsize/2}else if(direction==="south"){posX=x-tipbox_width/2;posY=y+pad;divpad=tipdiv.style("padding-top").replace("px","")*1;shiftX=+tipbox_width/2-fontsize;shiftY=-fontsize}tipdiv.style("left",posX+"px").style("top",posY+"px");triX=posX+shiftX;triY=posY+shiftY;return tridiv.style("left",triX+"px").style("top",triY+"px").style("width",tipbox_width).style("height",tipbox_height)};d3panels.tooltip_text=function(tipgroup,text){return tipgroup.select("div.d3panels-tooltip").html(text)};d3panels.tooltip_show=function(tipgroup,duration){return tipgroup.transition().duration(duration).style("opacity",1)};d3panels.tooltip_hide=function(tipgroup,duration){return tipgroup.transition().duration(duration).style("opacity",0)};d3panels.tooltip_destroy=function(tipgroup){return tipgroup.remove()};if(typeof define==="function"&&define.amd)this.d3panels=d3panels,define(d3panels);else if(typeof module==="object"&&module.exports)module.exports=d3panels;else this.d3panels=d3panels}();
\ No newline at end of file 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 d0b41d04..2a0a7b84 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -140,12 +140,17 @@ $('input[name=display_all]').change((function(_this) { }; })(this)); -//ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping -var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', - 'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', - 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', - 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', - 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'primary_samples'] +// This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping +var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', + 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + 'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', + 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', + 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', + 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'do_control', + 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', + 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', + 'mapmethod_rqtl', 'mapmodel_rqtl', 'temp_trait', 'group', 'species', + 'reaper_version', 'primary_samples'] $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { return function() { @@ -153,9 +158,12 @@ $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { var form_data, url; url = "/loading"; $('input[name=method]').val("rqtl_geno"); + $('input[name=pair_scan]').val("false"); $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val()); $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); + $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_geno').val()); + $('input[name=mapmethod_rqtl]').val($('#mapmethod_rqtl_geno').val()); $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); $('input[name=categorical_vars]').val(js_data.categorical_vars) $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); @@ -171,6 +179,30 @@ $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { }; })(this)); +$(".rqtl-pair-tab, #rqtl_pair_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_pair_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("rqtl_geno"); + $('input[name=pair_scan]').val("true"); + $('input[name=genofile]').val($('#genofile_rqtl_pair').val()); + $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_pair').val()); + $('input[name=mapmethod_rqtl]').val($('#mapmethod_rqtl_pair').val()); + $('input[name=num_perm]').val($('input[name=num_perm_rqtl_pair]').val()); + $('input[name=categorical_vars]').val(js_data.categorical_vars) + $('input[name=control_marker]').val($('input[name=control_rqtl_pair]').val()); + $('input[name=do_control]').val($('input[name=do_control_rqtl_pair]:checked').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + $(".gemma-tab, #gemma_compute").on("click", (function(_this) { return function() { if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ @@ -238,25 +270,25 @@ $("#use_composite_choice").change(composite_mapping_fields); $("#mapping_method_choice").change(mapping_method_fields); -$("#mapmodel_rqtl_geno").change(function() { +$("#mapmodel_rqtl_geno,#mapmodel_rqtl_pair").change(function() { if ($(this).val() == "np"){ $("#mapmethod_rqtl_geno").attr('disabled', 'disabled'); $("#mapmethod_rqtl_geno").css('background-color', '#CCC'); - $("#missing_geno").attr('disabled', 'disabled'); - $("#missing_geno").css('background-color', '#CCC'); + $("#missing_geno,#missing_geno_pair").attr('disabled', 'disabled'); + $("#missing_geno,#missing_geno_pair").css('background-color', '#CCC'); } else { $("#mapmethod_rqtl_geno").removeAttr('disabled'); $("#mapmethod_rqtl_geno").css('background-color', '#FFF'); - $("#missing_geno").removeAttr('disabled'); - $("#missing_geno").css('background-color', '#FFF'); + $("#missing_geno,#missing_geno_pair").removeAttr('disabled'); + $("#missing_geno,#missing_geno_pair").css('background-color', '#FFF'); } }); -$("#mapmethod_rqtl_geno").change(function() { +$("#mapmethod_rqtl_geno,#mapmethod_rqtl_pair").change(function() { if ($(this).val() == "mr"){ - $("#missing_geno_div").css('display', 'block'); + $("#missing_geno_div,#missing_geno_pair_div").css('display', 'block'); } else { - $("#missing_geno_div").css('display', 'none'); + $("#missing_geno_div,#missing_geno_pair_div").css('display', 'none'); } }); diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index fb825b90..dbd90bc7 100644 --- a/wqflask/wqflask/templates/pair_scan_results.html +++ b/wqflask/wqflask/templates/pair_scan_results.html @@ -1,70 +1,114 @@ {% extends "base.html" %} {% block title %}Pair Scan{% endblock %} {% block css %} - <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> - <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> +<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> +<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/d3panels.min.css" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/pair_scan.css" /> {% endblock %} {% block content %} <!-- Start of body --> - {{ header("Mapping", - '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }} +{{ header("Mapping", + '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }} - <div class="container"> - <div> - <h2> - Pair Scan - </h2> - </div> - <div id="chart_container"> - <div class="pair_scan_figure" id="pair_scan_figure"> - <a href="/tmp/{{ pair_scan_filename }}"> - <img alt="Embedded Image" src="data:image/png;base64, - {% for elem in pair_scan_array -%} - {% print("%c"|format(elem)) %} - {%- endfor %} - " /></a> - </div> - </div> - <div> - <h2> - Results - </h2> - <table cellpadding="0" cellspacing="0" border="0" id="pair_scan_results" class="table table-hover table-striped table-bordered"> - <thead> - <tr> - <td>Index</td> - <td>Locus</td> - <td>Chr 1</td> - <td>Mb</td> - <td>Chr 2</td> - </tr> - </thead> - <tbody> - {% for marker in trimmed_markers %} - <tr> - <td>{{loop.index}}</td> - <td>{{marker.name}}</td> - <td>{{marker.chr1}}</td> - <td>{{marker.Mb}}</td> - <td>{{marker.chr2}}</td> - </tr> - {% endfor %} - </tbody> - </table> - </div> +<div id="main_div" class="container"> + <div> + <h2> + Pair Scan + </h2> </div> + <div class="qtlcharts" id="chart_container"> + <div id="pairscan_chart"></div> + </div> + <div class="pairscan-container"> + <h2> + Results + </h2> + <table cellpadding="0" cellspacing="0" border="0" id="pair_scan_results" class="table table-hover table-striped table-bordered"> + <thead> + <tr> + <th colspan="3">Interval 1</th> + <th rowspan="3">LOD</th> + <th colspan="3">Interval 2</th> + </tr> + <tr> + <th rowspan="2">Position</th> + <th colspan="2">Flanking Markers</th> + <th rowspan="2">Position</th> + <th colspan="2">Flanking Markers</th> + </tr> + <tr> + <th>Proximal</th> + <th>Distal</th> + <th>Proximal</th> + <th>Distal</th> + </tr> + </thead> + <tbody> + {% for row in table_data %} + <tr> + <td>{{ row.pos1 }}</td> + <td>{{ row.proximal1 }}</td> + <td>{{ row.distal1 }}</td> + <td>{{ row.lod }}</td> + <td>{{ row.pos2 }}</td> + <td>{{ row.proximal2 }}</td> + <td>{{ row.distal2 }}</td> + </tr> + {% endfor %} + </tbody> + </table> + </div> +</div> {% endblock %} {% block js %} - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> +<script> + var figure_data = {{ figure_data | safe }} +</script> + +<script src="https://d3js.org/d3.v7.min.js"></script> +<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script> +<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> +<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> +<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> +<script language="javascript" type="text/javascript" src="/static/new/javascript/d3panels.min.js"></script> + +<script type="text/javascript"> + +var data, mychart; + +mychart = d3panels.lod2dheatmap({ + equalCells: true +}); -{% endblock %}
\ No newline at end of file +mychart(d3.select('div#pairscan_chart'), figure_data); + +table_conf = { + "columns":[ + { "width": "165px" }, + { "width": "130px" }, + { "width": "130px" }, + { "width": "50px" }, + { "width": "165px" }, + { "width": "130px" }, + { "width": "130px" }, + ], + "sDom": "itir", + "autoWidth": false, + "bSortClasses": false, + "order": [[3, "desc" ]], + "scrollY": "100vh", + "scroller": true, + "scrollCollapse": true + } + +trait_table = $('#pair_scan_results').DataTable(table_conf); + +</script> + +{% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 3af94ed6..fbb26ede 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -13,6 +13,9 @@ <li class="rqtl-geno-tab mapping-tab {% if dataset.group.mapping_id == '3' %}active{% endif %}"> <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> </li> + <li class="rqtl-pair-tab mapping-tab"> + <a href="#rqtl_pair" data-toggle="tab">Pair Scan</a> + </li> {% elif mapping_method == "QTLReaper" %} <li class="reaper-tab mapping-tab"> <a href="#interval_mapping" data-toggle="tab">Haley-Knott Regression</a> @@ -325,6 +328,89 @@ </div> </div> </div> + <div class="tab-pane" id="rqtl_pair"> + <div class="form-horizontal section-form-div"> + {% if genofiles and genofiles|length > 0 %} + <div class="mapping_method_fields form-group"> + <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> + <div class="col-xs-6 controls"> + <select id="genofile_rqtl_pair" class="form-control"> + {% for item in genofiles %} + <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> + {% endfor %} + </select> + </div> + </div> + {% endif %} + <div class="mapping_method_fields form-group"> + <label for="control_for" class="col-xs-3 control-label">Control for</label> + <div class="col-xs-6 controls"> + <input name="control_rqtl_pair" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" /> + <label class="radio-inline"> + <input type="radio" name="do_control_rqtl" value="true"> + Yes + </label> + <label class="radio-inline"> + <input type="radio" name="do_control_rqtl" value="false" checked=""> + No + </label> + </div> + </div> + <div class="mapping_method_fields form-group"> + <label for="mapmodel_rqtl_pair" class="col-xs-3 control-label">Model</label> + <div class="col-xs-4 controls"> + <select id="mapmodel_rqtl_pair" name="mapmodel_rqtl_pair" class="form-control"> + <option value="normal">Normal</option> + {% if binary == "true" %}<option value="binary">Binary</option>{% endif %} + <!--<option value="2part">2-part</option>--> + <option value="np">Non-parametric</option> + </select> + </div> + </div> + <div class="mapping_method_fields form-group"> + <label for="mapmethod_rqtl_pair" class="col-xs-3 control-label">Method</label> + <div class="col-xs-6 controls"> + <select id="mapmethod_rqtl_pair" name="mapmethod_rqtl_pair" class="form-control"> + <option value="hk" selected>Haley-Knott</option> + <option value="ehk">Extended Haley-Knott</option> + <option value="mr">Marker Regression</option> + <option value="em">Expectation-Maximization</option> + <option value="imp">Imputation</option> + </select> + </div> + </div> + <div id="missing_geno_pair_div" class="mapping_method_fields form-group" style="display: none;"> + <label for="missing_genotypes_pair" class="col-xs-3 control-label"></label> + <div class="col-xs-6 controls"> + <select id="missing_genotype_pair" name="missing_genotypes" class="form-control"> + <option value="mr">Remove Samples w/o Genotypes</option> + <option value="mr-imp">Single Imputation</option> + <option value="mr-argmax">Imputation w/ Viterbi Algorithm</option> + </select> + </div> + </div> + <div class="mapping_method_fields form-group"> + <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label> + <div class="col-xs-8 covar-options"> + {% if g.user_session.num_collections < 1 %} + No collections available. Please add traits to a collection to use them as covariates. + {% else %} + <div class="select-covar-div"> + <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button> + <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button> + </div> + <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea> + {% endif %} + </div> + </div> + <div class="mapping_method_fields form-group"> + <label class="col-xs-3 control-label"></label> + <div class="col-xs-6 controls"> + <button id="rqtl_pair_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Pair Scan" value="Compute">Compute</button> + </div> + </div> + </div> + </div> {% endif %} {% endfor %} </div> @@ -338,8 +424,10 @@ <dt>GEMMA</dt> <dd>Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.</dd> {% elif mapping_method == "R/qtl" %} - <dt class="map-method-text">R/qtl (version 1.44.9</dt> + <dt class="map-method-text">R/qtl (version 1.44.9)</dt> <dd>The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (<a href="https://www.ncbi.nlm.nih.gov/pubmed/12724300">PMID: 12724300</a>). Both R/qtl as implemented here, and R/qtl2 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>) are available as <span class="broken-link" href="https://kbroman.org/pages/software.html">R suites</span>.</dd> + <dt class="map-method-text">Pair Scan</dt> + <dd>Pair Scan using the R/qtl scantwo function.</dd> {% elif mapping_method == "QTLReaper" %} <dt class="map-method-text">Haley-Knott Regression</dt> <dd>Fast linear mapping method (<a href="https://www.ncbi.nlm.nih.gov/pubmed/16718932">PMID 16718932</a>) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (<a href="https://github.com/pjotrp/QTLReaper">QTL Reaper code</a>).</dd> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 59dba309..b2cf95fb 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -808,8 +808,8 @@ def mapping_results_page(): 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', - 'mapmethod_rqtl_geno', - 'mapmodel_rqtl_geno', + 'mapmethod_rqtl', + 'mapmodel_rqtl', 'temp_trait', 'n_samples', 'transform' @@ -846,23 +846,15 @@ def mapping_results_page(): rendered_template = render_template("mapping_error.html") return rendered_template - template_vars.js_data = json.dumps(template_vars.js_data, - default=json_default_handler, - indent=" ") + if not template_vars.pair_scan: + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ") result = template_vars.__dict__ if result['pair_scan']: with Bench("Rendering template"): - img_path = result['pair_scan_filename'] - logger.info("img_path:", img_path) - initial_start_vars = request.form - logger.info("initial_start_vars:", initial_start_vars) - imgfile = open(TEMPDIR + img_path, 'rb') - imgdata = imgfile.read() - imgB64 = base64.b64encode(imgdata) - bytesarray = array.array('B', imgB64) - result['pair_scan_array'] = bytesarray rendered_template = render_template( "pair_scan_results.html", **result) else: |