Merge pull request #82 from lrgr/events-and-sig-types

Events and sig types

src/api.js

@@ -1,5 +1,11 @@
 import * as d3 from 'd3';
 import { getHashCode } from './helpers';
+import { MUT_TYPES } from './constants';
+
+import Signature from './classes/Signature';
+import Project from './classes/Project';
+import SignatureGroup from './classes/SignatureGroup';
+import CancerType from './classes/CancerType';
 
 const globalPlotData = {};
 
@@ -31,23 +37,81 @@ export default class API {
         return fetch(url, { method: "POST" })
             .then(function(response) {
                 return response.json();
+            })
+            .then(function(allData) {
+                let signatures = {};
+                for(let mutType of MUT_TYPES) {
+                    signatures[mutType] = allData['sigs'][mutType].map((sigData) => {
+                        return new Signature(
+                            sigData['name'],
+                            sigData['description'],
+                            sigData['index'],
+                            sigData['publication'],
+                            mutType
+                        );
+                    });
+                }
+                let projects = {};
+                for(var projID of Object.keys(allData['projects'])) {
+                    let projData = allData['projects'][projID];
+                    projects[projID] = new Project(
+                        projID,
+                        projData['name'],
+                        projData['num_donors'],
+                        projData['source'],
+                        projData['has_clinical'],
+                        projData['has_extended'],
+                        projData['has_counts']
+                    );
+                }
+                let sigGroups = [];
+                for(let sigGroupData of allData['sigs_per_cancer_type']) {
+                    let sigGroup = new SignatureGroup(
+                        sigGroupData['id'], 
+                        sigGroupData['group']
+                    );
+                    for(let cancerTypeData of sigGroupData['cancer-types']) {
+                        let cancerType = new CancerType(
+                            cancerTypeData['id'], 
+                            cancerTypeData['name'],
+                            cancerTypeData['signatures']
+                        );
+                        sigGroup.addCancerType(cancerType);
+                    }
+                    sigGroups.push(sigGroup);
+                }
+                return {
+                    'sigs': signatures,
+                    'projects': projects,
+                    'sigs_per_cancer_type': sigGroups
+                };
             });
     }
 
-    // Fetches with cacheing
-    static fetchChromosomes() {
-        let url = API.api_base + "chromosomes";
+    static fetchAutocompleteGene(partialGeneId) {
+        let url = API.api_base + "autocomplete-gene";
 
-        return API.request(
-            fetch(url, { method: "POST" })
-                .then(function(response) {
-                    return response.json();
-                }), 
-            url,
-            null
-        );
+        let body = {
+            "gene_id_partial": partialGeneId
+        };
+
+        return fetch(url, { method: "POST", body: JSON.stringify(body) })
+            .then(function(response) {
+                return response.json();
+            });
     }
 
+    static fetchGeneEventTrack(dataOptions) {
+        let url = API.api_base + "genome-event-track";
+
+        return fetch(url, { method: "POST", body: JSON.stringify(dataOptions) })
+            .then(function(response) {
+                return response.json();
+            });
+    }
+
+    // Fetches with cacheing
+
     static fetchKaryotype() {
         let url = API.api_base + "karyotype";
 
@@ -98,8 +162,8 @@ export default class API {
         );
     }
 
-    static fetchSingleDonorExposures(dataOptions) {
-        let url = API.api_base + "exposures-single-donor";
+    static fetchSingleSampleExposures(dataOptions) {
+        let url = API.api_base + "exposures-single-sample";
 
         return API.request(
             d3.json(url, { method: "POST", body: JSON.stringify(dataOptions) }),
@@ -128,8 +192,8 @@ export default class API {
         );
     }
 
-    static fetchSingleDonorGenomeSignatureBins(dataOptions) {
-        let url = API.api_base + "signature-genome-bins-single-donor";
+    static fetchSingleSampleGenomeSignatureBins(dataOptions) {
+        let url = API.api_base + "signature-genome-bins-single-sample";
         dataOptions['regionWidth'] = 5000000;
 
         return API.request(
@@ -148,4 +212,6 @@ export default class API {
             dataOptions
         );
     }
+
+
 }

src/classes/CancerType.js

@@ -0,0 +1,28 @@
+import { MUT_TYPES } from './../constants.js';
+
+export default class CancerType {
+
+    constructor(id, name, signatures) {
+        this.name = name; // string
+        this.id = id; // string
+        this.signatures = {};
+        for(let mutType of MUT_TYPES) {
+            if(signatures.hasOwnProperty(mutType)) {
+                this.signatures[mutType] = signatures[mutType];
+            } else {
+                this.signatures[mutType] = [];
+            }
+        }
+    }
+
+    get signaturesFlat() {
+        let result = [];
+        for(let mutType of MUT_TYPES) {
+            for(let sig of this.signatures[mutType]) {
+                result.push(sig);
+            }
+        }
+        return result;
+    }
+
+}

src/classes/Project.js

@@ -0,0 +1,13 @@
+export default class Project {
+
+    constructor(id, name, numDonors, source, hasClinical, hasExtended, hasCounts) {
+        this.id = id;
+        this.name = name;
+        this.numDonors = numDonors;
+        this.source = source;
+        this.hasClinical = hasClinical;
+        this.hasExtended = hasExtended;
+        this.hasCounts = hasCounts;
+    }
+
+}

src/classes/Signature.js

@@ -0,0 +1,12 @@
+
+export default class Signature {
+
+    constructor(name, description, index, publication, mutType) {
+        this.name = name;
+        this.description = description;
+        this.index = index;
+        this.publication = publication;
+        this.mutType = mutType;
+    }
+
+}

src/classes/SignatureGroup.js

@@ -0,0 +1,13 @@
+export default class SignatureGroup {
+
+    constructor(id, name) {
+        this.id = id;
+        this.name = name;
+        this.cancerTypes = [];
+    }
+
+    addCancerType(cancerType) {
+        this.cancerTypes.push(cancerType);
+    }
+
+}

src/colors.js

@@ -0,0 +1,49 @@
+export const KARYOTYPE_COLORS = {
+    'gneg': '#E3E3E3',
+    'gpos25': '#8E8E8E',
+    'gpos50': '#555555',
+    'gpos75': '#393939',
+    'gpos100': '#000000',
+    'acen': '#963232',
+    'stalk': '#7F7F7F',
+    'gvar': '#000000'
+};
+
+export const MUTATION_COLORS = {
+    'C>A': '#21BDEC',
+    'C>G': '#000000',
+    'C>T': '#E02C2E',
+    'T>A': '#999999',
+    'T>C': '#A2CD69',
+    'T>G': '#EAC6C5',
+
+    'AC>NN': '#A7CEE2',
+    'AT>NN': '#2679B2',
+    'CC>NN': '#B3DE8E',
+    'CG>NN': '#399F34',
+    'CT>NN': '#F99B9B',
+    'GC>NN': '#E01F27',
+    'TA>NN': '#FCBE75',
+    'TC>NN': '#FD7F23',
+    'TG>NN': '#CAB3D5',
+    'TT>NN': '#694098',
+
+    'D1C': '#FCBD75',
+    'D1T': '#FD8024',
+    'I1C': '#B1DC8F',
+    'I1T': '#3BA036',
+    'DR2': '#FCCAB7',
+    'DR3': '#FA8A6E',
+    'DR4': '#EE463A',
+    'DR5+': '#BA1822',
+    'IR2': '#D1E1F1',
+    'IR3': '#96C4DE',
+    'IR4': '#4E99C7',
+    'IR5+': '#1D66A9',
+    'DM2': '#E2E2EF',
+    'DM3': '#B6B7D7',
+    'DM4': '#8684BB',
+    'DM5+': '#614399'
+};
+
+

src/components/App.vue

@@ -9,6 +9,7 @@
 import { debounce } from 'lodash';
 import { mapGetters } from 'vuex';
 import API from './../api.js';
+import { MUT_TYPES } from './../constants.js';
 
 // child components
 import PlotGrid from './PlotGrid.vue';
@@ -24,9 +25,6 @@ export default {
     let vm = this;
     vm.checkHash();
     
-    API.fetchChromosomes().then(function(chromosomeLengths) {
-        vm.$store.commit('setChromosomeLengths', chromosomeLengths);
-    });
 
     // resize bindings
     vm.$store.commit('setWindowWidth', window.innerWidth);
@@ -40,9 +38,9 @@ export default {
   computed: {
     ...mapGetters([
       'selectedChromosome',
-      'selectedSignatures',
+      'selectedSignatureNames',
       'selectedPlots',
-      'selectedDatasets',
+      'selectedDatasetNames',
       'currentMode',
       'currentModeTitle',
       'currentModeOptions'
@@ -52,32 +50,45 @@ export default {
     checkHash: function() {
       let vm = this;
       // check for data in hash
-      var paramStr = window.location.hash.substring(1) // remove the initial "#"
-      if(paramStr.length > 0 && paramStr.substring(0, 3) != "bib") {
-        var params = JSON.parse(decodeURIComponent(paramStr));
-        if(params.datasets && params.signatures && params.plots && params.chr) {
-          vm.$store.commit('setSelectedChromosome', {
-            'name': params.chr.name,
-            'start': params.chr.start,
-            'end': params.chr.end
-          });
-          vm.$store.commit('setSelectedSignatures', params.signatures);
-          vm.$store.commit('setSelectedDatasets', params.datasets);
-          vm.$store.commit('setSelectedPlots', params.plots);
+      API.fetchDataListing().then((listing) => {
+        var paramStr = window.location.hash.substring(1); // remove the initial "#"
+        if(paramStr.length > 0 && paramStr.substring(0, 3) != "bib") {
+          var params = JSON.parse(decodeURIComponent(paramStr));
+          if(params.datasets && params.signatures && params.plots && params.chr) {
+            vm.$store.commit('setSelectedChromosome', {
+              'name': params.chr.name,
+              'start': params.chr.start,
+              'end': params.chr.end
+            });
+            
+            let selectedSignatures = {};
+            for(let mutType of MUT_TYPES) {
+              selectedSignatures[mutType] = params.signatures[mutType].map((selectedName) => {
+                return listing['sigs'][mutType].find((sig) => (sig.name === selectedName));
+              });
+            }
+            vm.$store.commit('setSelectedSignatures', selectedSignatures);
+            let selectedDatasets = [];
+            for(let dataset of params.datasets) {
+              selectedDatasets.push(listing['projects'][dataset]);
+            }
+            vm.$store.commit('setSelectedDatasets', selectedDatasets);
+            vm.$store.commit('setSelectedPlots', params.plots);
+          }
+          if(params.mode && params.mode.mode && params.mode.title && params.mode.options) {
+            vm.$store.commit('setMode', {
+                mode: params.mode.mode,
+                title: params.mode.title,
+                options: params.mode.options
+            });
+          }
         }
-        if(params.mode && params.mode.mode && params.mode.title && params.mode.options) {
-          vm.$store.commit('setMode', {
-              mode: params.mode.mode,
-              title: params.mode.title,
-              options: params.mode.options
-          });
-        }
-      }
+      })
     },
     setHash: function() {
       let hashData = {
-        'datasets': this.selectedDatasets,
-        'signatures': this.selectedSignatures,
+        'datasets': this.selectedDatasetNames,
+        'signatures': this.selectedSignatureNames,
         'plots': this.selectedPlots.map((plotInfo) => {
           return {
             "type": plotInfo.type,
@@ -101,13 +112,13 @@ export default {
     }
   },
   watch: {
-    selectedSignatures: {
+    selectedSignatureNames: {
       handler: function() {
         this.setHash();
       },
       deep: true
     },
-    selectedDatasets: {
+    selectedDatasetNames: {
       handler: function() {
         this.setHash();
       },

src/components/ChromosomeSelect.vue

@@ -9,7 +9,7 @@
 </template>
 
 <script>
-import { CHROMOSOMES } from './../constants.js'
+import { CHROMOSOMES, CHROMOSOME_LENGTHS } from './../constants.js'
 
 export default {
   name: 'ChromosomeSelect',
@@ -30,7 +30,7 @@ export default {
       setChromosome: function(event) {
           var chrLen = 0;
           if(event != '*') {
-              chrLen = this.$store.getters.chromosomeLength(event);
+              chrLen = CHROMOSOME_LENGTHS[event];
           }
           var chrOptions = {
               'name': event,