npm - @sjcrh/proteinpaint-client - Versions diffs - 2.76.1 → 2.76.2 - Mend

@sjcrh/proteinpaint-client 2.76.1 → 2.76.2

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package/dist/{matrix.sort-9440c86a.js → matrix.sort-1ac05842.js} RENAMED Viewed

	@@ -1 +1 @@
1	- import{b as e}from"./termsetting-ad8c4f3a.js";import{at as t,ak as r,ap as s,bE as i,bD as n}from"./app-2cd97738.js";import"./tslib.es6-c3c2d88f.js";import"path";function o(t,r,s,i={}){const n=r;a(n);if(t.config.chartType=="hierCluster"&&t.config.settings.hierCluster.clusterSamples){return t.hcSampleSorter}if(n.sortSamplesBy=="asListed"){return(e,r)=>t.asListedSampleOrder.indexOf(e.sample)-t.asListedSampleOrder.indexOf(r.sample)}if(n.sortSamplesBy=="name"){return l}const o=n.sortOptions[n.sortSamplesBy];if(!o)throw`unsupported s.sortSamplesBy='${n.sortSamplesBy}'`;t.selectedTermsToSortAgainst=t.termOrder.filter((e=>e.tw.sortSamples));const p=t.selectedTermsToSortAgainst.map((e=>e.tw)).sort(((e,t)=>e.sortSamples.priority-t.sortSamples.priority));const m=[];const h=o.sortPriority;if(h){for(const e of p){const t=structuredClone(e);if(t.sortSamples?.by){m.push(Object.assign({},t));continue}for(const e of h){if(i.skipSorter?.(e,t))continue;if(!e.types.includes(t.term.type))continue;for(const r of e.tiebreakers){const e=Object.assign(structuredClone(t.sortSamples\|\|{}),r);const s=Object.assign(structuredClone(t),{sortSamples:e});m.push(s)}}}}if(h){for(const e of h){for(const r of t.termOrder){if(p.find((e=>e.$id===r.tw.$id)))continue;if(i.skipSorter?.(e,r.tw))continue;if(!e.types.includes(r.tw.term.type))continue;for(const t of e.tiebreakers){m.push(Object.assign({},r.tw,{sortSamples:t}))}}}}else{const r=t.app.vocabApi.vocab?.dslabel=="PNET"?[]:t.termOrder.filter((t=>!t.tw.sortSamples&&e(t.tw.term.type)&&!p.find((e=>e.$id===t.tw.$id)))).map((e=>Object.assign({sortSamples:{by:"values"}},e.tw)));const s=t.app.vocabApi.vocab?.dslabel=="PNET"?[]:t.termOrder.filter((t=>!t.tw.sortSamples&&!e(t.tw.term.type)&&!p.find((e=>e.$id===t.tw.$id)))).map((e=>Object.assign({sortSamples:{by:"hits"}},e.tw)));m.push(...s,...r)}if(i.tiebreaker)m.push(i.tiebreaker);m.push(...n.sortSamplesTieBreakers.map((e=>e)));const b=[];t.maxSampleSet=new Set;for(const e of m){if(typeof e==="function")b.push(e);else if(e.$id=="sample")b.push(l);else if(e.sortSamples.by=="hits")b.push(u(e,t,s));else if(e.term.type!="geneVariant")b.push(d(e,t,s));else if(e.sortSamples.by=="values")b.push(d(e,t,s));else if(e.sortSamples.by=="dt")b.push(f(e));else if(e.sortSamples.by=="class")b.push(c(e,t));else throw`unsupported sortSamplesBy entry by='${e.sortSamples.by}'`}if(!b.find((e=>e.$id==="sample"))){b.push(l)}return(e,t)=>{for(const r of b){const s=r(e,t);if(s!==0)return s}}}function a(e){if(!e.sortOptions)e.sortOptions="custom";if(["selectedTerms","class","dt","hits"].includes(e.sortSamplesBy))e.sortSamplesBy="custom"}function l(e,t){if(e._ref_.label&&t._ref_.label){return e._ref_.label<t._ref_.label?-1:e._ref_.label>t._ref_.label?1:0}if(!e.sample&&!t.sample&&e.row.sample){return e.row.sample<t.row.sample?-1:e.row.sample>t.row.sample?1:0}return e.sample<t.sample?-1:e.sample>t.sample?1:0}function u(e,t,r,s){const{$id:i,sortSamples:n}=e;const o={};for(const e of r){if(!o[e.sample])o[e.sample]=0;if(i in e){o[e.sample]+=e[i].countedValues?.length\|\|0}}return(e,t)=>o[e.sample]==o[t.sample]?0:o[e.sample]>o[t.sample]?-1:1}function d(e,t,r,s){const{$id:i,sortSamples:n}=e;const o=t.termOrder.find((e=>e.tw.$id===i));if(o.grp.type=="hierCluster"){return(e,t)=>{if(i in e&&i in t){return e[i]?.values[0].value-t[i]?.values[0].value}if(i in e)return-1;if(i in t)return 1;return 0}}if(o.tw.q?.mode=="continuous"){return(e,t)=>{if(i in e&&i in t){return e[i]?.value-t[i]?.value}if(i in e)return-1;if(i in t)return 1;return 0}}const a=[];if(o?.term?.values){for(const e of term.values){a.push(e.key)}a.sort(((e,t)=>term.values[e].order<term.values[e].order?-1:1))}else if(o?.ref?.bins){a.push(...o.ref.bins.map((e=>e.name)))}else{for(const e of r){if(!(i in e))continue;const t=e[i].override?.key\|\|e[i].key;if(a.indexOf(t)==-1)a.push(t)}}return(e,t)=>{if(!e[i]&&!t[i])return 0;if(!e[i])return t[i].override?-1:1;if(!t[i])return e[i].override?1:-1;if(e[i].override&&t[i].override){const r="order"in e[i].override?e[i].override.order:a.indexOf(e[i].override.key);const s="order"in t[i].override?t[i].override.order:a.indexOf(t[i].override.key);return r-s}if(!e[i].override&&!t[i].override){return a.indexOf(e[i].key)-a.indexOf(t[i].key)}if(!e[i].override)return-1;if(!t[i].override)return 1;return 0}}function f(e,t,r,s){const{$id:i,sortSamples:n,term:o}=e;const a=n.order;const l=a.length+1;const u=new Map;function d(e){if(!(i in e)){u.set(e.sample,l);return}if(n.filter&&!p(e[i].values,n.filter.values)){u.set(e.sample,l);return}const t=e[i].values.map((e=>a.indexOf(e.dt))).filter((e=>e!==-1));u.set(e.sample,t.length?Math.min(...t):l)}return(e,t)=>{if(!u.has(e.sample))d(e);if(!u.has(t.sample))d(t);return u.get(e.sample)-u.get(t.sample)}}function c(e,t,r,s){const{$id:i,sortSamples:n}=e;if(n.disabled)return()=>0;const o=t.config.settings.matrix;const a=o.showMatrixMutation!="none"&&!o.allMatrixMutationHidden;const l=o.showMatrixCNV!="none"&&!o.allMatrixCNVHidden;const u=n.order.filter(a&&l?e=>!o.hiddenVariants.includes(e):!a&&!l?()=>false:a?e=>o.mutationClasses.includes(e)&&!o.hiddenVariants.includes(e):l?e=>e.startsWith("CNV_")&&!o.hiddenVariants.includes(e):e=>!e.startsWith("CNV_"));if(!u.length&&n.ignoreEmptyFilteredOrder)return()=>0;const d="z";const f=new Map;function c(e){if(!(i in e)){f.set(e.sample,d);return}const t=e[i].renderedValues\|\|e[i].filteredValues\|\|e[i].values;if(n.filter&&!p(t,n.filter.values)){f.set(e.sample,d);return}const r=t.map((e=>e.class));if(!u.find((e=>r.includes(e)))){f.set(e.sample,d);return}else if(!n.isOrdered){f.set(e.sample,"1")}else{const t=u.map((e=>r.includes(e)?"1":"x"));f.set(e.sample,t)}}return(e,t)=>{if(!f.has(e.sample))c(e);if(!f.has(t.sample))c(t);const r=f.get(e.sample);const s=f.get(t.sample);return r<s?-1:r>s?1:0}}function p(e,t){for(const r of e){for(const e of t){if((!e.dt\|\|r.dt===e.dt)&&(!e.mclassLst\|\|e.mclassLst.includes(r.class))&&(!e.class\|\|e.class===r.class)&&(!e.origin\|\|r.origin===e.origin)){return true}}}}function m(e,t,r){if(r?.type=="hierCluster")return e.hcTermSorter;if(t.sortTermsBy=="asListed"){return(e,t)=>e.index-t.index}if(t.sortTermsBy!="sampleCount"){throw`unsupported s.sortTermsBy='${t.sortTermsBy}'`}return(t,r)=>{if(e.app.vocabApi.vocab?.dslabel==="GDC"){if(t.tw?.term?.id&&!r.tw?.term?.id)return-1;if(!t.tw?.term?.id&&r.tw?.term?.id)return 1}if(r.counts.samples!==t.counts.samples)return r.counts.samples-t.counts.samples;if(r.counts.hits!==t.counts.hits)return r.counts.hits-t.counts.hits;return t.index-r.index}}function h(e,o={},a){const l=a\|\|e?.matrix?.settings\|\|{};const u=Object.assign({sample:"sample"},o,l.controlLabels\|\|{});const d={};if(l.sortPriority){const e=1;Object.values(d).forEach((t=>{if(t.order>=e)t.order+=1}));d.custom={label:l.sortPriority.label\|\|"Custom sort",value:"custom",order:e,sortPriority:l.sortPriority}}d.a=l.sortOptions?.a?v(l.sortOptions.a,u):{value:"a",order:1,sortPriority:[{label:`For each gene mutation, sort ${u.samples} by matching data`,types:["geneVariant"],tiebreakers:[{skip:!l.mutationClasses.includes("Fuserna"),label:`${u.Samples} with Fusion RNASeq > without`,filter:{values:[{dt:t}]},by:"class",isOrdered:false,order:["Fuserna"]},{label:`${u.Samples} with truncating mutations > without`,filter:{values:[{dt:r}]},by:"class",isOrdered:false,order:[...l.truncatingMutations],notUsed:[]},{label:`${u.Samples} with CNV data > without`,mayToggle:true,filter:{values:[{dt:s}]},by:"class",isOrdered:true,disabled:true,order:[i,n]},{disabled:false,mayToggle:true,label:`${u.Samples} with protein-changing mutations > without`,filter:{values:[{dt:r}]},by:"class",isOrdered:false,order:l.proteinChangingMutations.filter((e=>!l.truncatingMutations.includes(e))),notUsed:l.truncatingMutations}]},{label:`For each dictionary variable, sort ${u.samples} by matching data`,types:["categorical","integer","float","survival"],tiebreakers:[{label:"Values",by:"values"}]}]};d.name={label:`By ${u.sample} name, ID, or label`,value:"name",order:Object.values(d).length};return d}function b(e){const t=e.settings.matrix;if(t.sortSampleGrpsBy=="hits")return(e,t)=>{if(e.lst.length&&!t.lst.length)return-1;if(!e.lst.length&&t.lst.length)return 1;return t.totalCountedValues-e.totalCountedValues};if(t.sortSampleGrpsBy=="sampleCount")return(e,t)=>{if(e.lst.length&&!t.lst.length)return-1;if(!e.lst.length&&t.lst.length)return 1;if(e.lst.length==t.lst.length){return y(e,t)}return t.lst.length-e.lst.length};if(!e.config.divideBy?.$id)return y;const r=e.data.refs.byTermId[e.config.divideBy.$id];if(r&&!r.keyOrder)r.keyOrder=r.bins?r.bins.map((e=>e.name)):[];const s=e.data.refs.byTermId[e.config.divideBy.$id]?.keyOrder;if(!s)return y;return(e,t)=>{e.order=s.indexOf(e.id);if(e.order==-1)delete e.order;t.order=s.indexOf(t.id);if(t.order==-1)delete t.order;if("order"in e&&"order"in t)return e.order-t.order;if("order"in e)return-1;if("order"in t)return 1;if(e.tw?.term?.values?.[e.id]?.order&&t.tw?.term?.values?.[t.id]?.order){return e.tw.term.values[e.id].order-t.tw.term.values[t.id].order}return y(e,t)}}function y(e,t){return e.name<t.name?-1:1}function g(e){const t=e.settings.matrix;const r=t.sortOptions[t.sortSamplesBy].sortPriority?t.sortOptions[t.sortSamplesBy]:t.sortOptions.a;const s=[];r.sortPriority.forEach((e=>{if(e.types.includes("geneVariant")){e.tiebreakers.forEach((e=>{if(e.by=="class"&&e.order){s.push(...e.order.filter((e=>e!=="WT"&&e!=="Blank")))}}))}}));const i=(e,t)=>{const r=s.indexOf(e.class);const i=s.indexOf(t.class);return r==-1&&i==-1?0:s.indexOf(e.class)==-1?1:s.indexOf(t.class)==-1?-1:s.indexOf(e.class)-s.indexOf(t.class)};return i}function v(e,o){const a=o;let l;for(const t of e.sortPriority){if(t.types.includes("categorical")){if(!t.label)t.label=`For each dictionary variable, sort ${a.samples} by matching data`;continue}if(!t.types?.includes("geneVariant"))continue;if(!l){l=t;if(!t.label)t.label=`For each gene mutation, sort ${a.samples} by matching data`}else{l.tiebreakers.push(...t.tiebreakers);t.toBeDeleted=true}}for(const e of l.tiebreakers){if(e.filter?.values?.find((e=>e.dt==t))){const t={label:`${a.Samples} with Fusion RNASeq > without`,isOrdered:true,disabled:false,mayToggle:true};Object.assign(e,t,e)}else if(e.filter?.values?.find((e=>e.dt==r))){const t=e.order.includes(i)\|\|e.order.includes(n)?`${a.Samples} with SSM + CNV > SSM only`:`${a.Samples} with mutations`;const r={label:t,isOrdered:true,disabled:false,mayToggle:true};Object.assign(e,r,e)}else if(e.order.length==2&&e.order.includes(i)&&e.order.includes(n)){const t={label:`${a.Samples} with CNV only > without`,filter:{values:[{dt:s}]},by:"class",isOrdered:true,disabled:false,mayToggle:true};Object.assign(e,t,e)}}e.sortPriority=e.sortPriority.filter((e=>!e.toBeDeleted));return e}export{g as getMclassSorter,b as getSampleGroupSorter,o as getSampleSorter,h as getSortOptions,m as getTermSorter,v as reshapeSortPriority};
1	+ import{b as e}from"./termsetting-492eefa7.js";import{at as t,ak as r,ap as s,bE as i,bD as n}from"./app-6fb77603.js";import"./tslib.es6-c3c2d88f.js";import"path";function o(t,r,s,i={}){const n=r;a(n);if(t.config.chartType=="hierCluster"&&t.config.settings.hierCluster.clusterSamples){return t.hcSampleSorter}if(n.sortSamplesBy=="asListed"){return(e,r)=>t.asListedSampleOrder.indexOf(e.sample)-t.asListedSampleOrder.indexOf(r.sample)}if(n.sortSamplesBy=="name"){return l}const o=n.sortOptions[n.sortSamplesBy];if(!o)throw`unsupported s.sortSamplesBy='${n.sortSamplesBy}'`;t.selectedTermsToSortAgainst=t.termOrder.filter((e=>e.tw.sortSamples));const p=t.selectedTermsToSortAgainst.map((e=>e.tw)).sort(((e,t)=>e.sortSamples.priority-t.sortSamples.priority));const m=[];const b=o.sortPriority;if(b){for(const e of p){const t=structuredClone(e);if(t.sortSamples?.by){m.push(Object.assign({},t));continue}for(const e of b){if(i.skipSorter?.(e,t))continue;if(!e.types.includes(t.term.type))continue;for(const r of e.tiebreakers){const e=Object.assign(structuredClone(t.sortSamples\|\|{}),r);const s=Object.assign(structuredClone(t),{sortSamples:e});m.push(s)}}}}if(b){for(const e of b){for(const r of t.termOrder){if(p.find((e=>e.$id===r.tw.$id)))continue;if(i.skipSorter?.(e,r.tw))continue;if(!e.types.includes(r.tw.term.type))continue;for(const t of e.tiebreakers){m.push(Object.assign({},r.tw,{sortSamples:t}))}}}}else{const r=t.app.vocabApi.vocab?.dslabel=="PNET"?[]:t.termOrder.filter((t=>!t.tw.sortSamples&&e(t.tw.term.type)&&!p.find((e=>e.$id===t.tw.$id)))).map((e=>Object.assign({sortSamples:{by:"values"}},e.tw)));const s=t.app.vocabApi.vocab?.dslabel=="PNET"?[]:t.termOrder.filter((t=>!t.tw.sortSamples&&!e(t.tw.term.type)&&!p.find((e=>e.$id===t.tw.$id)))).map((e=>Object.assign({sortSamples:{by:"hits"}},e.tw)));m.push(...s,...r)}if(i.tiebreaker)m.push(i.tiebreaker);m.push(...n.sortSamplesTieBreakers.map((e=>e)));const h=[];t.maxSampleSet=new Set;for(const e of m){if(typeof e==="function")h.push(e);else if(e.$id=="sample")h.push(l);else if(e.sortSamples.by=="hits")h.push(u(e,t,s));else if(e.term.type!="geneVariant")h.push(d(e,t,s));else if(e.sortSamples.by=="values")h.push(d(e,t,s));else if(e.sortSamples.by=="dt")h.push(f(e));else if(e.sortSamples.by=="class")h.push(c(e,t));else throw`unsupported sortSamplesBy entry by='${e.sortSamples.by}'`}if(!h.find((e=>e.$id==="sample"))){h.push(l)}return(e,t)=>{for(const r of h){const s=r(e,t);if(s!==0)return s}}}function a(e){if(!e.sortOptions)e.sortOptions="custom";if(["selectedTerms","class","dt","hits"].includes(e.sortSamplesBy))e.sortSamplesBy="custom"}function l(e,t){if(e._ref_.label&&t._ref_.label){return e._ref_.label<t._ref_.label?-1:e._ref_.label>t._ref_.label?1:0}if(!e.sample&&!t.sample&&e.row.sample){return e.row.sample<t.row.sample?-1:e.row.sample>t.row.sample?1:0}return e.sample<t.sample?-1:e.sample>t.sample?1:0}function u(e,t,r,s){const{$id:i,sortSamples:n}=e;const o={};for(const e of r){if(!o[e.sample])o[e.sample]=0;if(i in e){o[e.sample]+=e[i].countedValues?.length\|\|0}}return(e,t)=>o[e.sample]==o[t.sample]?0:o[e.sample]>o[t.sample]?-1:1}function d(e,t,r,s){const{$id:i,sortSamples:n}=e;const o=t.termOrder.find((e=>e.tw.$id===i));if(o.grp.type=="hierCluster"){return(e,t)=>{if(i in e&&i in t){return e[i]?.values[0].value-t[i]?.values[0].value}if(i in e)return-1;if(i in t)return 1;return 0}}if(o.tw.q?.mode=="continuous"){return(e,t)=>{if(i in e&&i in t){return e[i]?.value-t[i]?.value}if(i in e)return-1;if(i in t)return 1;return 0}}const a=[];if(o?.term?.values){for(const e of term.values){a.push(e.key)}a.sort(((e,t)=>term.values[e].order<term.values[e].order?-1:1))}else if(o?.ref?.bins){a.push(...o.ref.bins.map((e=>e.name)))}else{for(const e of r){if(!(i in e))continue;const t=e[i].override?.key\|\|e[i].key;if(a.indexOf(t)==-1)a.push(t)}}return(e,t)=>{if(!e[i]&&!t[i])return 0;if(!e[i])return t[i].override?-1:1;if(!t[i])return e[i].override?1:-1;if(e[i].override&&t[i].override){const r="order"in e[i].override?e[i].override.order:a.indexOf(e[i].override.key);const s="order"in t[i].override?t[i].override.order:a.indexOf(t[i].override.key);return r-s}if(!e[i].override&&!t[i].override){return a.indexOf(e[i].key)-a.indexOf(t[i].key)}if(!e[i].override)return-1;if(!t[i].override)return 1;return 0}}function f(e,t,r,s){const{$id:i,sortSamples:n,term:o}=e;const a=n.order;const l=a.length+1;const u=new Map;function d(e){if(!(i in e)){u.set(e.sample,l);return}if(n.filter&&!p(e[i].values,n.filter.values)){u.set(e.sample,l);return}const t=e[i].values.map((e=>a.indexOf(e.dt))).filter((e=>e!==-1));u.set(e.sample,t.length?Math.min(...t):l)}return(e,t)=>{if(!u.has(e.sample))d(e);if(!u.has(t.sample))d(t);return u.get(e.sample)-u.get(t.sample)}}function c(e,t,r,s){const{$id:i,sortSamples:n}=e;if(n.disabled)return()=>0;const o=t.config.settings.matrix;const a=o.showMatrixMutation!="none"&&!o.allMatrixMutationHidden;const l=o.showMatrixCNV!="none"&&!o.allMatrixCNVHidden;const u=n.order.filter(a&&l?e=>!o.hiddenVariants.includes(e):!a&&!l?()=>false:a?e=>o.mutationClasses.includes(e)&&!o.hiddenVariants.includes(e):l?e=>e.startsWith("CNV_")&&!o.hiddenVariants.includes(e):e=>!e.startsWith("CNV_"));if(!u.length&&n.ignoreEmptyFilteredOrder)return()=>0;const d="z";const f=new Map;function c(e){if(!(i in e)){f.set(e.sample,d);return}const t=e[i].renderedValues\|\|e[i].filteredValues\|\|e[i].values;if(n.filter&&!p(t,n.filter.values)){f.set(e.sample,d);return}const r=t.map((e=>e.class));if(!u.find((e=>r.includes(e)))){f.set(e.sample,d);return}else if(!n.isOrdered){f.set(e.sample,"1")}else{const t=u.map((e=>r.includes(e)?"1":"x"));f.set(e.sample,t)}}return(e,t)=>{if(!f.has(e.sample))c(e);if(!f.has(t.sample))c(t);const r=f.get(e.sample);const s=f.get(t.sample);return r<s?-1:r>s?1:0}}function p(e,t){for(const r of e){for(const e of t){if((!e.dt\|\|r.dt===e.dt)&&(!e.mclassLst\|\|e.mclassLst.includes(r.class))&&(!e.class\|\|e.class===r.class)&&(!e.origin\|\|r.origin===e.origin)){return true}}}}function m(e,t,r){if(r?.type=="hierCluster")return e.hcTermSorter;if(t.sortTermsBy=="asListed"){return(e,t)=>e.index-t.index}if(t.sortTermsBy!="sampleCount"){throw`unsupported s.sortTermsBy='${t.sortTermsBy}'`}return(t,r)=>{if(e.app.vocabApi.vocab?.dslabel==="GDC"){if(t.tw?.term?.id&&!r.tw?.term?.id)return-1;if(!t.tw?.term?.id&&r.tw?.term?.id)return 1}if(r.counts.samples!==t.counts.samples)return r.counts.samples-t.counts.samples;if(r.counts.hits!==t.counts.hits)return r.counts.hits-t.counts.hits;return t.index-r.index}}function b(e,o={},a){const l=a\|\|e?.matrix?.settings\|\|{};const u=Object.assign({sample:"sample"},o,l.controlLabels\|\|{});const d={};if(l.sortPriority){const e=1;Object.values(d).forEach((t=>{if(t.order>=e)t.order+=1}));d.custom={label:l.sortPriority.label\|\|"Custom sort",value:"custom",order:e,sortPriority:l.sortPriority}}d.a=l.sortOptions?.a?v(l.sortOptions.a,u):{value:"a",order:1,sortPriority:[{label:`For each gene mutation, sort ${u.samples} by matching data`,types:["geneVariant"],tiebreakers:[{skip:!l.mutationClasses.includes("Fuserna"),label:`${u.Samples} with Fusion RNASeq > without`,filter:{values:[{dt:t}]},by:"class",isOrdered:false,order:["Fuserna"]},{label:`${u.Samples} with truncating mutations > without`,filter:{values:[{dt:r}]},by:"class",isOrdered:false,order:[...l.truncatingMutations],notUsed:[]},{label:`${u.Samples} with CNV data > without`,mayToggle:true,filter:{values:[{dt:s}]},by:"class",isOrdered:true,disabled:true,order:[i,n]},{disabled:false,mayToggle:true,label:`${u.Samples} with protein-changing mutations > without`,filter:{values:[{dt:r}]},by:"class",isOrdered:false,order:l.proteinChangingMutations.filter((e=>!l.truncatingMutations.includes(e))),notUsed:l.truncatingMutations}]},{label:`For each dictionary variable, sort ${u.samples} by matching data`,types:["categorical","integer","float","survival"],tiebreakers:[{label:"Values",by:"values"}]}]};d.name={label:`By ${u.sample} name, ID, or label`,value:"name",order:Object.values(d).length};return d}function h(e){const t=e.settings.matrix;if(t.sortSampleGrpsBy=="hits")return(e,t)=>{if(e.lst.length&&!t.lst.length)return-1;if(!e.lst.length&&t.lst.length)return 1;return t.totalCountedValues-e.totalCountedValues};if(t.sortSampleGrpsBy=="sampleCount")return(e,t)=>{if(e.lst.length&&!t.lst.length)return-1;if(!e.lst.length&&t.lst.length)return 1;if(e.lst.length==t.lst.length){return y(e,t)}return t.lst.length-e.lst.length};if(!e.config.divideBy?.$id)return y;const r=e.data.refs.byTermId[e.config.divideBy.$id];if(r&&!r.keyOrder)r.keyOrder=r.bins?r.bins.map((e=>e.name)):[];const s=e.data.refs.byTermId[e.config.divideBy.$id]?.keyOrder;if(!s)return y;return(e,t)=>{e.order=s.indexOf(e.id);if(e.order==-1)delete e.order;t.order=s.indexOf(t.id);if(t.order==-1)delete t.order;if("order"in e&&"order"in t)return e.order-t.order;if("order"in e)return-1;if("order"in t)return 1;if(e.tw?.term?.values?.[e.id]?.order&&t.tw?.term?.values?.[t.id]?.order){return e.tw.term.values[e.id].order-t.tw.term.values[t.id].order}return y(e,t)}}function y(e,t){return e.name<t.name?-1:1}function g(e){const t=e.settings.matrix;const r=t.sortOptions[t.sortSamplesBy].sortPriority?t.sortOptions[t.sortSamplesBy]:t.sortOptions.a;const s=[];r.sortPriority.forEach((e=>{if(e.types.includes("geneVariant")){e.tiebreakers.forEach((e=>{if(e.by=="class"&&e.order){s.push(...e.order.filter((e=>e!=="WT"&&e!=="Blank")))}}))}}));const i=(e,t)=>{const r=s.indexOf(e.class);const i=s.indexOf(t.class);return r==-1&&i==-1?0:s.indexOf(e.class)==-1?1:s.indexOf(t.class)==-1?-1:s.indexOf(e.class)-s.indexOf(t.class)};return i}function v(e,o){const a=o;let l;for(const t of e.sortPriority){if(t.types.includes("categorical")){if(!t.label)t.label=`For each dictionary variable, sort ${a.samples} by matching data`;continue}if(!t.types?.includes("geneVariant"))continue;if(!l){l=t;if(!t.label)t.label=`For each gene mutation, sort ${a.samples} by matching data`}else{l.tiebreakers.push(...t.tiebreakers);t.toBeDeleted=true}}for(const e of l.tiebreakers){if(e.filter?.values?.find((e=>e.dt==t))){const t={label:`${a.Samples} with Fusion RNASeq > without`,isOrdered:true,disabled:false,mayToggle:true};Object.assign(e,t,e)}else if(e.filter?.values?.find((e=>e.dt==r))){const t=e.order.includes(i)\|\|e.order.includes(n)?`${a.Samples} with SSM + CNV > SSM only`:`${a.Samples} with mutations`;const r={label:t,isOrdered:true,disabled:false,mayToggle:true};Object.assign(e,r,e)}else if(e.order.length==2&&e.order.includes(i)&&e.order.includes(n)){const t={label:`${a.Samples} with CNV only > without`,filter:{values:[{dt:s}]},by:"class",isOrdered:true,disabled:false,mayToggle:true};Object.assign(e,t,e)}}e.sortPriority=e.sortPriority.filter((e=>!e.toBeDeleted));return e}export{g as getMclassSorter,h as getSampleGroupSorter,o as getSampleSorter,b as getSortOptions,m as getTermSorter,v as reshapeSortPriority};

package/dist/{matrix.sorterUi-2c5eb35f.js → matrix.sorterUi-1c60c145.js} RENAMED Viewed

	@@ -1 +1 @@
1	- import{M as t,P as e,d as a,z as i}from"./app-2cd97738.js";const n=`ABCDEFGHIJKLMNOPQRSTUVWXYZ`.split("");function r(r){const{controls:s,holder:l}=r;const o=s.parent;const d=structuredClone(o.config.settings.matrix);const p=d.controlLabels;const c=new t({padding:"",parent_menu:o.app.tip?.d.node()});let y=[],g,u={};const h={dom:{tip:c},opts:r,highlightColor:"none",label:`Sort ${p.Samples}`,title:`Set how to sort ${p.samples}`,type:"custom",expanded:r.expanded\|\|false,expandedSection:r.expandedSection\|\|"",init(t={},s={}){c.clear().hide();if(o.config.settings.matrix!=d)e(d,o.config.settings.matrix);if(d!==t)e(d,t);h.settings=d;h.activeOption=structuredClone(d.sortOptions[d.sortSamplesBy]);g=[{label:`For each selected row, sort ${p.samples} by matching data`,notDraggable:true,tiebreakers:[],handler:U},...h.activeOption.sortPriority,{label:`Sort ${p.samples} by name, alphabetically`,notDraggable:true,tiebreakers:[]}];Object.assign(r,s);r.holder.selectAll("").remove();const l=r.holder.append("div").style("text-align","right");l.append("button").html("Apply").on("click",j);l.append("button").html("Reset").on("click",((t,e)=>h.init()));const u=r.holder.append("table");const $=u.append("thead");$.append("th").html("Priority").style("text-align","left").style("max-width","0px");$.append("th").html("Description");$.append("th").html("Action");let I=0,M=0;for(const t of g){const e=t.tiebreakers?.[0]?.order\|\|t.handler;const r=u.append("thead").datum(t).property("draggable",!t.notDraggable).attr("droppable",true).on("dragstart",f).on("dragover",m).on("dragleave",x).on("drop",v);y.push(a(r));const s=r.append("tr").style("background-color","#eee").on("mouseover",V);s.append("th").style("padding","5px").style("vertical-align","top").style("font-weight",400).html(n[M++]).on("click",e?b:null);const l=s.append("th").style("padding","5px").style("vertical-align","top").style("text-align","left").style("cursor",e?"pointer":"").on("click",e?b:null);l.append("span").style("margin-right","12px").style("font-weight",400).html(t.label);s.append("th").style("padding","5px").style("vertical-align","top").style("text-align","center").style("font-weight",400).style("cursor",e?"pointer":"").append("span").html(e?"Details":" ").on("click",e?b:null);const o=u.append("tbody").datum(t).style("display",h.expandedSection=="all"\|\|h.expandedSection==t.label?"":"none");for(const e of t.tiebreakers){if(e.skip)continue;if(!t.types?.includes("geneVariant")){continue}const a=o.append("tr").on("mouseover",V).datum(e).attr("draggable",!e.disabled&&t.types?.length!==0).attr("droppable",!e.disabled&&t.types?.length!==0).on("dragstart",k).on("dragover",O).on("dragleave",D).on("drop",A);if(!e.disabled)I++;const n=a.append("td").attr("title",e.disabled?`This tiebreaker is currently not being used to sort ${p.cases}. Check the box to use.`:`The number indicates the order in which this tiebreaker is used. Unched the box to skip.`).datum(e);n.style("padding","5px").style("vertical-align","top").style("text-align","center");n.append("span").html(!e.disabled?I:"");const r=a.append("td").style("opacity",e.disabled?.5:1).style("padding","5px").style("vertical-align","top").style("max-width","500px");r.append("span").html(e.label\|\|"");if(!e.disabled){const t=r.append("label");t.append("span").html("<br>(use data list order ");if(!e.isOrdered)e.isOrdered=false;t.append("input").datum(e).attr("type","checkbox").property("checked",e.isOrdered).style("vertical-align","bottom").on("change",S);t.append("span").html(")");const a=e.order;r.append("div").attr("class","sjpp-matrix-sorter-ui-value").selectAll("div").data(a.map(((t,a)=>({lstName:"order",key:t,cls:i[t],tb:e,dragstart:P,dragover:w,dragleave:T,drop:_,filterByClass:d.filterByClass,index:a})))).enter().append("div").style("display",e.isOrdered?"block":"inline-block").each(C);if(e.notUsed?.length){const t=r.append("div");t.append("div").attr("data-testid","sjpp-matrix-sorter-ui-hidden-add").style("display","inline-block").style("padding","5x").style("vertical-align","top").style("padding","3px 5px").style("cursor","pointer").html(`+Add`).on("click",N)}}const s=a.append("td").style("text-align","center").style("vertical-align","top");if(e.mayToggle){s.append("button").datum(e).html(e.disabled?"Enable":"Disable").on("click",B)}}const c=o.append("tr").attr("draggable",true).on("mouseover",V);c.append("td").html(" ");const g=c.append("td").style("text-align","left").html(t.details&&!t.order?.length?t.details:" ");if(t.handler)t.handler(g,c,o);c.append("td").html(" ")}},toggleSection:b,trackDraggedSection:f,highlightSection:m,unhighlightSection:x,adjustSortPriority:v,trackDraggedTieBreaker:k,highlightTieBreaker:O,unhighlightTieBreaker:D,adjustTieBreakers:A,trackDraggedValue:P,highlightValue:w,unhighlightValue:T,adjustValueOrder:_,apply:j};function b(t,e={label:"all"}){h.expandedSection=h.expandedSection===e.label?"":e.label;h.expanded=!!h.expandedSection;h.init()}function f(t,e){u.type="sortPriority";u.data=e;u.index=h.activeOption.sortPriority.indexOf(e)}function m(t,e){if(u.type!="sortPriority"\|\|e==u.data)return;t.preventDefault();const i=h.activeOption.sortPriority.indexOf(e);const n=i<u.index?"border-top":i>u.index?"border-bottom":"";if(!n)return;a(this).selectAll("th").style(n,"2px solid blue")}function x(t,e){if(u.type!="sortPriority")return;t.preventDefault();a(this).selectAll("th").style("border","none")}function v(t,e){if(e==u.data)return;const a=h.activeOption.sortPriority.indexOf(e);const i=o.config.settings.matrix;h.activeOption.sortPriority.splice(u.index,1);h.activeOption.sortPriority.splice(a,0,u.data);h.init({sortOptions:{[i.sortSamplesBy]:h.activeOption}})}function k(t,e){u.type="tiebreaker";u.data=e;u.sectionData=t.target.closest("tbody").__data__;u.priorityIndex=h.activeOption.sortPriority.indexOf(u.sectionData);u.index=u.sectionData.tiebreakers.indexOf(e)}function O(t,e){if(u.type!="tiebreaker"\|\|e==u.data)return;t.preventDefault();const i=u.sectionData.tiebreakers.indexOf(e);const n=i<u.index?"border-top":i>u.index?"border-bottom":"";if(!n)return;a(this).selectAll("td:nth-child(2)").style(n,"2px solid blue")}function D(t,e){if(u.type!="tiebreaker")return;t.preventDefault();a(this).selectAll("td:nth-child(2)").style("border","none")}function S(t,e){t.stopPropagation();e.isOrdered=!e.isOrdered;h.init({sortOptions:{[d.sortSamplesBy]:h.activeOption}})}function B(t,e){t.stopPropagation();e.disabled=!e.disabled;h.init({sortOptions:{[d.sortSamplesBy]:h.activeOption}})}function A(t,e){if(u.type!="tiebreaker"\|\|e==u.data)return;t.preventDefault();const a=u.sectionData.tiebreakers.indexOf(e);const i=o.config.settings.matrix;u.sectionData.tiebreakers.splice(u.index,1);u.sectionData.tiebreakers.splice(a,0,u.data);h.init({sortOptions:{[i.sortSamplesBy]:h.activeOption}})}function C(t){const e=[];if(t.tb.notUsed?.includes(t.key))e.push(`- Click on this label to include in used data values.`);if(t.filterByClass[t.key])e.unshift("- Click on the corresponding entry in the matrix legend or Mutation/CNV menus to unhide");if(e.length)e.unshift(`To use this data value for sorting ${p.samples}:`);t.tb.notUsed?.includes(t.key);const i=t.filterByClass[t.key]=="value"?.5:1;const n=a(this).attr("aria-label",e.length?e.join("\n"):`Click to not use this data value to sort ${p.samples}`).attr("draggable",t.tb.isOrdered?true:false).attr("droppable",t.tb.isOrdered?true:false).style("width","fit-content").style("margin-right","10px").style("overflow","hidden").style("white-space","nowrap").style("opacity",i).style("cursor","pointer").on("dragstart",t.dragstart).on("dragover",t.dragover).on("dragleave",t.dragleave).on("drop",t.drop).on("mouseenter",(()=>r.style("opacity",1))).on("mouseleave",(()=>r.style("opacity",0))).on("click",(()=>{if(e.length){const a="sjpp-matrix-sorter-value-note";n.selectAll(`.${a}`).remove();const i=n.append("div").attr("class",a).style("max-width","200px").style("padding","5px");i.html(e.join("<br>"));if(t.filterByClass[t.key])return}const a=t.lstName=="order"?"notUsed":"order";if(!t.tb[a])t.tb[a]=[];const i=t.tb[a];t.tb[t.lstName].splice(t.index,1);if(t.lstName=="order")i.unshift(t.key);else i.push(t.key);h.init({sortOptions:{[d.sortSamplesBy]:h.activeOption}})}));n.append("div").style("display","inline-block").style("cursor","pointer").style("width","12px").style("height","12px").style("margin-right","3px").style("background-color",t.cls.color);n.append("span").style("cursor","pointer").style("text-decoration",t.filterByClass[t.key]=="case"?"line-through":"").html(t.cls.label+(t.filterByClass[t.key]?" (<i>not used since this value is hidden</i>)":""));const r=n.append("div").style("display","inline-block").style("width","12px").style("cursor","pointer").style("opacity",0).style("color",t.lstName=="order"?"red":"green").html(t.lstName=="order"?"&cross;":"&check;")}function P(t,e){t.stopPropagation?.();u.type="value";u.data=e;u.sectionData=t.target.closest("tbody").__data__;u.priorityIndex=h.activeOption.sortPriority.indexOf(u.sectionData);u.tiebreaker=t.target.closest("tr").__data__;u.tbIndex=u.sectionData.tiebreakers.indexOf(u.priorityIndex);u.order=u.tiebreaker.order}function w(t,e){t.stopPropagation?.();if(u.type!="value"\|\|e==u.data)return;if(e.tb!=u.data.tb)return;t.preventDefault();u.order.indexOf(e);a(this).style("border","2px solid blue")}function T(t,e){t.stopPropagation?.();if(u.type!="value")return;t.preventDefault();a(this).style("border","none")}function _(t,e){t.stopPropagation?.();if(u.type!="value"\|\|e==u.data)return;t.preventDefault();const a=h.settings;u.data.tb[u.data.lstName].splice(u.data.index,1);e.tb[e.lstName].splice(e.index,0,u.data.key);const i=a.hiddenVariants.indexOf(u.data.key);const n=structuredClone(a.hiddenVariants);const r=structuredClone(a.filterByClass);if(i!=-1){n.splice(i,1);r[u.data.key]=false}h.init({hiddenVariants:n,filterByClass:r,sortOptions:{[a.sortSamplesBy]:h.activeOption}})}function N(t,e){t?.stopPropagation();const a=c.clear().d.append("div").attr("data-testid","sjpp-matrix-sorter-ui-hidden-vals").style("margin-top","3px").style("vertical-align","top").style("padding-left","12px");a.selectAll("div").data(e.notUsed.map(((t,a)=>({lstName:"notUsed",key:t,cls:i[t],tb:e,dragstart:P,dragover:w,dragleave:T,drop:_,filterByClass:d.filterByClass,index:a})))).enter().append("div").style("display","block").each(C);c.showunder(t.target)}function j(){o.app.tip?.hide();o.app.dispatch({type:"plot_edit",id:o.id,config:{settings:{matrix:{sortOptions:{[d.sortSamplesBy]:h.activeOption}}}}})}function V(){}function U(t,e){if(!o.selectedTermsToSortAgainst?.length){t.html(`Click on a matrix row label and the left triangle to add an entry here`);return}const i=o.selectedTermsToSortAgainst.map((t=>({t:t,label:t.tw.term.name+(t.tw.term.type=="geneVariant"?" alterations":" values")})));const n=a(e.node().parentNode);n.selectAll("tr").remove();n.selectAll("tr").data(i).enter().append("tr").selectAll("td").data(((t,e)=>[{label:e+1,textAlign:"center",cursor:"",t:t.t},{label:t.label,textAlign:"left",cursor:""},{label:"Delete",textAlign:"center",cursor:"pointer",click:o.unsortSamplesAgainstTerm,data:t}])).enter().append("td").style("text-align",(t=>t.textAlign)).style("cursor",(t=>t.cursor)).html((t=>t.label)).on("click",((t,e)=>e.click?.(t,e)))}h.init();h.api={main:h.init,destroy:()=>{r.holder.selectAll("").remove()}};if(r.debug)h.api.Inner=h;return h.api}export{r as getSorterUi};
1	+ import{M as t,P as e,d as a,z as i}from"./app-6fb77603.js";const n=`ABCDEFGHIJKLMNOPQRSTUVWXYZ`.split("");function r(r){const{controls:s,holder:l}=r;const o=s.parent;const d=structuredClone(o.config.settings.matrix);const p=d.controlLabels;const c=new t({padding:"",parent_menu:o.app.tip?.d.node()});let y=[],g,u={};const h={dom:{tip:c},opts:r,highlightColor:"none",label:`Sort ${p.Samples}`,title:`Set how to sort ${p.samples}`,type:"custom",expanded:r.expanded\|\|false,expandedSection:r.expandedSection\|\|"",init(t={},s={}){c.clear().hide();if(o.config.settings.matrix!=d)e(d,o.config.settings.matrix);if(d!==t)e(d,t);h.settings=d;h.activeOption=structuredClone(d.sortOptions[d.sortSamplesBy]);g=[{label:`For each selected row, sort ${p.samples} by matching data`,notDraggable:true,tiebreakers:[],handler:U},...h.activeOption.sortPriority,{label:`Sort ${p.samples} by name, alphabetically`,notDraggable:true,tiebreakers:[]}];Object.assign(r,s);r.holder.selectAll("").remove();const l=r.holder.append("div").style("text-align","right");l.append("button").html("Apply").on("click",j);l.append("button").html("Reset").on("click",((t,e)=>h.init()));const u=r.holder.append("table");const $=u.append("thead");$.append("th").html("Priority").style("text-align","left").style("max-width","0px");$.append("th").html("Description");$.append("th").html("Action");let I=0,M=0;for(const t of g){const e=t.tiebreakers?.[0]?.order\|\|t.handler;const r=u.append("thead").datum(t).property("draggable",!t.notDraggable).attr("droppable",true).on("dragstart",f).on("dragover",m).on("dragleave",x).on("drop",v);y.push(a(r));const s=r.append("tr").style("background-color","#eee").on("mouseover",V);s.append("th").style("padding","5px").style("vertical-align","top").style("font-weight",400).html(n[M++]).on("click",e?b:null);const l=s.append("th").style("padding","5px").style("vertical-align","top").style("text-align","left").style("cursor",e?"pointer":"").on("click",e?b:null);l.append("span").style("margin-right","12px").style("font-weight",400).html(t.label);s.append("th").style("padding","5px").style("vertical-align","top").style("text-align","center").style("font-weight",400).style("cursor",e?"pointer":"").append("span").html(e?"Details":" ").on("click",e?b:null);const o=u.append("tbody").datum(t).style("display",h.expandedSection=="all"\|\|h.expandedSection==t.label?"":"none");for(const e of t.tiebreakers){if(e.skip)continue;if(!t.types?.includes("geneVariant")){continue}const a=o.append("tr").on("mouseover",V).datum(e).attr("draggable",!e.disabled&&t.types?.length!==0).attr("droppable",!e.disabled&&t.types?.length!==0).on("dragstart",k).on("dragover",O).on("dragleave",D).on("drop",A);if(!e.disabled)I++;const n=a.append("td").attr("title",e.disabled?`This tiebreaker is currently not being used to sort ${p.cases}. Check the box to use.`:`The number indicates the order in which this tiebreaker is used. Unched the box to skip.`).datum(e);n.style("padding","5px").style("vertical-align","top").style("text-align","center");n.append("span").html(!e.disabled?I:"");const r=a.append("td").style("opacity",e.disabled?.5:1).style("padding","5px").style("vertical-align","top").style("max-width","500px");r.append("span").html(e.label\|\|"");if(!e.disabled){const t=r.append("label");t.append("span").html("<br>(use data list order ");if(!e.isOrdered)e.isOrdered=false;t.append("input").datum(e).attr("type","checkbox").property("checked",e.isOrdered).style("vertical-align","bottom").on("change",S);t.append("span").html(")");const a=e.order;r.append("div").attr("class","sjpp-matrix-sorter-ui-value").selectAll("div").data(a.map(((t,a)=>({lstName:"order",key:t,cls:i[t],tb:e,dragstart:P,dragover:w,dragleave:T,drop:_,filterByClass:d.filterByClass,index:a})))).enter().append("div").style("display",e.isOrdered?"block":"inline-block").each(C);if(e.notUsed?.length){const t=r.append("div");t.append("div").attr("data-testid","sjpp-matrix-sorter-ui-hidden-add").style("display","inline-block").style("padding","5x").style("vertical-align","top").style("padding","3px 5px").style("cursor","pointer").html(`+Add`).on("click",N)}}const s=a.append("td").style("text-align","center").style("vertical-align","top");if(e.mayToggle){s.append("button").datum(e).html(e.disabled?"Enable":"Disable").on("click",B)}}const c=o.append("tr").attr("draggable",true).on("mouseover",V);c.append("td").html(" ");const g=c.append("td").style("text-align","left").html(t.details&&!t.order?.length?t.details:" ");if(t.handler)t.handler(g,c,o);c.append("td").html(" ")}},toggleSection:b,trackDraggedSection:f,highlightSection:m,unhighlightSection:x,adjustSortPriority:v,trackDraggedTieBreaker:k,highlightTieBreaker:O,unhighlightTieBreaker:D,adjustTieBreakers:A,trackDraggedValue:P,highlightValue:w,unhighlightValue:T,adjustValueOrder:_,apply:j};function b(t,e={label:"all"}){h.expandedSection=h.expandedSection===e.label?"":e.label;h.expanded=!!h.expandedSection;h.init()}function f(t,e){u.type="sortPriority";u.data=e;u.index=h.activeOption.sortPriority.indexOf(e)}function m(t,e){if(u.type!="sortPriority"\|\|e==u.data)return;t.preventDefault();const i=h.activeOption.sortPriority.indexOf(e);const n=i<u.index?"border-top":i>u.index?"border-bottom":"";if(!n)return;a(this).selectAll("th").style(n,"2px solid blue")}function x(t,e){if(u.type!="sortPriority")return;t.preventDefault();a(this).selectAll("th").style("border","none")}function v(t,e){if(e==u.data)return;const a=h.activeOption.sortPriority.indexOf(e);const i=o.config.settings.matrix;h.activeOption.sortPriority.splice(u.index,1);h.activeOption.sortPriority.splice(a,0,u.data);h.init({sortOptions:{[i.sortSamplesBy]:h.activeOption}})}function k(t,e){u.type="tiebreaker";u.data=e;u.sectionData=t.target.closest("tbody").__data__;u.priorityIndex=h.activeOption.sortPriority.indexOf(u.sectionData);u.index=u.sectionData.tiebreakers.indexOf(e)}function O(t,e){if(u.type!="tiebreaker"\|\|e==u.data)return;t.preventDefault();const i=u.sectionData.tiebreakers.indexOf(e);const n=i<u.index?"border-top":i>u.index?"border-bottom":"";if(!n)return;a(this).selectAll("td:nth-child(2)").style(n,"2px solid blue")}function D(t,e){if(u.type!="tiebreaker")return;t.preventDefault();a(this).selectAll("td:nth-child(2)").style("border","none")}function S(t,e){t.stopPropagation();e.isOrdered=!e.isOrdered;h.init({sortOptions:{[d.sortSamplesBy]:h.activeOption}})}function B(t,e){t.stopPropagation();e.disabled=!e.disabled;h.init({sortOptions:{[d.sortSamplesBy]:h.activeOption}})}function A(t,e){if(u.type!="tiebreaker"\|\|e==u.data)return;t.preventDefault();const a=u.sectionData.tiebreakers.indexOf(e);const i=o.config.settings.matrix;u.sectionData.tiebreakers.splice(u.index,1);u.sectionData.tiebreakers.splice(a,0,u.data);h.init({sortOptions:{[i.sortSamplesBy]:h.activeOption}})}function C(t){const e=[];if(t.tb.notUsed?.includes(t.key))e.push(`- Click on this label to include in used data values.`);if(t.filterByClass[t.key])e.unshift("- Click on the corresponding entry in the matrix legend or Mutation/CNV menus to unhide");if(e.length)e.unshift(`To use this data value for sorting ${p.samples}:`);t.tb.notUsed?.includes(t.key);const i=t.filterByClass[t.key]=="value"?.5:1;const n=a(this).attr("aria-label",e.length?e.join("\n"):`Click to not use this data value to sort 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i.push(t.key);h.init({sortOptions:{[d.sortSamplesBy]:h.activeOption}})}));n.append("div").style("display","inline-block").style("cursor","pointer").style("width","12px").style("height","12px").style("margin-right","3px").style("background-color",t.cls.color);n.append("span").style("cursor","pointer").style("text-decoration",t.filterByClass[t.key]=="case"?"line-through":"").html(t.cls.label+(t.filterByClass[t.key]?" (<i>not used since this value is hidden</i>)":""));const r=n.append("div").style("display","inline-block").style("width","12px").style("cursor","pointer").style("opacity",0).style("color",t.lstName=="order"?"red":"green").html(t.lstName=="order"?"&cross;":"&check;")}function P(t,e){t.stopPropagation?.();u.type="value";u.data=e;u.sectionData=t.target.closest("tbody").__data__;u.priorityIndex=h.activeOption.sortPriority.indexOf(u.sectionData);u.tiebreaker=t.target.closest("tr").__data__;u.tbIndex=u.sectionData.tiebreakers.indexOf(u.priorityIndex);u.order=u.tiebreaker.order}function w(t,e){t.stopPropagation?.();if(u.type!="value"\|\|e==u.data)return;if(e.tb!=u.data.tb)return;t.preventDefault();u.order.indexOf(e);a(this).style("border","2px solid blue")}function T(t,e){t.stopPropagation?.();if(u.type!="value")return;t.preventDefault();a(this).style("border","none")}function _(t,e){t.stopPropagation?.();if(u.type!="value"\|\|e==u.data)return;t.preventDefault();const a=h.settings;u.data.tb[u.data.lstName].splice(u.data.index,1);e.tb[e.lstName].splice(e.index,0,u.data.key);const i=a.hiddenVariants.indexOf(u.data.key);const n=structuredClone(a.hiddenVariants);const r=structuredClone(a.filterByClass);if(i!=-1){n.splice(i,1);r[u.data.key]=false}h.init({hiddenVariants:n,filterByClass:r,sortOptions:{[a.sortSamplesBy]:h.activeOption}})}function N(t,e){t?.stopPropagation();const a=c.clear().d.append("div").attr("data-testid","sjpp-matrix-sorter-ui-hidden-vals").style("margin-top","3px").style("vertical-align","top").style("padding-left","12px");a.selectAll("div").data(e.notUsed.map(((t,a)=>({lstName:"notUsed",key:t,cls:i[t],tb:e,dragstart:P,dragover:w,dragleave:T,drop:_,filterByClass:d.filterByClass,index:a})))).enter().append("div").style("display","block").each(C);c.showunder(t.target)}function j(){o.app.tip?.hide();o.app.dispatch({type:"plot_edit",id:o.id,config:{settings:{matrix:{sortOptions:{[d.sortSamplesBy]:h.activeOption}}}}})}function V(){}function U(t,e){if(!o.selectedTermsToSortAgainst?.length){t.html(`Click on a matrix row label and the left triangle to add an entry here`);return}const i=o.selectedTermsToSortAgainst.map((t=>({t:t,label:t.tw.term.name+(t.tw.term.type=="geneVariant"?" alterations":" values")})));const n=a(e.node().parentNode);n.selectAll("tr").remove();n.selectAll("tr").data(i).enter().append("tr").selectAll("td").data(((t,e)=>[{label:e+1,textAlign:"center",cursor:"",t:t.t},{label:t.label,textAlign:"left",cursor:""},{label:"Delete",textAlign:"center",cursor:"pointer",click:o.unsortSamplesAgainstTerm,data:t}])).enter().append("td").style("text-align",(t=>t.textAlign)).style("cursor",(t=>t.cursor)).html((t=>t.label)).on("click",((t,e)=>e.click?.(t,e)))}h.init();h.api={main:h.init,destroy:()=>{r.holder.selectAll("").remove()}};if(r.debug)h.api.Inner=h;return h.api}export{r as getSorterUi};

package/dist/{mavb-9d86df89.js → mavb-da8d1a0a.js} RENAMED Viewed

	@@ -1 +1 @@
1	- import{M as t,bn as e,bo as a,Z as n,j as l,U as o,I as r,ag as s,a9 as i,d as c,ah as d,f as p}from"./app-2cd97738.js";import{b as f}from"./block.lazyload-eda77d9b.js";import{d as u}from"./lasso-e8b9500e.js";import{b as g,a as m}from"./axis-747c801e.js";import"./drag-d8daa62f.js";import"./nodrag-ab7d5a9f.js";import"./pointer-c7475677.js";const h="#ffa200";const v=new t;function x(t,e,a,n){if(!t.dataname){t.dataname="Differential expression"}if(t.input){const l=t.input;delete t.input;const o=y({genome:t.genome,filename:t.dataname,holder:a,tracks:t.tracks,hostURL:t.hostURL,jwt:n},l.trim().split("\n"));if(o){e("Error with diferential gene expressionn data: "+o)}return}let l;if(t.url){l=new Request(t.hostURL+"/urltextfile",{method:"POST",body:JSON.stringify({url:t.url,jwt:n})});delete t.url}else if(t.file){l=new Request(t.hostURL+"/textfile",{method:"POST",body:JSON.stringify({file:t.file,jwt:n})});delete t.file}else{e("neither .input nor .url given for MA-Volcano plot");return}const o=a.append("div").style("margin","20px").style("color","#aaa").style("font-size","1.5em").text("Loading differential gene expression data ...");fetch(l).then((t=>t.json())).then((e=>{if(e.error)throw{message:e.error};if(!e.text)throw{message:"no data loaded"};const l=y({genome:t.genome,filename:t.dataname,holder:a,tracks:t.tracks,hostURL:t.hostURL,jwt:n},e.text.trim().split("\n"));if(l)throw{message:"Error with differential gene expression data: "+l}})).catch((t=>{e(t.message);if(t.stack)console.log(t.stack)})).then((()=>{o.remove()}))}function b(t,n,l,o,r){let s,i,c,d,p,f;if(o!==undefined)[i,c,d,p,f]=e(o,t);else{[s,i,c,d,p,f]=a(100,100,t);s.header.text("Differential gene expression viewer");s.body.style("margin","10px")}i.append("div").style("margin-top","30px").style("color","#858585").html(`\n\t\t<p>Interactive MA and Volcano plot for exploring differentially expressed genes.</p>\n\t\t<a href=https://docs.google.com/document/d/1gEhywyMzMQRM10NFvsObw1yDSWxVY7pxYjsQ2-nd6x4/edit?usp=sharing target=_blank>File format</a>\n\t\t`);function u(t,e){p.style("color",e?"red":"black").text(t)}const g=()=>{d.selectAll("").remove();const e=d.append("input").attr("type","file").on("change",(e=>{const a=e.target.files[0];if(!a){g();return}if(!a.size){u("Invalid file "+a.name);g();return}const i=new FileReader;i.onload=e=>{const i=c.options[c.selectedIndex].innerHTML;const d=y({genome:t[i],filename:a.name,hostURL:n,jwt:l,holder:o,sandbox_header:r},e.target.result.trim().split("\n"));if(d){u(d,1);g();return}if(s)s.pane.remove()};i.onerror=function(){u("Error reading file "+a.name,1);g();return};i.readAsText(a,"utf8")}));setTimeout((()=>e.node().focus()),1100)};g()}function y(t,e){if(t.tracks){for(const e of t.tracks){e.iscustom=true}}const[a,o]=k(e[0].trim());if(a){return a}t.hastvalue=o.includes("tvalue");const r=[];let s=0;let i=0;let c=0;for(let a=1;a<e.length;a++){const n=e[a];if(n=="")continue;if(n[0]=="#")continue;const l=n.trim().split("\t");const d={};for(let t=0;t<o.length;t++){d[o[t]]=l[t]}if(!d.gene){return"(line "+(a+1)+") missing gene"}d.gene=d.gene.replace(/"/g,"");if(!d.logfoldchange){return"(line "+(a+1)+") missing log fold change"}{const t=Number.parseFloat(d.logfoldchange);if(Number.isNaN(t)){c++;continue}d.logfoldchange=t}if(!d.averagevalue){return"(line "+(a+1)+") missing average value"}{const t=Number.parseFloat(d.averagevalue);if(Number.isNaN(t)){return"(line "+(a+1)+") invalid value for average value: "+d.averagevalue}d.averagevalue=t}if(!d.pvalue){s++;continue}else{const t=Number.parseFloat(d.pvalue);if(Number.isNaN(t)){s++;continue}d.pvalue=t}if(d.pvalueadj){const t=Number.parseFloat(d.pvalueadj);if(Number.isNaN(t)){i++;continue}d.pvalueadj=t}if(t.hastvalue){if(!d.tvalue){return"(line "+(a+1)+") missing T value"}{const t=Number.parseFloat(d.tvalue);if(Number.isNaN(t)){return"(line "+(a+1)+") invalid value for T value: 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plot").style("display","block").on("click",(t=>{o(a.node(),"MAplot")}));c.append("button").text("Get volcano plot").style("display","block").on("click",(t=>{o(l.node(),"Volcano")}))}function w(t,e){const a=[];let n=0,l=0;for(const t of e.data){n=Math.min(n,t.logfoldchange);l=Math.max(l,t.logfoldchange);a.push(t.averagevalue)}a.sort(((t,e)=>t-e));const o=a[0];const i=a[a.length-1];let c,d,p,f,u,v,x,b=50,y=50,k;const _=t.append("svg");const w=_.append("g");const M=_.append("g");const A=_.append("text").text("Average expression value").attr("fill","black").attr("text-anchor","middle");const E=_.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");e.ma_dotarea=_.append("g");const P=e.ma_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const U=r().domain([o,i]);const z=r().domain([n,l]);let F;if(e.hastvalue){F=r().domain([e.tvaluemin,e.tvaluemax])}const 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value)").attr("fill","black").attr("text-anchor","middle");e.vo_dotarea=y.append("g");const A=e.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const E=r().domain([a,n]);const P=r().domain([l,o]);let U;if(e.hastvalue)U=r().domain([e.tvaluemin,e.tvaluemax]);const z=e.vo_dotarea.selectAll().data(e.data).enter().append("g").each((function(t){t.vo_g=this}));const F=z.append("circle").attr("stroke","black").attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",h).attr("fill-opacity",0).each((function(t){t.vo_circle=this})).on("mouseover",N).on("mouseout",R).on("click",((t,a)=>{L(a,e,t.clientX,t.clientY)}));const S=e.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function T(t,a){d=t;p=a;i=Math.max(50,d/8);c=Math.max(50,p/8);b=Math.max(d,p)/80;const n=b*3;if(U)U.range([b,n]);F.each((t=>{t.vo_radius=U?U(Math.abs(t.tvalue)):b}));f=Math.max(n,d/50);u=Math.max(n,p/50);k.attr("transform","translate("+i+","+v+")");_.attr("transform","translate("+(i+f)+","+(v+p+u)+")");w.attr("x",i+f+d/2).attr("y",v+p+u+c-5);M.attr("transform","translate(15,"+(v+p/2)+") rotate(-90)");e.vo_dotarea.attr("transform","translate("+(i+f)+","+v+")");A.attr("width",d).attr("height",p);E.range([0,d]);P.range([p,0]);z.attr("transform",(t=>"translate("+E(t.logfoldchange)+","+P(t.pvalue==0?o:-Math.log(t.pvalue,10))+")"));F.attr("r",(t=>t.vo_radius));S.attr("x1",E(0)).attr("x2",E(0)).attr("y2",p);y.attr("width",i+f+d+x).attr("height",v+p+u+c);s({axis:k.call(g().scale(P)),color:"black",showline:true});s({axis:_.call(m().scale(E)),color:"black",showline:true})}T(400,400);if(e.data[0].pvalueadj!=undefined){const a=t.append("div").style("margin","20px");a.append("span").text("Select P value for Volcano plot:");const n=a.append("select").style("margin-left","5px").on("change",(t=>{l=0;o=0;const a=n.node().selectedIndex==0;for(const t of e.data){const e=a?t.pvalue:t.pvalueadj;if(e==0)continue;const n=-Math.log(e,10);l=Math.min(l,n);o=Math.max(o,n)}P.domain([l,o]);s({axis:k.call(g().scale(P)),color:"black",showline:true});z.attr("transform",(t=>{const e=a?t.pvalue:t.pvalueadj;return"translate("+E(t.logfoldchange)+","+P(e==0?o:-Math.log(e,10))+")"}));M.text(a?"-log(P value)":"-log(adjusted P value)")}));n.append("option").text("Unadjusted P value");n.append("option").text("Adjusted P value")}j(z.selectAll("circle"),y,"ma_circle");return y}function j(t,e,a){const n=u().items(t).targetArea(e);function l(){e.selectAll(".possible").style("fill-opacity",0).classed("not_possible",true).classed("selected",false).each((t=>{c(t[a]).attr("fill-opacity",0)}))}function o(){n.possibleItems().style("fill-opacity",.9).classed("not_possible",false).classed("possible",true).each((t=>{c(t[a]).attr("fill-opacity",.9)}))}function r(){}n.on("start",l).on("draw",o).on("end",r);e.call(n)}function N(t,e){v.clear().show(t.clientX,t.clientY);const a=[{k:"gene",v:e.gene},{k:"average value",v:e.averagevalue},{k:"log fold change",v:e.logfoldchange},{k:"P value",v:e.pvalue}];if(e.pvalueadj!=undefined){a.push({k:"adjusted P value",v:e.pvalueadj})}if(e.tvalue!=undefined){a.push({k:"T value",v:e.tvalue})}for(const t in e){if(t=="gene"\|\|t=="averagevalue"\|\|t=="logfoldchange"\|\|t=="pvalue"\|\|t=="pvalueadj"\|\|t=="tvalue"){continue}const n=e[t];if(typeof n!="string"){continue}a.push({k:t,v:n})}i(v.d,a);if(!e.ma_label){c(e.ma_circle).attr("fill-opacity",.9);c(e.vo_circle).attr("fill-opacity",.9)}}function R(t,e){v.hide();if(!e.ma_label){c(e.ma_circle).attr("fill-opacity",0);c(e.vo_circle).attr("fill-opacity",0)}}function A(t,e){if(t.ma_label){t.ma_label.remove();t.ma_labelbg.remove();t.ma_label=null;t.vo_label.remove();t.vo_labelbg.remove();t.vo_label=null;c(t.ma_circle).attr("fill-opacity",0);c(t.vo_circle).attr("fill-opacity",0);return}e.ma_dotarea.node().appendChild(t.ma_g);t.ma_labelbg=c(t.ma_g).append("text").text(t.gene).attr("x",t.ma_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("font-family",d).attr("fill","none").attr("stroke","white").attr("stroke-width",3);t.ma_label=c(t.ma_g).append("text").text(t.gene).attr("x",t.ma_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("fill","black").attr("font-family",d).on("mousedown",((t,e)=>{E(e.ma_label,e.ma_labelbg,t)}));e.vo_dotarea.node().appendChild(t.vo_g);t.vo_labelbg=c(t.vo_g).append("text").text(t.gene).attr("x",t.vo_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("font-family",d).attr("fill","none").attr("stroke","white").attr("stroke-width",3);t.vo_label=c(t.vo_g).append("text").text(t.gene).attr("x",t.vo_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("fill","black").attr("font-family",d).on("mousedown",((t,e)=>{E(e.vo_label,e.vo_labelbg,t)}));c(t.ma_circle).attr("fill-opacity",.8);c(t.vo_circle).attr("fill-opacity",.8)}function E(t,e,a){event.preventDefault();const n=Number.parseFloat(t.attr("x"));const l=Number.parseFloat(t.attr("y"));const o=a.clientX;const r=a.clientY;const s=c(document.body);s.on("mousemove",(a=>{t.attr("x",n+a.clientX-o).attr("y",l+a.clientY-r);e.attr("x",n+a.clientX-o).attr("y",l+a.clientY-r)})).on("mouseup",(t=>{s.on("mousemove",null).on("mouseup",null)}))}function L(t,e,a,l){if(e.tracks){if(!t.ma_label){const o=n({x:a+20,y:l-50});o.header.text(t.gene);P(e,t.gene,o.body)}}A(t,e)}function P(t,e,a){fetch(new Request(t.hostURL+"/genelookup",{method:"POST",body:JSON.stringify({deep:1,input:e,genome:t.genome.name,jwt:t.jwt})})).then((t=>t.json())).then((n=>{if(n.error)throw{message:n.error};if(!n.gmlst\|\|n.gmlst.length==0)throw{message:"No genes can be found for "+e};const l=new Map;for(const t of n.gmlst){if(!l.has(t.chr)){l.set(t.chr,{chr:t.chr,start:t.start,stop:t.stop})}l.get(t.chr).start=Math.min(t.start,l.get(t.chr).start);l.get(t.chr).stop=Math.max(t.stop,l.get(t.chr).stop)}const o=[...l][0][1];const r=[...t.tracks];p(t.genome,r);f({holder:a,hostURL:t.hostURL,jwt:t.jwt,genome:t.genome,chr:o.chr,start:o.start,stop:o.stop,tklst:r,nobox:true})})).catch((t=>{l(a,t.message);if(t.stack)console.log(t.stack)}))}export{x as mavbparseinput,b as mavbui};
1	+ import{M as t,bn as e,bo as a,Z as n,j as l,U as o,I as r,ag as s,a9 as i,d as c,ah as d,f as p}from"./app-6fb77603.js";import{b as f}from"./block.lazyload-d2951c91.js";import{d as u}from"./lasso-1a02a545.js";import{b as g,a as m}from"./axis-747c801e.js";import"./drag-2e9c80bb.js";import"./nodrag-b2737073.js";import"./pointer-c7475677.js";const h="#ffa200";const v=new t;function x(t,e,a,n){if(!t.dataname){t.dataname="Differential expression"}if(t.input){const l=t.input;delete t.input;const o=y({genome:t.genome,filename:t.dataname,holder:a,tracks:t.tracks,hostURL:t.hostURL,jwt:n},l.trim().split("\n"));if(o){e("Error with diferential gene expressionn data: "+o)}return}let l;if(t.url){l=new Request(t.hostURL+"/urltextfile",{method:"POST",body:JSON.stringify({url:t.url,jwt:n})});delete t.url}else if(t.file){l=new Request(t.hostURL+"/textfile",{method:"POST",body:JSON.stringify({file:t.file,jwt:n})});delete t.file}else{e("neither .input nor .url given for MA-Volcano plot");return}const o=a.append("div").style("margin","20px").style("color","#aaa").style("font-size","1.5em").text("Loading differential gene expression data ...");fetch(l).then((t=>t.json())).then((e=>{if(e.error)throw{message:e.error};if(!e.text)throw{message:"no data loaded"};const l=y({genome:t.genome,filename:t.dataname,holder:a,tracks:t.tracks,hostURL:t.hostURL,jwt:n},e.text.trim().split("\n"));if(l)throw{message:"Error with differential gene expression data: "+l}})).catch((t=>{e(t.message);if(t.stack)console.log(t.stack)})).then((()=>{o.remove()}))}function b(t,n,l,o,r){let s,i,c,d,p,f;if(o!==undefined)[i,c,d,p,f]=e(o,t);else{[s,i,c,d,p,f]=a(100,100,t);s.header.text("Differential gene expression viewer");s.body.style("margin","10px")}i.append("div").style("margin-top","30px").style("color","#858585").html(`\n\t\t<p>Interactive MA and Volcano plot for exploring differentially expressed genes.</p>\n\t\t<a href=https://docs.google.com/document/d/1gEhywyMzMQRM10NFvsObw1yDSWxVY7pxYjsQ2-nd6x4/edit?usp=sharing target=_blank>File format</a>\n\t\t`);function u(t,e){p.style("color",e?"red":"black").text(t)}const g=()=>{d.selectAll("").remove();const e=d.append("input").attr("type","file").on("change",(e=>{const a=e.target.files[0];if(!a){g();return}if(!a.size){u("Invalid file "+a.name);g();return}const i=new FileReader;i.onload=e=>{const i=c.options[c.selectedIndex].innerHTML;const d=y({genome:t[i],filename:a.name,hostURL:n,jwt:l,holder:o,sandbox_header:r},e.target.result.trim().split("\n"));if(d){u(d,1);g();return}if(s)s.pane.remove()};i.onerror=function(){u("Error reading file "+a.name,1);g();return};i.readAsText(a,"utf8")}));setTimeout((()=>e.node().focus()),1100)};g()}function y(t,e){if(t.tracks){for(const e of t.tracks){e.iscustom=true}}const[a,o]=k(e[0].trim());if(a){return a}t.hastvalue=o.includes("tvalue");const r=[];let s=0;let i=0;let c=0;for(let a=1;a<e.length;a++){const n=e[a];if(n=="")continue;if(n[0]=="#")continue;const l=n.trim().split("\t");const d={};for(let t=0;t<o.length;t++){d[o[t]]=l[t]}if(!d.gene){return"(line "+(a+1)+") missing gene"}d.gene=d.gene.replace(/"/g,"");if(!d.logfoldchange){return"(line "+(a+1)+") missing log fold change"}{const t=Number.parseFloat(d.logfoldchange);if(Number.isNaN(t)){c++;continue}d.logfoldchange=t}if(!d.averagevalue){return"(line "+(a+1)+") missing average value"}{const t=Number.parseFloat(d.averagevalue);if(Number.isNaN(t)){return"(line "+(a+1)+") invalid value for average value: "+d.averagevalue}d.averagevalue=t}if(!d.pvalue){s++;continue}else{const t=Number.parseFloat(d.pvalue);if(Number.isNaN(t)){s++;continue}d.pvalue=t}if(d.pvalueadj){const t=Number.parseFloat(d.pvalueadj);if(Number.isNaN(t)){i++;continue}d.pvalueadj=t}if(t.hastvalue){if(!d.tvalue){return"(line "+(a+1)+") missing T value"}{const t=Number.parseFloat(d.tvalue);if(Number.isNaN(t)){return"(line "+(a+1)+") invalid value for T value: "+d.tvalue}d.tvalue=t}}r.push(d)}if(r.length==0){return"No valid data"}if(t.holder==undefined){const e=n({x:100,y:100});e.header.text(t.filename);t.holder=e.body}else{t.holder.selectAll("").remove();if(t.sandbox_header!==undefined)t.holder.append("div").html('<span style="opacity:.5;font-size:.7em">FILE: </span> '+t.filename)}t.data=r;if(c+s+i>0){const e=t.holder.append("div").style("width","800px");if(c){l(e,c+" lines dropped for invalid log fold change value")}if(s){l(e,s+" lines dropped for invalid P value")}if(i){l(e,i+" lines dropped for invalid adjusted P value")}}_(t);return null}function k(t){const e=t.toLowerCase().split("\t");const a=t.split("\t");if(a.length<=1){return["invalid file header"]}const n=(...t)=>{for(const a of t){const t=e.indexOf(a);if(t!=-1)return t}return-1};let l=n("gene");if(l==-1)return["gene missing from header"];a[l]="gene";l=n("logfc","log.foldchange");if(l==-1)return["log.foldchange missing from header"];a[l]="logfoldchange";l=n("aveexpr","average.value");if(l==-1)return["average.value missing from header"];a[l]="averagevalue";l=n("t","t.value");if(l!=-1){a[l]="tvalue"}l=n("p.value");if(l==-1)return["p.value missing from header"];a[l]="pvalue";l=n("p.value.adjusted","adj.p.val","adjustedp-value(fdr)");if(l!=-1){a[l]="pvalueadj"}return[null,a]}function _(t){if(t.hastvalue){let e=Math.abs(t.data[0].tvalue);let a=0;for(const n of t.data){const t=Math.abs(n.tvalue);e=Math.min(e,t);a=Math.max(a,t)}t.tvaluemin=e;t.tvaluemax=a}const e=t.holder.append("div").style("display","inline-block").style("vertical-align","top").style("margin","20px");const a=w(e,t);const n=t.holder.append("div").style("display","inline-block").style("vertical-align","top").style("margin","20px");const l=M(n,t);const r=t.holder.append("div").style("margin","20px");const s=r.append("textarea").style("display","inline-block").attr("rows",5).attr("cols",10).style("resize","both").attr("placeholder","Enter genes, separate by space or newline");const i=r.append("div").style("display","inline-block").style("margin-left","10px").style("vertical-align","top");i.append("button").style("display","block").text("Show gene labels").on("click",(e=>{const a=s.property("value").trim();if(a=="")return;const n=new Set;for(const t of a.split(/[\s\n\t]+/)){n.add(t.toUpperCase())}if(n.size==0)return;for(const e of t.data){if(!e.ma_label&&n.has(e.gene.toUpperCase())){A(e,t)}}}));i.append("button").style("display","block").text("Remove all labels").on("click",(e=>{for(const e of t.data){if(e.ma_label){A(e,t)}}}));i.append("div").style("margin-top","10px").style("color","#858585").style("font-size",".8em").html('<span style="font-size:1.3em">TIP:</span> click circles to toggle highlight on genes;<br>drag to move a gene label around.');const c=r.append("div").style("display","inline-block").style("margin-left","30px").style("vertical-align","top");c.append("button").text("Get MA plot").style("display","block").on("click",(t=>{o(a.node(),"MAplot")}));c.append("button").text("Get volcano plot").style("display","block").on("click",(t=>{o(l.node(),"Volcano")}))}function w(t,e){const a=[];let n=0,l=0;for(const t of e.data){n=Math.min(n,t.logfoldchange);l=Math.max(l,t.logfoldchange);a.push(t.averagevalue)}a.sort(((t,e)=>t-e));const o=a[0];const i=a[a.length-1];let c,d,p,f,u,v,x,b=50,y=50,k;const _=t.append("svg");const w=_.append("g");const M=_.append("g");const A=_.append("text").text("Average expression value").attr("fill","black").attr("text-anchor","middle");const E=_.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");e.ma_dotarea=_.append("g");const P=e.ma_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const U=r().domain([o,i]);const z=r().domain([n,l]);let F;if(e.hastvalue){F=r().domain([e.tvaluemin,e.tvaluemax])}const S=e.ma_dotarea.selectAll().data(e.data).enter().append("g").each((function(t){t.ma_g=this}));const T=S.append("circle").attr("stroke","black").attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",h).attr("fill-opacity",0).each((function(t){t.ma_circle=this})).on("mouseover",N).on("mouseout",R).on("click",((t,a)=>{L(a,e,t.clientX,t.clientY)}));const I=e.ma_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");const O=_.append("g");const Y=O.append("line").attr("stroke",h).attr("shape-rendering","crispEdges");const X=O.append("line").attr("stroke",h).attr("shape-rendering","crispEdges");const C=O.append("line").attr("stroke",h).attr("shape-rendering","crispEdges");const V=O.append("rect").attr("fill","white").attr("stroke",h).attr("shape-rendering","crispEdges");const D=O.append("line").attr("stroke",h).attr("shape-rendering","crispEdges");const q=a[Math.ceil(a.length.05)];const J=a[Math.ceil(a.length.95)];const G=a[Math.ceil(a.length.25)];const Q=a[Math.ceil(a.length.75)];const H=a[Math.ceil(a.length/2)];function W(t,a){p=t;f=a;c=Math.max(50,p/8);d=Math.max(50,f/8);k=Math.max(p,f)/80;const n=k3;U.range([0,p]);z.range([f,0]);if(F)F.range([k,n]);T.each((t=>{t.ma_radius=F?F(Math.abs(t.tvalue)):k}));x=k3;u=Math.max(n,p/50);v=Math.max(n,f/50);w.attr("transform","translate("+c+","+b+")");M.attr("transform","translate("+(c+u)+","+(b+f+v+x+v)+")");A.attr("x",c+u+p/2).attr("y",b+f+v+x+v+d-5);E.attr("transform","translate(15,"+(b+f/2)+") rotate(-90)");e.ma_dotarea.attr("transform","translate("+(c+u)+","+b+")");P.attr("width",p).attr("height",f);S.attr("transform",(t=>"translate("+U(t.averagevalue)+","+z(t.logfoldchange)+")"));T.attr("r",(t=>t.ma_radius));I.attr("x2",p).attr("y1",z(0)).attr("y2",z(0));O.attr("transform","translate("+(c+u)+","+(b+f+v)+")");const l=U(q),o=U(G),r=U(H),i=U(Q),h=U(J);X.attr("x1",l).attr("x2",l).attr("y2",x);C.attr("x1",h).attr("x2",h).attr("y2",x);D.attr("x1",r).attr("x2",r).attr("y2",x);V.attr("x",o).attr("width",i-o).attr("height",x);Y.attr("x1",l).attr("x2",h).attr("y1",x/2).attr("y2",x/2);_.attr("width",c+u+p+y).attr("height",b+f+v+x+v+d);s({axis:w.call(g().scale(z)),color:"black",showline:true});s({axis:M.call(m().scale(U)),color:"black",showline:true})}W(400,400);j(S.selectAll("circle"),_,"vo_circle");return _}function M(t,e){let a=0,n=0,l=0,o=0;for(const t of e.data){a=Math.min(a,t.logfoldchange);n=Math.max(n,t.logfoldchange);if(t.pvalue==0){continue}else{const e=-Math.log(t.pvalue,10);l=Math.min(l,e);o=Math.max(o,e)}}let i,c,d,p,f,u,v=50,x=50,b;const y=t.append("svg");const k=y.append("g");const _=y.append("g");const w=y.append("text").text("log2(fold change)").attr("fill","black").attr("text-anchor","middle");const M=y.append("text").text("-log(P value)").attr("fill","black").attr("text-anchor","middle");e.vo_dotarea=y.append("g");const A=e.vo_dotarea.append("rect").attr("stroke","#ededed").attr("fill","none").attr("shape-rendering","crispEdges");const E=r().domain([a,n]);const P=r().domain([l,o]);let U;if(e.hastvalue)U=r().domain([e.tvaluemin,e.tvaluemax]);const z=e.vo_dotarea.selectAll().data(e.data).enter().append("g").each((function(t){t.vo_g=this}));const F=z.append("circle").attr("stroke","black").attr("stroke-opacity",.2).attr("stroke-width",1).attr("fill",h).attr("fill-opacity",0).each((function(t){t.vo_circle=this})).on("mouseover",N).on("mouseout",R).on("click",((t,a)=>{L(a,e,t.clientX,t.clientY)}));const S=e.vo_dotarea.append("line").attr("stroke","#ccc").attr("shape-rendering","crispEdges");function T(t,a){d=t;p=a;i=Math.max(50,d/8);c=Math.max(50,p/8);b=Math.max(d,p)/80;const n=b*3;if(U)U.range([b,n]);F.each((t=>{t.vo_radius=U?U(Math.abs(t.tvalue)):b}));f=Math.max(n,d/50);u=Math.max(n,p/50);k.attr("transform","translate("+i+","+v+")");_.attr("transform","translate("+(i+f)+","+(v+p+u)+")");w.attr("x",i+f+d/2).attr("y",v+p+u+c-5);M.attr("transform","translate(15,"+(v+p/2)+") rotate(-90)");e.vo_dotarea.attr("transform","translate("+(i+f)+","+v+")");A.attr("width",d).attr("height",p);E.range([0,d]);P.range([p,0]);z.attr("transform",(t=>"translate("+E(t.logfoldchange)+","+P(t.pvalue==0?o:-Math.log(t.pvalue,10))+")"));F.attr("r",(t=>t.vo_radius));S.attr("x1",E(0)).attr("x2",E(0)).attr("y2",p);y.attr("width",i+f+d+x).attr("height",v+p+u+c);s({axis:k.call(g().scale(P)),color:"black",showline:true});s({axis:_.call(m().scale(E)),color:"black",showline:true})}T(400,400);if(e.data[0].pvalueadj!=undefined){const a=t.append("div").style("margin","20px");a.append("span").text("Select P value for Volcano plot:");const n=a.append("select").style("margin-left","5px").on("change",(t=>{l=0;o=0;const a=n.node().selectedIndex==0;for(const t of e.data){const e=a?t.pvalue:t.pvalueadj;if(e==0)continue;const n=-Math.log(e,10);l=Math.min(l,n);o=Math.max(o,n)}P.domain([l,o]);s({axis:k.call(g().scale(P)),color:"black",showline:true});z.attr("transform",(t=>{const e=a?t.pvalue:t.pvalueadj;return"translate("+E(t.logfoldchange)+","+P(e==0?o:-Math.log(e,10))+")"}));M.text(a?"-log(P value)":"-log(adjusted P value)")}));n.append("option").text("Unadjusted P value");n.append("option").text("Adjusted P value")}j(z.selectAll("circle"),y,"ma_circle");return y}function j(t,e,a){const n=u().items(t).targetArea(e);function l(){e.selectAll(".possible").style("fill-opacity",0).classed("not_possible",true).classed("selected",false).each((t=>{c(t[a]).attr("fill-opacity",0)}))}function o(){n.possibleItems().style("fill-opacity",.9).classed("not_possible",false).classed("possible",true).each((t=>{c(t[a]).attr("fill-opacity",.9)}))}function r(){}n.on("start",l).on("draw",o).on("end",r);e.call(n)}function N(t,e){v.clear().show(t.clientX,t.clientY);const a=[{k:"gene",v:e.gene},{k:"average value",v:e.averagevalue},{k:"log fold change",v:e.logfoldchange},{k:"P value",v:e.pvalue}];if(e.pvalueadj!=undefined){a.push({k:"adjusted P value",v:e.pvalueadj})}if(e.tvalue!=undefined){a.push({k:"T value",v:e.tvalue})}for(const t in e){if(t=="gene"\|\|t=="averagevalue"\|\|t=="logfoldchange"\|\|t=="pvalue"\|\|t=="pvalueadj"\|\|t=="tvalue"){continue}const n=e[t];if(typeof n!="string"){continue}a.push({k:t,v:n})}i(v.d,a);if(!e.ma_label){c(e.ma_circle).attr("fill-opacity",.9);c(e.vo_circle).attr("fill-opacity",.9)}}function R(t,e){v.hide();if(!e.ma_label){c(e.ma_circle).attr("fill-opacity",0);c(e.vo_circle).attr("fill-opacity",0)}}function A(t,e){if(t.ma_label){t.ma_label.remove();t.ma_labelbg.remove();t.ma_label=null;t.vo_label.remove();t.vo_labelbg.remove();t.vo_label=null;c(t.ma_circle).attr("fill-opacity",0);c(t.vo_circle).attr("fill-opacity",0);return}e.ma_dotarea.node().appendChild(t.ma_g);t.ma_labelbg=c(t.ma_g).append("text").text(t.gene).attr("x",t.ma_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("font-family",d).attr("fill","none").attr("stroke","white").attr("stroke-width",3);t.ma_label=c(t.ma_g).append("text").text(t.gene).attr("x",t.ma_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("fill","black").attr("font-family",d).on("mousedown",((t,e)=>{E(e.ma_label,e.ma_labelbg,t)}));e.vo_dotarea.node().appendChild(t.vo_g);t.vo_labelbg=c(t.vo_g).append("text").text(t.gene).attr("x",t.vo_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("font-family",d).attr("fill","none").attr("stroke","white").attr("stroke-width",3);t.vo_label=c(t.vo_g).append("text").text(t.gene).attr("x",t.vo_radius+5).attr("y",0).attr("dominant-baseline","central").attr("font-size",14).attr("fill","black").attr("font-family",d).on("mousedown",((t,e)=>{E(e.vo_label,e.vo_labelbg,t)}));c(t.ma_circle).attr("fill-opacity",.8);c(t.vo_circle).attr("fill-opacity",.8)}function E(t,e,a){event.preventDefault();const n=Number.parseFloat(t.attr("x"));const l=Number.parseFloat(t.attr("y"));const o=a.clientX;const r=a.clientY;const s=c(document.body);s.on("mousemove",(a=>{t.attr("x",n+a.clientX-o).attr("y",l+a.clientY-r);e.attr("x",n+a.clientX-o).attr("y",l+a.clientY-r)})).on("mouseup",(t=>{s.on("mousemove",null).on("mouseup",null)}))}function L(t,e,a,l){if(e.tracks){if(!t.ma_label){const o=n({x:a+20,y:l-50});o.header.text(t.gene);P(e,t.gene,o.body)}}A(t,e)}function P(t,e,a){fetch(new Request(t.hostURL+"/genelookup",{method:"POST",body:JSON.stringify({deep:1,input:e,genome:t.genome.name,jwt:t.jwt})})).then((t=>t.json())).then((n=>{if(n.error)throw{message:n.error};if(!n.gmlst\|\|n.gmlst.length==0)throw{message:"No genes can be found for "+e};const l=new Map;for(const t of n.gmlst){if(!l.has(t.chr)){l.set(t.chr,{chr:t.chr,start:t.start,stop:t.stop})}l.get(t.chr).start=Math.min(t.start,l.get(t.chr).start);l.get(t.chr).stop=Math.max(t.stop,l.get(t.chr).stop)}const o=[...l][0][1];const r=[...t.tracks];p(t.genome,r);f({holder:a,hostURL:t.hostURL,jwt:t.jwt,genome:t.genome,chr:o.chr,start:o.start,stop:o.stop,tklst:r,nobox:true})})).catch((t=>{l(a,t.message);if(t.stack)console.log(t.stack)}))}export{x as mavbparseinput,b as mavbui};

package/dist/{mds.fimo-bffccb9f.js → mds.fimo-8604c3f8.js} RENAMED Viewed

	@@ -1 +1 @@
1	- import{M as t,k as e,p as a,q as n,ah as r,a9 as o,ag as i,I as s,w as l}from"./app-2cd97738.js";import{c as p}from"./axis-747c801e.js";const f=80;const c=5;async function d(t){window.obj=t;t.errdiv=t.div.append("div");try{g(t);await h(t)}catch(e){t.errdiv.text(e.message\|\|e);if(e.stack)console.log(e.stack)}}function g(a){a.motifrowheight=16;a.gaincolor="red";a.losscolor="blue";a.flankspan=15;if(!a.fimo_thresh)a.fimo_thresh=.001;if(!a.minabslogp)a.minabslogp=1;a.tip=new t;const n=a.div.append("table").style("border-spacing","3px").style("border-collapse","separate").style("margin","10px");{const t=n.append("tr");t.append("td").text("Flanking sequence (#nt)");const r=t.append("td");r.append("input").attr("type","number").style("margin","0px 10px").style("width","100px").property("value",a.flankspan).on("keyup",(t=>{if(!e(t))return;const n=Number.parseInt(t.target.value);if(n<10){window.alert("Enter integer above 10");return}if(n==a.flankspan)return;a.flankspan=n;h(a)}));r.append("span").style("font-size","0.7em").style("opacity",.5).text("Press ENTER to update")}{const t=n.append("tr");t.append("td").text("P-value cutoff");const r=t.append("td");r.append("input").attr("type","number").style("margin","0px 10px").style("width","100px").property("value",a.fimo_thresh).on("keyup",(t=>{if(!e(t))return;const n=Number.parseFloat(t.target.value);if(n<=0){window.alert("Enter a p value between 0 to 1");return}if(n==a.fimo_thresh)return;a.fimo_thresh=n;h(a)}));r.append("span").style("font-size","0.7em").style("opacity",.5).text("Press ENTER to update")}{const t=n.append("tr");t.append("td").text("Minimum log10 p-value difference");const r=t.append("td");r.append("input").attr("type","number").style("margin","0px 10px").style("width","100px").property("value",a.minabslogp).on("keyup",(t=>{if(!e(t))return;const n=Number.parseFloat(t.target.value);if(n<=0){window.alert("Enter a number above 0");return}if(n==a.minabslogp)return;a.minabslogp=n;h(a)}));r.append("span").style("font-size","0.7em").style("opacity",.5).text("Press ENTER to update")}a.wait=a.div.append("div");a.svg=a.div.append("svg");a.dynamic_g=a.svg.append("g");a.legend={};a.legend.logpvaluediv=a.div.append("div");m(a)}function m(t){if(!t.factor_profiles)return;if(!Array.isArray(t.factor_profiles))throw"factor_profiles is not array";for(const e of t.factor_profiles){if(!e.name)throw"name missing for a profile";if(!e.leftpad)e.leftpad=20;if(!e.width)e.width=300;e.headerg=t.svg.append("g");e.textlabel=e.headerg.append("text").text(e.name).attr("x",e.width/2).attr("text-anchor","middle").attr("y",-30);if(e.isgenevalue){e.color="green";e.axisg=e.headerg.append("g");continue}if(e.isgenevalueonesample){if(!e.samplename)throw"samplename missing for isgenevalueonesample";e.barcolor="#62945B";e.axisg=e.headerg.append("g");continue}throw"unknown profile type"}}function h(t){a(t.wait.text("Loading..."));t.dynamic_g.selectAll("").remove();const e={genome:t.genome.name,m:t.m,fimo_thresh:t.fimo_thresh,flankspan:t.flankspan,minabslogp:t.minabslogp};return n("fimo",e).then((e=>{if(e.error)throw"Error: cannot do motif finding: "+e.error;if(t.callback_once){t.callback_once();delete t.callback_once}if(!e.items\|\|e.items.length==0)throw"Found no motif change due to this mutation";t.wait.style("display","none");for(const t of e.items){if(t.attr){t.gene=t.attr["Transcription factor"]}else{t.gene=t.name}}return u(e,t)})).catch((e=>{t.wait.style("display","block").text(e.message\|\|e);if(e.stack)console.log(e.stack)}))}async function u(t,e){x(t,e);if(e.factor_profiles){await b(t,e);let a=Number.parseInt(e.svg.attr("width"));for(const n of e.factor_profiles){n.headerg.attr("transform","translate("+(a+n.leftpad)+","+f+")");n.motifs=[];for(const e of t.items){const t=e.layer1_g.append("g").attr("transform","translate("+(a+n.leftpad)+",0)");n.motifs.push({motif:e,g:t,message:t.append("text").text("Loading...").attr("dominant-baseline","central").attr("fill","#ccc")})}a+=n.leftpad+n.width;e.svg.attr("width",a+5);await _(e,n);for(const e of t.items){e.bgbox.attr("width",a);e.coverbox.attr("width",a)}}}}function x(t,e){const a=14;const n=at.refseq.length;{const n=(e.m.pos-t.refstart+.5)a;const r=e.dynamic_g.append("g").attr("transform","translate("+n+","+f+")");r.append("rect").attr("x",-a/2).attr("y",-10).attr("width",a).attr("height",10).attr("fill","#666");r.append("text").attr("y",-15).attr("text-anchor","middle").text(e.m.chr+":"+e.m.pos+" "+e.m.ref+">"+e.m.alt)}let o=f+c;const i=1;const s=e.dynamic_g.append("g").attr("transform","translate(0,"+o+")");for(const[o,l]of t.items.entries()){l.g=s.append("g").attr("transform","translate(0,"+(e.motifrowheight(o+.5)+io)+")");l.layer1_g=l.g.append("g");l.layer2_g=l.g.append("g");l.bgbox=l.layer1_g.append("rect").attr("y",-e.motifrowheight/2).attr("width",n).attr("height",e.motifrowheight).attr("fill","white");const p=(l.start-t.refstart)a;const f=(Math.min(l.stop,t.refstop)-l.start)a;l.layer1_g.append("rect").attr("x",p).attr("y",-e.motifrowheight/2).attr("width",f).attr("height",e.motifrowheight).attr("fill",l.gain?e.gaincolor:e.losscolor).attr("fill-opacity",l.logpvaluediff/(l.gain?t.valuemax:t.valuemin));let c;if(l.strand=="+"){c="> "+l.name+" >"}else{c="< "+l.name+" <"}l.layer1_g.append("text").text(c).attr("x",p+f/2).attr("dominant-baseline","central").attr("text-anchor","middle").attr("stroke","white").attr("stroke-width",3).attr("font-size",e.motifrowheight-3).attr("font-family",r).style("white-space","pre");l.layer1_g.append("text").text(c).attr("x",p+f/2).attr("dominant-baseline","central").attr("text-anchor","middle").attr("font-size",e.motifrowheight-3).attr("font-family",r).style("white-space","pre");l.coverbox=l.layer2_g.append("rect").attr("y",-e.motifrowheight/2).attr("width",n).attr("height",e.motifrowheight).attr("fill","white").attr("fill-opacity",0).on("mouseover",(t=>{l.bgbox.attr("fill","#f9fabd");y(l,e,t)})).on("mouseout",(()=>{l.bgbox.attr("fill","white");e.tip.hide()}))}o+=(i+e.motifrowheight)t.items.length+20;v(t,e);e.svg.attr("width",n).attr("height",o)}function y(t,e,a){e.tip.clear();if(t.attr){e.tip.d.append("div").text("MOTIF").style("font-weight","bold");const a=[{k:"P-values",v:w(t,e)},{k:"Strand",v:t.strand}];o(e.tip.d,a);e.tip.d.append("div").text("FACTOR").style("font-weight","bold");const n=[];for(const e in t.attr){n.push({k:e,v:t.attr[e]})}o(e.tip.d,n)}else{const a=[{k:"TF",v:t.name},{k:"P-values",v:w(t,e)},{k:"Strand",v:t.strand}];o(e.tip.d,a)}e.tip.show(a.clientX,a.clientY)}function w(t,e){return(t.pvalue_ref==undefined?'<span style="opacity:.5;padding:2px"><span style="font-size:.7em">REF</span> not found</span>':'<span style="background-color:'+e.losscolor+';padding:2px;color:white;"><span style="font-size:.7em">REF</span> '+t.pvalue_ref+"</span>")+"<br>"+(t.pvalue_alt==undefined?'<span style="opacity:.5;padding:2px"><span style="font-size:.7em">ALT</span> not found</span>':'<span style="background-color:'+e.gaincolor+';padding:2px;color:white;"><span style="font-size:.7em">ALT</span> '+t.pvalue_alt+"</span>")}function v(t,e){e.legend.logpvaluediv.selectAll("").remove();const a=50,n=4,o=12,l=55,f=20;e.legend.logpvaluediv.append("span").text("Log10 p-value difference");const c=e.legend.logpvaluediv.append("svg").attr("width",(a+l)2).attr("height",o+n+f);const d=c.append("g").attr("transform","translate("+a+","+(o+n)+")");i({axis:d.call(p().scale(s().domain([t.valuemin,0,t.valuemax]).range([0,l,l2])).tickValues([t.valuemin,0,t.valuemax]).tickSize(n))});const g=Math.random().toString();const m=Math.random().toString();const h=c.append("defs");{const t=h.append("linearGradient").attr("id",m);t.append("stop").attr("offset","0%").attr("stop-color",e.losscolor);t.append("stop").attr("offset","100%").attr("stop-color","white")}{const t=h.append("linearGradient").attr("id",g);t.append("stop").attr("offset","0%").attr("stop-color","white");t.append("stop").attr("offset","100%").attr("stop-color",e.gaincolor)}c.append("rect").attr("x",a).attr("y",o+n).attr("width",l).attr("height",f).attr("fill","url(#"+m+")");c.append("rect").attr("x",a+l).attr("y",o+n).attr("width",l).attr("height",f).attr("fill","url(#"+g+")");c.append("text").attr("x",a-5).attr("y",o+n+f/2).attr("font-family",r).attr("font-size",o).attr("text-anchor","end").attr("dominant-baseline","central").attr("fill","black").text("Loss");c.append("text").attr("x",a+l2+5).attr("y",o+n+f/2).attr("font-family",r).attr("font-size",o).attr("dominant-baseline","central").attr("fill","black").text("Gain")}async function b(t,e){e.gene2position={};const a=new Set;for(const e of t.items){a.add(e.gene)}for(const t of a){const a=await k(t,e);if(a){e.gene2position[t]=a}}}function k(t,e){return n("genelookup",{genome:e.genome.name,input:t,deep:1}).then((t=>{if(!t.gmlst)return null;const e=l(t.gmlst);return e[0]}))}function _(t,e){if(e.isgenevalue){return M(t,e)}if(e.isgenevalueonesample){return E(t,e)}throw"unknown profile type"}async function E(t,e){const r={genome:t.genome.name,genes:[],sample:e.samplename};if(e.mdslabel){r.dslabel=e.mdslabel;r.querykey=e.querykey;if(e.samplegroup_attrlst){r.getgroup=e.samplegroup_attrlst}}else{r.iscustom=1;r.file=e.file;r.url=e.url;r.indexURL=e.indexURL}for(const e in t.gene2position){const a=t.gene2position[e];r.genes.push({gene:e,chr:a.chr,start:a.start,stop:a.stop})}return n("mdsgenevalueonesample",r).then((a=>{if(a.error)throw a.error;for(const t of e.motifs){t.message.text("No data")}if(a.nodata)return;if(!a.result)throw"error";let n=0,r=0;for(const t in a.result){n=Math.min(n,a.result[t]);r=Math.max(r,a.result[t])}const o=s().domain([n,r]).range([0,e.width]);i({axis:e.axisg.call(p().scale(o).ticks(4)),showline:1});for(const n of e.motifs){const r=a.result[n.motif.gene];if(Number.isFinite(r)){n.message.text("");n.g.append("rect").attr("y",-t.motifrowheight/2).attr("width",Math.max(1,o(r))).attr("height",t.motifrowheight).attr("shape-rendering","crispEdges").attr("fill",e.barcolor)}}e.textlabel.attr("x",e.width/2).attr("text-anchor","middle").attr("y",-30)})).catch((e=>{if(e.stack)console.log(e.stack);a(t.wait.text(e.message\|\|e))}))}async function M(t,e){e.gene2result=new Map;for(const a in t.gene2position){const n=await L(t,e,a);if(n){z(t,e,a,n);e.gene2result.set(a,n);F(t,e)}}N(t,e)}function z(t,e,a,n){if(n.nodata)return;for(const t of e.motifs){if(t.motif.gene!=a)continue;t.boxplot={out:[]};if(n.w1!=undefined){t.boxplot.hline=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.linew1=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.linew2=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.box=t.g.append("rect").attr("fill","white").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.linep50=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges")}if(n.out){for(const a of n.out){const n=t.g.append("circle").attr("stroke",e.color).attr("fill","white").attr("fill-opacity",0);t.boxplot.out.push({value:a.value,circle:n})}}}}function F(t,e){let a=0,n=0;for(const t of e.gene2result.values()){a=Math.min(a,t.min);n=Math.max(n,t.max)}const r=s().domain([a,n]).range([0,e.width]);const o=t.motifrowheight-2;for(const[t,a]of e.gene2result){for(const n of e.motifs){if(n.motif.gene!=t)continue;const e=n.boxplot;if(!e)continue;if(e.hline){const t=r(a.w1);const n=r(a.w2);const i=r(a.p25);const s=r(a.p50);const l=r(a.p75);e.hline.transition().attr("x1",t).attr("x2",n);e.linew1.transition().attr("x1",t).attr("x2",t).attr("y1",-o/2).attr("y2",o/2);e.linew2.transition().attr("x1",n).attr("x2",n).attr("y1",-o/2).attr("y2",o/2);e.box.transition().attr("x",i).attr("y",-o/2).attr("width",l-i).attr("height",o);e.linep50.transition().attr("x1",s).attr("x2",s).attr("y1",-o/2).attr("y2",o/2)}for(const t of e.out){t.circle.transition().attr("cx",r(t.value)).attr("r",o/3)}}}i({axis:e.axisg.transition().call(p().scale(r).ticks(4)),showline:1})}function L(t,e,a){const r=t.gene2position[a];const o={genome:t.genome.name,gene:a,chr:r.chr,start:r.start,stop:r.stop,getgroup2boxplot:1};if(e.mdslabel){o.dslabel=e.mdslabel;o.querykey=e.querykey;if(e.samplegroup_attrlst){o.getgroup=e.samplegroup_attrlst}}else{o.iscustom=1;o.file=e.file;o.url=e.url;o.indexURL=e.indexURL}return n("mdsgeneboxplot",o).then((t=>{if(t.error)throw"Error: "+t.error;if(t.nodata)throw"No data";for(const t of e.motifs){if(t.motif.gene==a){t.message.text("")}}return t})).catch((t=>{if(t.stack)console.log(t.stack);for(const n of e.motifs){if(n.motif.gene==a){n.message.text(t.message\|\|t)}}}))}function N(t,e){let a=0;for(const t of e.gene2result.values()){a=Math.max(a,t.n)}e.textlabel.text(e.name+" (n="+a+")").attr("x",e.width/2).attr("text-anchor","middle").attr("y",-30)}export{d as init};
1	+ import{M as t,k as e,p as a,q as n,ah as r,a9 as o,ag as i,I as s,w as l}from"./app-6fb77603.js";import{c as p}from"./axis-747c801e.js";const f=80;const c=5;async function d(t){window.obj=t;t.errdiv=t.div.append("div");try{g(t);await h(t)}catch(e){t.errdiv.text(e.message\|\|e);if(e.stack)console.log(e.stack)}}function g(a){a.motifrowheight=16;a.gaincolor="red";a.losscolor="blue";a.flankspan=15;if(!a.fimo_thresh)a.fimo_thresh=.001;if(!a.minabslogp)a.minabslogp=1;a.tip=new t;const n=a.div.append("table").style("border-spacing","3px").style("border-collapse","separate").style("margin","10px");{const t=n.append("tr");t.append("td").text("Flanking sequence (#nt)");const r=t.append("td");r.append("input").attr("type","number").style("margin","0px 10px").style("width","100px").property("value",a.flankspan).on("keyup",(t=>{if(!e(t))return;const n=Number.parseInt(t.target.value);if(n<10){window.alert("Enter integer above 10");return}if(n==a.flankspan)return;a.flankspan=n;h(a)}));r.append("span").style("font-size","0.7em").style("opacity",.5).text("Press ENTER to update")}{const t=n.append("tr");t.append("td").text("P-value cutoff");const r=t.append("td");r.append("input").attr("type","number").style("margin","0px 10px").style("width","100px").property("value",a.fimo_thresh).on("keyup",(t=>{if(!e(t))return;const n=Number.parseFloat(t.target.value);if(n<=0){window.alert("Enter a p value between 0 to 1");return}if(n==a.fimo_thresh)return;a.fimo_thresh=n;h(a)}));r.append("span").style("font-size","0.7em").style("opacity",.5).text("Press ENTER to update")}{const t=n.append("tr");t.append("td").text("Minimum log10 p-value difference");const r=t.append("td");r.append("input").attr("type","number").style("margin","0px 10px").style("width","100px").property("value",a.minabslogp).on("keyup",(t=>{if(!e(t))return;const n=Number.parseFloat(t.target.value);if(n<=0){window.alert("Enter a number above 0");return}if(n==a.minabslogp)return;a.minabslogp=n;h(a)}));r.append("span").style("font-size","0.7em").style("opacity",.5).text("Press ENTER to update")}a.wait=a.div.append("div");a.svg=a.div.append("svg");a.dynamic_g=a.svg.append("g");a.legend={};a.legend.logpvaluediv=a.div.append("div");m(a)}function m(t){if(!t.factor_profiles)return;if(!Array.isArray(t.factor_profiles))throw"factor_profiles is not array";for(const e of t.factor_profiles){if(!e.name)throw"name missing for a profile";if(!e.leftpad)e.leftpad=20;if(!e.width)e.width=300;e.headerg=t.svg.append("g");e.textlabel=e.headerg.append("text").text(e.name).attr("x",e.width/2).attr("text-anchor","middle").attr("y",-30);if(e.isgenevalue){e.color="green";e.axisg=e.headerg.append("g");continue}if(e.isgenevalueonesample){if(!e.samplename)throw"samplename missing for isgenevalueonesample";e.barcolor="#62945B";e.axisg=e.headerg.append("g");continue}throw"unknown profile type"}}function h(t){a(t.wait.text("Loading..."));t.dynamic_g.selectAll("").remove();const e={genome:t.genome.name,m:t.m,fimo_thresh:t.fimo_thresh,flankspan:t.flankspan,minabslogp:t.minabslogp};return n("fimo",e).then((e=>{if(e.error)throw"Error: cannot do motif finding: "+e.error;if(t.callback_once){t.callback_once();delete t.callback_once}if(!e.items\|\|e.items.length==0)throw"Found no motif change due to this mutation";t.wait.style("display","none");for(const t of e.items){if(t.attr){t.gene=t.attr["Transcription factor"]}else{t.gene=t.name}}return u(e,t)})).catch((e=>{t.wait.style("display","block").text(e.message\|\|e);if(e.stack)console.log(e.stack)}))}async function u(t,e){x(t,e);if(e.factor_profiles){await v(t,e);let a=Number.parseInt(e.svg.attr("width"));for(const n of e.factor_profiles){n.headerg.attr("transform","translate("+(a+n.leftpad)+","+f+")");n.motifs=[];for(const e of t.items){const t=e.layer1_g.append("g").attr("transform","translate("+(a+n.leftpad)+",0)");n.motifs.push({motif:e,g:t,message:t.append("text").text("Loading...").attr("dominant-baseline","central").attr("fill","#ccc")})}a+=n.leftpad+n.width;e.svg.attr("width",a+5);await _(e,n);for(const e of t.items){e.bgbox.attr("width",a);e.coverbox.attr("width",a)}}}}function x(t,e){const a=14;const n=at.refseq.length;{const n=(e.m.pos-t.refstart+.5)a;const r=e.dynamic_g.append("g").attr("transform","translate("+n+","+f+")");r.append("rect").attr("x",-a/2).attr("y",-10).attr("width",a).attr("height",10).attr("fill","#666");r.append("text").attr("y",-15).attr("text-anchor","middle").text(e.m.chr+":"+e.m.pos+" "+e.m.ref+">"+e.m.alt)}let o=f+c;const i=1;const s=e.dynamic_g.append("g").attr("transform","translate(0,"+o+")");for(const[o,l]of t.items.entries()){l.g=s.append("g").attr("transform","translate(0,"+(e.motifrowheight(o+.5)+io)+")");l.layer1_g=l.g.append("g");l.layer2_g=l.g.append("g");l.bgbox=l.layer1_g.append("rect").attr("y",-e.motifrowheight/2).attr("width",n).attr("height",e.motifrowheight).attr("fill","white");const p=(l.start-t.refstart)a;const f=(Math.min(l.stop,t.refstop)-l.start)a;l.layer1_g.append("rect").attr("x",p).attr("y",-e.motifrowheight/2).attr("width",f).attr("height",e.motifrowheight).attr("fill",l.gain?e.gaincolor:e.losscolor).attr("fill-opacity",l.logpvaluediff/(l.gain?t.valuemax:t.valuemin));let c;if(l.strand=="+"){c="> "+l.name+" >"}else{c="< "+l.name+" <"}l.layer1_g.append("text").text(c).attr("x",p+f/2).attr("dominant-baseline","central").attr("text-anchor","middle").attr("stroke","white").attr("stroke-width",3).attr("font-size",e.motifrowheight-3).attr("font-family",r).style("white-space","pre");l.layer1_g.append("text").text(c).attr("x",p+f/2).attr("dominant-baseline","central").attr("text-anchor","middle").attr("font-size",e.motifrowheight-3).attr("font-family",r).style("white-space","pre");l.coverbox=l.layer2_g.append("rect").attr("y",-e.motifrowheight/2).attr("width",n).attr("height",e.motifrowheight).attr("fill","white").attr("fill-opacity",0).on("mouseover",(t=>{l.bgbox.attr("fill","#f9fabd");y(l,e,t)})).on("mouseout",(()=>{l.bgbox.attr("fill","white");e.tip.hide()}))}o+=(i+e.motifrowheight)t.items.length+20;b(t,e);e.svg.attr("width",n).attr("height",o)}function y(t,e,a){e.tip.clear();if(t.attr){e.tip.d.append("div").text("MOTIF").style("font-weight","bold");const a=[{k:"P-values",v:w(t,e)},{k:"Strand",v:t.strand}];o(e.tip.d,a);e.tip.d.append("div").text("FACTOR").style("font-weight","bold");const n=[];for(const e in t.attr){n.push({k:e,v:t.attr[e]})}o(e.tip.d,n)}else{const a=[{k:"TF",v:t.name},{k:"P-values",v:w(t,e)},{k:"Strand",v:t.strand}];o(e.tip.d,a)}e.tip.show(a.clientX,a.clientY)}function w(t,e){return(t.pvalue_ref==undefined?'<span style="opacity:.5;padding:2px"><span style="font-size:.7em">REF</span> not found</span>':'<span style="background-color:'+e.losscolor+';padding:2px;color:white;"><span style="font-size:.7em">REF</span> '+t.pvalue_ref+"</span>")+"<br>"+(t.pvalue_alt==undefined?'<span style="opacity:.5;padding:2px"><span style="font-size:.7em">ALT</span> not found</span>':'<span style="background-color:'+e.gaincolor+';padding:2px;color:white;"><span style="font-size:.7em">ALT</span> '+t.pvalue_alt+"</span>")}function b(t,e){e.legend.logpvaluediv.selectAll("").remove();const a=50,n=4,o=12,l=55,f=20;e.legend.logpvaluediv.append("span").text("Log10 p-value difference");const c=e.legend.logpvaluediv.append("svg").attr("width",(a+l)2).attr("height",o+n+f);const d=c.append("g").attr("transform","translate("+a+","+(o+n)+")");i({axis:d.call(p().scale(s().domain([t.valuemin,0,t.valuemax]).range([0,l,l2])).tickValues([t.valuemin,0,t.valuemax]).tickSize(n))});const g=Math.random().toString();const m=Math.random().toString();const h=c.append("defs");{const t=h.append("linearGradient").attr("id",m);t.append("stop").attr("offset","0%").attr("stop-color",e.losscolor);t.append("stop").attr("offset","100%").attr("stop-color","white")}{const t=h.append("linearGradient").attr("id",g);t.append("stop").attr("offset","0%").attr("stop-color","white");t.append("stop").attr("offset","100%").attr("stop-color",e.gaincolor)}c.append("rect").attr("x",a).attr("y",o+n).attr("width",l).attr("height",f).attr("fill","url(#"+m+")");c.append("rect").attr("x",a+l).attr("y",o+n).attr("width",l).attr("height",f).attr("fill","url(#"+g+")");c.append("text").attr("x",a-5).attr("y",o+n+f/2).attr("font-family",r).attr("font-size",o).attr("text-anchor","end").attr("dominant-baseline","central").attr("fill","black").text("Loss");c.append("text").attr("x",a+l2+5).attr("y",o+n+f/2).attr("font-family",r).attr("font-size",o).attr("dominant-baseline","central").attr("fill","black").text("Gain")}async function v(t,e){e.gene2position={};const a=new Set;for(const e of t.items){a.add(e.gene)}for(const t of a){const a=await k(t,e);if(a){e.gene2position[t]=a}}}function k(t,e){return n("genelookup",{genome:e.genome.name,input:t,deep:1}).then((t=>{if(!t.gmlst)return null;const e=l(t.gmlst);return e[0]}))}function _(t,e){if(e.isgenevalue){return M(t,e)}if(e.isgenevalueonesample){return E(t,e)}throw"unknown profile type"}async function E(t,e){const r={genome:t.genome.name,genes:[],sample:e.samplename};if(e.mdslabel){r.dslabel=e.mdslabel;r.querykey=e.querykey;if(e.samplegroup_attrlst){r.getgroup=e.samplegroup_attrlst}}else{r.iscustom=1;r.file=e.file;r.url=e.url;r.indexURL=e.indexURL}for(const e in t.gene2position){const a=t.gene2position[e];r.genes.push({gene:e,chr:a.chr,start:a.start,stop:a.stop})}return n("mdsgenevalueonesample",r).then((a=>{if(a.error)throw a.error;for(const t of e.motifs){t.message.text("No data")}if(a.nodata)return;if(!a.result)throw"error";let n=0,r=0;for(const t in a.result){n=Math.min(n,a.result[t]);r=Math.max(r,a.result[t])}const o=s().domain([n,r]).range([0,e.width]);i({axis:e.axisg.call(p().scale(o).ticks(4)),showline:1});for(const n of e.motifs){const r=a.result[n.motif.gene];if(Number.isFinite(r)){n.message.text("");n.g.append("rect").attr("y",-t.motifrowheight/2).attr("width",Math.max(1,o(r))).attr("height",t.motifrowheight).attr("shape-rendering","crispEdges").attr("fill",e.barcolor)}}e.textlabel.attr("x",e.width/2).attr("text-anchor","middle").attr("y",-30)})).catch((e=>{if(e.stack)console.log(e.stack);a(t.wait.text(e.message\|\|e))}))}async function M(t,e){e.gene2result=new Map;for(const a in t.gene2position){const n=await L(t,e,a);if(n){z(t,e,a,n);e.gene2result.set(a,n);F(t,e)}}N(t,e)}function z(t,e,a,n){if(n.nodata)return;for(const t of e.motifs){if(t.motif.gene!=a)continue;t.boxplot={out:[]};if(n.w1!=undefined){t.boxplot.hline=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.linew1=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.linew2=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.box=t.g.append("rect").attr("fill","white").attr("stroke",e.color).attr("shape-rendering","crispEdges");t.boxplot.linep50=t.g.append("line").attr("stroke",e.color).attr("shape-rendering","crispEdges")}if(n.out){for(const a of n.out){const n=t.g.append("circle").attr("stroke",e.color).attr("fill","white").attr("fill-opacity",0);t.boxplot.out.push({value:a.value,circle:n})}}}}function F(t,e){let a=0,n=0;for(const t of e.gene2result.values()){a=Math.min(a,t.min);n=Math.max(n,t.max)}const r=s().domain([a,n]).range([0,e.width]);const o=t.motifrowheight-2;for(const[t,a]of e.gene2result){for(const n of e.motifs){if(n.motif.gene!=t)continue;const e=n.boxplot;if(!e)continue;if(e.hline){const t=r(a.w1);const n=r(a.w2);const i=r(a.p25);const s=r(a.p50);const l=r(a.p75);e.hline.transition().attr("x1",t).attr("x2",n);e.linew1.transition().attr("x1",t).attr("x2",t).attr("y1",-o/2).attr("y2",o/2);e.linew2.transition().attr("x1",n).attr("x2",n).attr("y1",-o/2).attr("y2",o/2);e.box.transition().attr("x",i).attr("y",-o/2).attr("width",l-i).attr("height",o);e.linep50.transition().attr("x1",s).attr("x2",s).attr("y1",-o/2).attr("y2",o/2)}for(const t of e.out){t.circle.transition().attr("cx",r(t.value)).attr("r",o/3)}}}i({axis:e.axisg.transition().call(p().scale(r).ticks(4)),showline:1})}function L(t,e,a){const r=t.gene2position[a];const o={genome:t.genome.name,gene:a,chr:r.chr,start:r.start,stop:r.stop,getgroup2boxplot:1};if(e.mdslabel){o.dslabel=e.mdslabel;o.querykey=e.querykey;if(e.samplegroup_attrlst){o.getgroup=e.samplegroup_attrlst}}else{o.iscustom=1;o.file=e.file;o.url=e.url;o.indexURL=e.indexURL}return n("mdsgeneboxplot",o).then((t=>{if(t.error)throw"Error: "+t.error;if(t.nodata)throw"No data";for(const t of e.motifs){if(t.motif.gene==a){t.message.text("")}}return t})).catch((t=>{if(t.stack)console.log(t.stack);for(const n of e.motifs){if(n.motif.gene==a){n.message.text(t.message\|\|t)}}}))}function N(t,e){let a=0;for(const t of e.gene2result.values()){a=Math.max(a,t.n)}e.textlabel.text(e.name+" (n="+a+")").attr("x",e.width/2).attr("text-anchor","middle").attr("y",-30)}export{d as init};

package/dist/{mds.samplescatterplot-b3908cc7.js → mds.samplescatterplot-3f09ae0e.js} RENAMED Viewed

	@@ -1 +1 @@
1	- import{d as e,M as t,j as s,a7 as a,a8 as l,I as o,a9 as n,k as i,N as r,Z as c,v as p,aa as d,q as m,ab as f,p as u,ac as y,ad as b,f as v}from"./app-2cd97738.js";import{s as x}from"./legacy-d3-polyfill-bdb2d792.js";import{b as g}from"./block.lazyload-eda77d9b.js";import{d as h}from"./lasso-e8b9500e.js";import{d as _}from"./zoom-d6ef6f3f.js";import{f as k}from"./FilterStateless-b1c6ee04.js";import{e as w}from"./FilterRxComp-0f35b322.js";import"./termsetting-ad8c4f3a.js";import{g as O}from"./filter-b3d3964e.js";import"./drag-d8daa62f.js";import"./nodrag-ab7d5a9f.js";import"./pointer-c7475677.js";import"./table-f50a9344.js";import"./tslib.es6-c3c2d88f.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-01e8cce6.js";import"path";function j(e){const t={waitTime:0,pad:5,nameKey:"",steps:[{type:"restyle",applyTo:"all",css:{selector:"text",key:"font-size",value:"12px"}},{type:"move",repeat:2,pad:0,css:{selector:"text"},boxSorter:(e,t)=>{if(e.x1>t.x1)return-1;if(t.x1>e.x1)return 1;if(e.y1>t.y1)return-1;if(t.y1>e.y1)return 1;return 0}}]};return Object.assign(t,e)}async function z(e,t={}){if(!e\|\|!e.size())return;const s=j(t);if(!s.steps\|\|!s.steps.length)return;if(!s.svg)s.svg=e.node().closest("svg");await R(s.waitTime);s.svgBox=s.svg.getBoundingClientRect();const a=S(e,s);const l=A(a);window.boxes=a;if(l){const t=s.steps.shift();const o=t.applyTo=="all"?a:t.type=="move"?a.filter((e=>e.collisions.length)):a.filter((e=>e.collisions.length===l));if(o.length){if(t.boxSorter)o.sort(t.boxSorter);for(const e of o){const l=S(e.label,s)[0];Object.assign(e,l);F(e,a.filter((t=>t!=e)));await C[t.type](e,t,a,s)}}if(typeof t.repeat=="number"&&t.repeat>0){t.repeat+=-1;s.steps.unshift(t)}if(s.steps.length)setTimeout((()=>z(e,s)),0);else a.forEach(B)}else a.forEach(B)}function S(t,s){const a=[];t.each((function(t){const l=this;const o=l.getBoundingClientRect();const 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a.entries()){if(e<=2)continue;t.sample_attributes[s]={label:s}}}if(!t.colorbyattributes&&a.length>3)t.colorbyattributes=[{key:a[3]}]}else{throw"unknown data encoding in .analysisdata{}"}e.sample2dot=new Map;for(const s of e.dots){if(!Number.isFinite(s.x)\|\|!Number.isFinite(s.y))throw"non-numeric x/y for a sample";if(t.samplekey){s.sample=s[t.samplekey];delete s[t.samplekey]}if(t.sample_attributes){s.s={};for(const e in t.sample_attributes){s.s[e]=s[e];delete s[e]}}e.sample2dot.set(s.sample,s)}e.sample_attributes=t.sample_attributes;e.colorbyattributes=t.colorbyattributes;e.attr_levels=t.attr_levels;if(t.user_samples){if(!Array.isArray(t.user_samples))throw".user_samples[] is not array";e.dots_user=[];for(const s of t.user_samples){if(!Number.isFinite(s.x)\|\|!Number.isFinite(s.y))throw"non-numeric x/y for a USER sample";if(t.samplekey){s.sample=s[t.samplekey];delete 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a=[{k:"Sample",v:s.sample}];if(t.sample_attributes){for(const e in t.sample_attributes){const l=t.sample_attributes[e];s.s[e];a.push({k:l.label,v:s.s[e]})}}n(t.tip.clear().d,a);t.tip.show(e.clientX,e.clientY)})).on("mouseout",((e,s)=>{e.target.setAttribute("stroke","none");t.tip.hide()})).on("click",((e,s)=>{Q(s,t,e)}));t.dotselection=S;let A,M,F,N,E;const T=t.userlabel_grp={userlabels:N,userlabel_borders:E};if(t.dots_user){A=O.selectAll().data(t.dots_user).enter().append("g").attr("class","sample_dot");M=A.append("circle").attr("stroke","none").attr("fill",(e=>e.color)).attr("r",q).on("mouseover",((e,s)=>{const a=[{k:"Sample",v:s.sample}];if(t.sample_attributes){for(const e in t.sample_attributes){const 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OF GENE CRITERIA").attr("class","sja_clbtext").on("click",(()=>{if(m.style("display")=="none"){u(m)}else{y(m)}}));const f=m.append("div");const b=f.append("div").style("display","table-cell").style("width","110px");b.append("div").text("Consequences").style("padding-right","15px");const v=f.append("div").style("display","table-cell").style("border-left","solid 1px #ededed");r.forEach((e=>{const t=v.append("div");const s=t.append("input").attr("type","checkbox").attr("name","mut_type").attr("value",e.db_col).style("margin","3px").style("margin-left","4px").property("checked",e.default);s.on("change",(()=>{if(s.node().checked){l.push(s.node().value)}else{l=l.filter((e=>e!==s.node().value))}}));t.append("label").attr("for",e.db_col).html(e.label)}));const x=v.append("input").attr("type","checkbox").attr("name","noncnv").attr("value","cnv").style("margin","3px").style("margin-left","4px").property("checked",p?true:false).on("change",(()=>{if(x.node().checked){k.property("disabled",false);w.property("disabled",false)}else{k.property("disabled",true);w.property("disabled",true)}}));v.append("label").attr("for","cnv").text("CNV");const g=v.append("div").style("display","block").style("padding","3px 15px");const h=[...new Set(c.map((e=>e.sizecutoff)))];const _=[...new Set(c.map((e=>e.log2cutoff)))];g.append("label").attr("for","cnv_size").style("margin","2px 10px").text("Size cutoff");const k=g.append("select").attr("name","cnv_size");h.forEach((e=>{k.append("option").attr("value",e).text(e)}));k.property("selectedIndex",p.sizecutoff=="1Mb"?0:p.sizecutoff=="2Mb"?1:2);g.append("label").attr("for","log2_ratio").style("margin","2px 10px").text("log2(ratio) cutoff");const w=g.append("select").attr("name","log2_ratio");_.forEach((e=>{w.append("option").attr("value",e.toFixed(1)).text(e.toFixed(1))}));w.property("selectedIndex",p.log2cutoff==.1?0:p.log2cutoff==.2?1:2);const O=m.append("div").style("padding-top","10px");const j=O.append("div").style("display","table-cell").style("width","110px");j.append("div").text("No. of Genes").style("padding-right","15px");const z=O.append("div").style("display","table-cell").style("padding","3px").style("border-left","solid 1px #ededed");const S=[10,15,20,30,40];const A=z.append("select").attr("name","gene_n");S.forEach((e=>{A.append("option").attr("value",e).text(e)}));A.property("selectedIndex",S.findIndex((e=>e==n)));m.append("button").style("margin","10px").style("padding","3px 10px").text("Calculate").on("click",(()=>{const s=v.node().querySelectorAll("input:checked");l=[];s.forEach((e=>{if(e.value!=="cnv"&&!l.includes(e.value))l.push(e.value);else if(e.value=="cnv"){const e=k.node().value;const t=w.node().value;o=c.find((s=>s.sizecutoff==e&&s.log2cutoff==t));l.push(o.db_col)}}));n=A.node().value;oe(e,t,l,n);a=[...l]}))}else a=["total"];oe(e,t,a,n)}async function oe(e,t,s,l){try{const o={genome:e.genome.name,dslabel:e.mds.label,samples:t,selectedMutTypes:s,nGenes:l};const n=await a("mdsgenecount",{method:"POST",body:JSON.stringify(o)});if(n.error)throw n.error;if(!n.genes)throw".genes missing";if(!n.genes.length){e.pane.wait.html("No gene retrived with mutations.");e.pane.matrix_criteria_div.style("display","none");return}ne({obj:e,genes:n.genes,samples:t,holder:e.pane.body});e.pane.wait.remove()}catch(t){e.pane.wait.text("Error: "+(t.message\|\|t));if(t.stack)console.log(t.stack)}}function ne(e){const{obj:t,genes:s,samples:a}=e;const l=t.pane.sample_matrix_div;l.selectAll("*").remove();for(const e of s){e.ismutation=true;e.genename=e.gene;e.label=e.gene;delete e.gene;e.querykeylst=["svcnv","snvindel"];t.features_on_rows?e.height=50:e.width=50}const o={genome:t.genome,dslabel:t.mds.label,features:s,features_on_rows:t.features_on_rows,ismutation_allsymbolic:true,hostURL:sessionStorage.getItem("hostURL")\|\|"",limitbysamplesetgroup:{samples:a},jwt:sessionStorage.getItem("jwt")\|\|"",holder:l.append("div").style("margin","20px")};import("./samplematrix-1192e5e2.js").then((e=>{const t=new e.Samplematrix(o);t._pane=l}))}function ie(e){const{obj:t,dot:s,sampletracks:a,holder:l}=e;const o={genome:t.genome,hostURL:sessionStorage.getItem("hostURL")\|\|"",jwt:sessionStorage.getItem("jwt")\|\|"",holder:l,chr:t.genome.defaultcoord.chr,start:t.genome.defaultcoord.start,stop:t.genome.defaultcoord.stop,nobox:1,tklst:[]};if(t.tracks){for(const e of t.tracks)o.tklst.push(e)}const n=t.mds.queries[t.querykey];if(n){const e={singlesample:{name:s.sample},mds:t.mds,querykey:t.querykey};for(const t in n){e[t]=n[t]}o.tklst.push(e);if(n.checkexpressionrank){const e={type:b.mdsexpressionrank,name:s.sample+" gene expression rank",dslabel:t.mds.label,querykey:n.checkexpressionrank.querykey,sample:s.sample};if(n.groupsamplebyattr){const t=n.groupsamplebyattr.attrlst;if(t&&t.length){e.attributes=[];for(const a of t){e.attributes.push({k:a.k,label:a.label,kvalue:s.s[a.k]})}}}o.tklst.push(e)}}if(a){for(const e of a)o.tklst.push(e)}v(t.genome,o.tklst);g(o)}export{X as init};
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n=S(t.label,l)[0];a.indexOf(t);F(n,a.filter((e=>e!=t)));if(s.applyTo=="all"){Object.assign(t,n)}else{if(n.overlapSum>=t.overlapSum){t.label.selectAll(s.css.selector).each((function(t){e(this).attr(s.css.key,o.get(this))}))}else{Object.assign(t,n)}}}async function T(t,s,a,l){const o=Object.keys(t.maxFree).filter((e=>t.maxFree[e]>0));if(!o.length)return;const n=new Map;if(t.maxOverlaps.y&&t.maxOverlaps.y.val>0){if(t.maxOverlaps.y.dir=="s"&&o.includes("n")){t.label.selectAll(s.css.selector).each((function(a){const l=e(this);n.set(this,l.attr("y")\|\|0);l.attr("y",Math.max(-t.maxFree.n,-t.maxOverlaps.y.val)-s.pad)}))}if(t.maxOverlaps.y.dir=="n"&&o.includes("s")){t.label.selectAll(s.css.selector).each((function(a){const l=e(this);n.set(this,l.attr("y")\|\|0);l.attr("y",Math.min(t.maxFree.s,t.maxOverlaps.y.val)+s.pad)}))}}if(n.size){await R(l.waitTime);const o=S(t.label,l)[0];F(o,a.filter((e=>e!=t)));if(o.overlapSum>=t.overlapSum){t.label.selectAll(s.css.selector).each((function(t){e(this).attr("y",n.get(this))}))}else{Object.assign(t,o);if(!t.collisions.length)return}}if(t.maxOverlaps.x&&t.maxOverlaps.x.val>0){if(t.maxOverlaps.x.dir=="e"&&o.includes("w")){t.label.selectAll(s.css.selector).each((function(a){const l=e(this);n.set(this,l.attr("x")\|\|0);l.attr("x",Math.max(-t.maxFree.w,-t.maxOverlaps.x.val)-s.pad)}))}if(t.maxOverlaps.x.dir=="w"&&o.includes("e")){t.label.selectAll(s.css.selector).each((function(a){const l=e(this);n.set(this,l.attr("x")\|\|0);l.attr("x",Math.min(t.maxFree.e,t.maxOverlaps.x.val)+s.pad)}))}}if(!n.size)return;await R(l.waitTime);const i=S(t.label,l)[0];F(i,a.filter((e=>e!=t)));if(i.overlapSum>=t.overlapSum){t.label.selectAll(s.css.selector).each((function(t){e(this).attr("x",n.get(this))}))}else{Object.assign(t,i)}}const C={restyle:E,move:T};function B(e){return}function R(e){return new 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#858585");if(a){e.dotselection.transition().attr("r",(e=>e.s[t.key]==s?q:L))}else{e.dotselection.filter((e=>e.s[t.key]==s)).transition().attr("r",q)}}));o.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background",l.color).style("margin-right","3px").text(l.count);o.append("div").style("display","inline-block").style("color",l.color).text(l.name\|\|s);l.cell=o}}}function V(t){const s=t.dots.filter((e=>t.filteredSamples.has(e.sample)));const a=Array.from(s,(e=>e.s));const l=t.attr_levels?.[0].label\|\|t.attr_levels?.[0].key;const o=[...new Set(Array.from(a,(e=>e[l])))];const n=t.attr_levels?.[1].label\|\|t.attr_levels?.[1].key;const i=[...new Set(Array.from(a,(e=>e[n])))];const r=t.legendtable.node().querySelectorAll(".sja_lb_div");for(const t of r){const s=e(t).select(".sja_l1lb").node().innerText.split(/\s{2}n=/)[0];if(!o.includes(s))e(t).style("display","none");else{e(t).style("display","block");const s=e(t).node().querySelectorAll(".sja_clb");for(const t of s){const s=e(t).node().querySelectorAll("div")[1];if(!i.includes(s.innerText))e(t).style("display","none");else e(t).style("display","inline-block")}}}}function Q(e,t,s){if(t.dslabel){ee(e,t,s);return}if(t.mds){$(e,t,s);return}}async function $(e,t,s){const a=c({x:s.clientX,y:s.clientY});a.header.text(e.sample);const l=p(a.body);try{const s=await d();const o={genome:t.genome.name,dslabel:t.mds.label,querykey:t.mds.querykey,getsample4disco:e.sample};const n=await m("/mdssvcnv",o);if(n.error)throw n.error;if(!n.text)throw".text missing";const i=a.body.append("div");const r=await s.dtDisco({holderSelector:i,chromosomeType:t.genome.name,majorchr:t.genome.majorchr,settings:{showControls:false,selectedSamples:[]},callbacks:{geneLabelClick:{type:"genomepaint",hostURL:sessionStorage.getItem("hostURL")\|\|"",genome:t.genome.name,dslabel:t.mds.label,sample:e.sample}}});const c={sampleName:e.sample,data:JSON.parse(n.text)};r.main(c);l.remove()}catch(e){l.text("Error: "+(e.message\|\|e));if(e.stack)console.log(e.stack)}}function ee(e,t,s){const a=c({x:s.clientX,y:s.clientY});a.header.text(e.sample);const l=a.body.append("div").style("margin","20px").text("Loading ...");m("/mdssvcnv",{genome:t.genome.name,dslabel:t.dslabel,querykey:t.querykey,gettrack4singlesample:e.sample}).then((s=>{l.remove();ie({obj:t,dot:e,sampletracks:s.tracks,holder:a.body})}))}function te(e,t){const s=e.scattersvg;let a;if(e.lasso_active){a=h().items(t.selectAll("circle")).targetArea(s);a.on("start",l).on("draw",o).on("end",n);s.call(a)}else{s.selectAll(".lasso").remove();s.on("mousedown.drag",null)}function l(){if(!e.lasso_active)return;a.items().attr("r",2).style("fill-opacity",".5").classed("not_possible",true).classed("selected",false)}function o(){if(!e.lasso_active)return;a.possibleItems().attr("r",q).style("fill-opacity","1").classed("not_possible",false).classed("possible",true)}function n(t){if(!e.lasso_active)return;const l=s.selectAll(".possible").data().map((e=>e.sample));if(l.length)i(t,l);else e.menu.hide();a.items().classed("not_possible",false).classed("possible",false);a.selectedItems().attr("r",q);a.notSelectedItems().attr("r",l.length==0?q:L).style("fill-opacity","1")}function i(t,s){e.menu.clear().show(t.sourceEvent.clientX-90,t.sourceEvent.clientY);if(e.mds&&e.mds.gene2mutcount){e.menu.d.append("div").attr("class","sja_menuoption").text("Recurrently mutated genes").on("click",(async()=>{e.menu.hide();await ae(e,s)}))}for(const t of e.lasso.postSelectMenuOptions){e.menu.d.append("div").attr("class","sja_menuoption").text(t.label).on("click",(async()=>{e.menu.hide();const a={samples:s,sample_attributes:e.sample_attributes,sample2dot:e.sample2dot};if(t.callback=="listSamples")se(a);else t.callback(a)}))}e.menu.d.append("div").attr("class","sja_menuoption").text("Cancel").on("click",(()=>{a.items().classed("not_possible",false).classed("possible",false).attr("r",q).style("fill-opacity","1");e.menu.hide()}));e.menu.d.append("div").style("padding","10px").style("font-size",".8em").style("width","150px").text(s.length+" samples selected")}}function se(e){const{samples:t,sample_attributes:s,sample2dot:a}=e;const l=Object.keys(s);let o=l.map((e=>s[e].label?s[e].label:e));o.unshift("Sample");const n=o.join("\t");const i=[n];for(const e of t){if(a.get(e).s){let t=[];t.push(e);for(const s of l)t.push(a.get(e).s[s]);i.push(t.join("\t"))}}f("List of selected samples",[{text:i.join("\n")}])}function ae(e,t){e.pane=c({x:event.clientX,y:event.clientY});e.pane.header.text("Recurrently Mutated Genes");e.pane.wait=p(e.pane.body);e.pane.matrix_criteria_div=e.pane.body.append("div");e.pane.sample_matrix_div=e.pane.body.append("div");le(e,t)}function le(e,t){let s=[],a=[],l=[],o,n=15;const i=e.pane.matrix_criteria_div;if(e.mds.mutCountType){s=e.mds.mutCountType;const r=s.filter((e=>!e.db_col.includes("cnv")));const c=s.filter((e=>e.db_col.includes("cnv")));const p=c.find((e=>e.default));o=p;a=s.filter((e=>e.default)).map((e=>e.db_col));l=[...a];const d=i.append("div").style("margin","5px 20px");const m=i.append("div").style("margin","5px 20px").style("padding","5px").style("border-top","solid 1px #ededed").style("border-bottom","solid 1px #ededed").style("background-color","#FCFBF7").style("font-size",".8em");d.append("span").style("margin-right","20px").style("font-size",".8em").text("MUTATION COUNT & NO. OF GENE CRITERIA").attr("class","sja_clbtext").on("click",(()=>{if(m.style("display")=="none"){u(m)}else{y(m)}}));const f=m.append("div");const b=f.append("div").style("display","table-cell").style("width","110px");b.append("div").text("Consequences").style("padding-right","15px");const v=f.append("div").style("display","table-cell").style("border-left","solid 1px #ededed");r.forEach((e=>{const t=v.append("div");const s=t.append("input").attr("type","checkbox").attr("name","mut_type").attr("value",e.db_col).style("margin","3px").style("margin-left","4px").property("checked",e.default);s.on("change",(()=>{if(s.node().checked){l.push(s.node().value)}else{l=l.filter((e=>e!==s.node().value))}}));t.append("label").attr("for",e.db_col).html(e.label)}));const x=v.append("input").attr("type","checkbox").attr("name","noncnv").attr("value","cnv").style("margin","3px").style("margin-left","4px").property("checked",p?true:false).on("change",(()=>{if(x.node().checked){k.property("disabled",false);w.property("disabled",false)}else{k.property("disabled",true);w.property("disabled",true)}}));v.append("label").attr("for","cnv").text("CNV");const g=v.append("div").style("display","block").style("padding","3px 15px");const h=[...new Set(c.map((e=>e.sizecutoff)))];const _=[...new Set(c.map((e=>e.log2cutoff)))];g.append("label").attr("for","cnv_size").style("margin","2px 10px").text("Size cutoff");const k=g.append("select").attr("name","cnv_size");h.forEach((e=>{k.append("option").attr("value",e).text(e)}));k.property("selectedIndex",p.sizecutoff=="1Mb"?0:p.sizecutoff=="2Mb"?1:2);g.append("label").attr("for","log2_ratio").style("margin","2px 10px").text("log2(ratio) cutoff");const w=g.append("select").attr("name","log2_ratio");_.forEach((e=>{w.append("option").attr("value",e.toFixed(1)).text(e.toFixed(1))}));w.property("selectedIndex",p.log2cutoff==.1?0:p.log2cutoff==.2?1:2);const O=m.append("div").style("padding-top","10px");const j=O.append("div").style("display","table-cell").style("width","110px");j.append("div").text("No. of Genes").style("padding-right","15px");const z=O.append("div").style("display","table-cell").style("padding","3px").style("border-left","solid 1px #ededed");const S=[10,15,20,30,40];const A=z.append("select").attr("name","gene_n");S.forEach((e=>{A.append("option").attr("value",e).text(e)}));A.property("selectedIndex",S.findIndex((e=>e==n)));m.append("button").style("margin","10px").style("padding","3px 10px").text("Calculate").on("click",(()=>{const s=v.node().querySelectorAll("input:checked");l=[];s.forEach((e=>{if(e.value!=="cnv"&&!l.includes(e.value))l.push(e.value);else if(e.value=="cnv"){const e=k.node().value;const t=w.node().value;o=c.find((s=>s.sizecutoff==e&&s.log2cutoff==t));l.push(o.db_col)}}));n=A.node().value;oe(e,t,l,n);a=[...l]}))}else a=["total"];oe(e,t,a,n)}async function oe(e,t,s,l){try{const o={genome:e.genome.name,dslabel:e.mds.label,samples:t,selectedMutTypes:s,nGenes:l};const n=await a("mdsgenecount",{method:"POST",body:JSON.stringify(o)});if(n.error)throw n.error;if(!n.genes)throw".genes missing";if(!n.genes.length){e.pane.wait.html("No gene retrived with mutations.");e.pane.matrix_criteria_div.style("display","none");return}ne({obj:e,genes:n.genes,samples:t,holder:e.pane.body});e.pane.wait.remove()}catch(t){e.pane.wait.text("Error: "+(t.message\|\|t));if(t.stack)console.log(t.stack)}}function ne(e){const{obj:t,genes:s,samples:a}=e;const l=t.pane.sample_matrix_div;l.selectAll("*").remove();for(const e of s){e.ismutation=true;e.genename=e.gene;e.label=e.gene;delete e.gene;e.querykeylst=["svcnv","snvindel"];t.features_on_rows?e.height=50:e.width=50}const o={genome:t.genome,dslabel:t.mds.label,features:s,features_on_rows:t.features_on_rows,ismutation_allsymbolic:true,hostURL:sessionStorage.getItem("hostURL")\|\|"",limitbysamplesetgroup:{samples:a},jwt:sessionStorage.getItem("jwt")\|\|"",holder:l.append("div").style("margin","20px")};import("./samplematrix-0841387f.js").then((e=>{const t=new e.Samplematrix(o);t._pane=l}))}function ie(e){const{obj:t,dot:s,sampletracks:a,holder:l}=e;const o={genome:t.genome,hostURL:sessionStorage.getItem("hostURL")\|\|"",jwt:sessionStorage.getItem("jwt")\|\|"",holder:l,chr:t.genome.defaultcoord.chr,start:t.genome.defaultcoord.start,stop:t.genome.defaultcoord.stop,nobox:1,tklst:[]};if(t.tracks){for(const e of t.tracks)o.tklst.push(e)}const n=t.mds.queries[t.querykey];if(n){const e={singlesample:{name:s.sample},mds:t.mds,querykey:t.querykey};for(const t in n){e[t]=n[t]}o.tklst.push(e);if(n.checkexpressionrank){const e={type:b.mdsexpressionrank,name:s.sample+" gene expression rank",dslabel:t.mds.label,querykey:n.checkexpressionrank.querykey,sample:s.sample};if(n.groupsamplebyattr){const t=n.groupsamplebyattr.attrlst;if(t&&t.length){e.attributes=[];for(const a of t){e.attributes.push({k:a.k,label:a.label,kvalue:s.s[a.k]})}}}o.tklst.push(e)}}if(a){for(const e of a)o.tklst.push(e)}v(t.genome,o.tklst);g(o)}export{X as init};