@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/oncomatrix-UGFXSXQJ.js

@@ -0,0 +1,293 @@
+import {
+  appInit
+} from "./chunk-MXNSW55L.js";
+import "./chunk-WS5XVKPJ.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-HZETQJGD.js";
+import {
+  fillTermWrapper,
+  vocabInit
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import {
+  dofetch3
+} from "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// gdc/oncomatrix.js
+var gdcGenome = "hg38";
+var gdcDslabel = "GDC";
+async function init(arg, holder, genomes) {
+  const toolGenome = arg.genome || gdcGenome;
+  const toolDslabel = arg.dslabel || gdcDslabel;
+  const genome = genomes[toolGenome];
+  try {
+    if (!genome) throw toolGenome + " missing";
+    const settings = arg.settings || {};
+    if (typeof settings != "object") throw "arg.settings{} not object";
+    if (!settings.matrix) settings.matrix = {};
+    if (typeof settings.matrix != "object") throw "arg.settings.matrix{} not object";
+    if (!settings.matrix.geneFilter) settings.matrix.geneFilter = "CGC";
+    if (!Number.isInteger(settings.matrix.maxGenes)) settings.matrix.maxGenes = 50;
+    if (arg.filter0 && typeof arg.filter0 != "object") throw "arg.filter0 not object";
+    const vocabApi = await vocabInit({
+      state: { vocab: { genome: toolGenome, dslabel: toolDslabel } }
+    });
+    vocabApi.getTermdbConfig();
+    const plotAppApi = await appInit({
+      holder: select_default(arg.holder).select(".sja_root_holder"),
+      genome,
+      state: copyMerge(
+        {
+          genome: toolGenome,
+          dslabel: toolDslabel,
+          termfilter: { filter0: arg.filter0 },
+          plots: [
+            // initialize with a geneset component, in case the genes lst is empty.
+            // This will be replaced with the actual matrix/hierCluster app once
+            // a valid geneset is selected.
+            {
+              chartType: "geneset",
+              toolName: "OncoMatrix",
+              settings: {
+                maxGenes: settings.matrix.maxGenes,
+                geneFilter: settings.matrix.geneFilter
+              }
+            }
+          ]
+        },
+        arg.state || {}
+      ),
+      app: arg.opts?.app || {},
+      geneset: {
+        mode: "geneVariant",
+        // consistent mode value as GeneSetEdit
+        genome,
+        genes: arg.genes,
+        reactsTo(action) {
+          if (action.type.startsWith("plot_")) return action.id === this.id;
+          if (action.type.startsWith("filter")) return true;
+          if (action.type == "app_refresh") return true;
+        },
+        showWaitMessage(div) {
+          div.style("margin", "20px");
+          div.append("div").text("Loading the top mutated genes in the current cohort...");
+        },
+        async callback(_genesetCompApi, twlst) {
+          if (!_genesetCompApi) return;
+          genesetCompApi = _genesetCompApi;
+          if (!matrixApi) {
+            const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "matrix");
+            if (plotConfig) matrixApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
+          }
+          const termgroups = [
+            ...arg.termgroups || [],
+            {
+              //name: 'Gene Expression',
+              lst: twlst
+            }
+          ];
+          if (matrixApi) {
+            plotAppApi.dispatch({
+              type: "plot_edit",
+              id: matrixApi.id,
+              config: { termgroups }
+            });
+          } else {
+            plotAppApi.dispatch({
+              type: "plot_create",
+              config: {
+                chartType: "matrix",
+                // avoid making a dictionary request when there is no gene data;
+                // if there is gene data, then the arg.termgroups can be submitted and rehydrated on app/store.init()
+                termgroups,
+                divideBy: arg.divideBy || void 0,
+                // moved default settings to gdc.hg38.js termdb[chartType].settings
+                // but can still override in the runpp() argument
+                settings
+              }
+            });
+          }
+        }
+      },
+      recover: {
+        undoHtml: "Undo",
+        redoHtml: "Redo",
+        resetHtml: "Restore",
+        hide(state) {
+          return state.plots[0]?.chartType != "matrix";
+        },
+        adjustTrackedState: (state) => {
+          const s = structuredClone(state);
+          delete s.termfilter.filter0;
+          if (s.plots) {
+            for (const plot of s.plots) {
+              if (!plot.termgroups) continue;
+              for (const grp of plot.termgroups) {
+                if (!grp.lst) continue;
+                for (const tw of grp.lst) {
+                  if (!tw?.term) continue;
+                  delete tw.term.category2samplecount;
+                  delete tw.term.values;
+                }
+              }
+            }
+          }
+          return s;
+        }
+      },
+      matrix: copyMerge(
+        {
+          reactsTo(action) {
+            if (action.type.startsWith("plot_")) return action.id === this.id;
+            if (action.type.startsWith("filter")) return true;
+            if (action.type == "app_refresh") return true;
+          },
+          // these will display the inputs together in the Genes menu,
+          // instead of being rendered outside of the matrix holder
+          customInputs: {
+            genes: [
+              {
+                label: `Maximum # Genes`,
+                title: "Limit the number of displayed genes",
+                type: "number",
+                chartType: "matrix",
+                settingsKey: "maxGenes",
+                callback: async (value) => {
+                  for (const key in arg.opts?.app?.callbacks) {
+                    if (key.startsWith("preDispatch")) {
+                      arg.opts?.app?.callbacks[key]();
+                      break;
+                    }
+                  }
+                  const genes = await getGenes(
+                    arg,
+                    { maxGenes: value, geneFilter: settings.matrix.geneFilter },
+                    vocabApi
+                  );
+                  api.update({
+                    termgroups: [{ lst: genes }],
+                    settings: {
+                      matrix: { maxGenes: value }
+                    }
+                  });
+                }
+              }
+            ]
+          },
+          callbacks: {
+            "firstRender.gdcMatrix": async (matrixApi2) => {
+              matrixApi2.on("firstRender.gdcMatrix", null);
+              if (!genesetCompApi) return;
+              plotAppApi.dispatch({
+                type: "plot_delete",
+                id: genesetCompApi.id
+              });
+              genesetCompApi = void 0;
+            }
+          }
+        },
+        arg.opts?.matrix || {}
+      )
+    });
+    let matrixApi, genesetCompApi;
+    const api = {
+      getState: () => plotAppApi.getState(),
+      destroy: () => plotAppApi.destroy(),
+      update: async (arg2) => {
+        if (!matrixApi) {
+          const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "matrix");
+          if (plotConfig) matrixApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
+        }
+        if (arg2.genes) {
+          plotAppApi.dispatch({
+            type: "plot_edit",
+            id: matrixApi.id,
+            config: {
+              termgroups: [
+                {
+                  lst: await Promise.all(
+                    arg2.genes.map(async (g) => {
+                      return await fillTermWrapper(
+                        {
+                          term: { gene: g.gene, type: "geneVariant", name: g.gene }
+                        },
+                        vocabApi
+                      );
+                    })
+                  )
+                }
+              ]
+            }
+          });
+        } else if ("filter0" in arg2) {
+          plotAppApi.dispatch({
+            type: "filter_replace",
+            filter0: arg2.filter0
+          });
+        } else if (matrixApi) {
+          plotAppApi.dispatch({
+            type: "plot_edit",
+            id: matrixApi.id,
+            config: arg2
+          });
+        }
+      },
+      triggerAbort: (_) => plotAppApi.triggerAbort(_)
+    };
+    return api;
+  } catch (e) {
+    throw e;
+  }
+}
+async function getGenes(arg, settings, vocabApi) {
+  const body = {
+    genome: gdcGenome,
+    dslabel: arg.dslabel || gdcDslabel,
+    maxGenes: settings.maxGenes,
+    geneFilter: settings.geneFilter
+  };
+  if (arg.filter0) body.filter0 = arg.filter0;
+  const data = await dofetch3("termdb/topMutatedGenes", { body });
+  if (data.error) throw data.error;
+  if (!data.genes) return;
+  return await Promise.all(
+    // do tempfix of "data.genes.slice(0,3).map" for faster testing
+    data.genes.map(async (i) => {
+      return fillTermWrapper({ term: { gene: i.gene, type: "geneVariant" } }, vocabApi);
+    })
+  );
+}
+export {
+  init
+};
+//# sourceMappingURL=oncomatrix-UGFXSXQJ.js.map

package/dist/oncomatrix-UGFXSXQJ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../gdc/oncomatrix.js"],
+  "sourcesContent": ["import { appInit } from '#plots/plot.app.js'\nimport { select } from 'd3-selection'\nimport { dofetch3 } from '#common/dofetch'\nimport { fillTermWrapper } from '#termsetting'\nimport { copyMerge } from '#rx'\nimport { vocabInit } from '#termdb/vocabulary'\n\n/*\ntest with http://localhost:3000/example.gdc.matrix.html\nrunpp({ launchGdcMatrix:true })\n\ndesigned to work for OncoMatrix app in GDC Analysis Tools Framework\n\ninitiates a \"plot\" app instance that wraps around the matrix component\nand returns the plot app API\n\n\n********* parameters\n\nholder\ngenomes = { hg38 : {} }\narg = {}\n\trunpp() argument object\n\n\t.filter0{}\n\t\tthe filter object from GDC Cohort Builder, for restricting cases in oncomatrix\n\t\t{\"op\":\"and\",\"content\":[{\"op\":\"in\",\"content\":{\"field\":\"cases.primary_site\",\"value\":[\"breast\",\"bronchus and lung\"]}}]}\n\t\tnot visualized on pp (invisible) and read only, passed to backend -> gdc api\n\t\t// NOTE 6/29/2023: this is the default only in the OncoMatrix demo mode,\n\t\t// and is supplied by the OncoMatrixWrapper in the GFF repo, no need to supply here\n\t\t// return { op: 'in', content: { field: 'cases.disease_type', value: ['Gliomas'] } }\n\n\t.genes[]\n\t\tfuture: list of genes to launch matrix\n\n\t.termgroups[]\n\t\tlist of terms to be added to the matrix by default\n\t\n\t.settings{matrix{}}\n\t\tany state that can be JSON-encoded/hydrated as part of getPlotConfig().settings.matrix. This is meant to hold plot-instance-specific state that only affects rendering and not data requests, but that distinction is not as clear with plots that use server-side rendering like violin plot.\n\t\t.maxGenes\n\t\t.maxSamples\n\n\t.opts{matrix{}}\n\t\tany options that cannot be JSON-stringified, like callbacks. These options will also be applied to all rehydrated or new plots of the same type, so not plot-instance-specific. this way of adding callback allows to work with an external portal, e.g. a callback from gdc to collect cases\n\t\t\t.allow2selectSamples: \n\t\t\t\t{\n\t\t\t\t  buttonText: \"Create Cohort\",\n\t\t\t\t  attributes: [\"case.case_id\"],\n\t\t\t\t  callback: console.log,\n\t\t\t\t}\n\n\t\t\t.cellClick(cell), where\n\t\t\t\tcell = {\n\t\t\t\t\tsampleData: the data.row by sample, part of the data.lst as returned by vocabApi.getAnnotatedSampleData()\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tsample: name/id string,\n\t\t\t\t\t\t\t[term1_$id]: {key, label, values, renderedValues, filteredValues, countedValues, sample},\n\t\t\t\t\t\t\t[....]\n\t\t\t\t\t\t},\n\n\t\t\t\t\tvalue: the data.row[term.id] value, data shape depends on the term.type,\n\t\t\t\t\t\t// for gene variant\n\t\t\t\t\t\t{\t\n\t\t\t\t\t\t\tdt, class, gene, pos, _SAMPLEID_, _SAMPLENAME\n\t\t\t\t\t\t}\n\t\t\t\t\t\t// not shown here: example values for other term types\n\n\t\t\t\t\tterm: the term for this matrix cell, equivalent to t.tw,\n\n\t\t\t\t\ts: the matrix.sampleOrder[] entry for this matrix cell,\n\n\t\t\t\t\tt: the matrix.termOrder[] entry for this matrix cell,\n\n\t\t\t\t\tsiblingCells: cell data for the same matrix sample/term, but excluding this cell \n\t\t\t\t}\n\n\n\n********* returns\n\nmatrix API object with following methods; pp react wrapper can call api.update() when user updates cohort in the GDC portal\nTODO revise to a simpler object\n\n{\n\ttype:'matrix'\n\tid:str\n\tgetComponents()\n\ton()\n\tupdate()\n\tdestroy()\n}\n*/\n\nconst gdcGenome = 'hg38'\nconst gdcDslabel = 'GDC'\n\nexport async function init(arg, holder, genomes) {\n\tconst toolGenome = arg.genome || gdcGenome\n\tconst toolDslabel = arg.dslabel || gdcDslabel\n\tconst genome = genomes[toolGenome]\n\ttry {\n\t\tif (!genome) throw toolGenome + ' missing'\n\n\t\t// these options will allow session recovery by an embedder\n\t\tconst settings = arg.settings || {}\n\t\tif (typeof settings != 'object') throw 'arg.settings{} not object'\n\t\tif (!settings.matrix) settings.matrix = {}\n\t\tif (typeof settings.matrix != 'object') throw 'arg.settings.matrix{} not object'\n\t\t// set defaults\n\t\tif (!settings.matrix.geneFilter) settings.matrix.geneFilter = 'CGC' // filter to only use CGC genes by default\n\t\tif (!Number.isInteger(settings.matrix.maxGenes)) settings.matrix.maxGenes = 50\n\n\t\tif (arg.filter0 && typeof arg.filter0 != 'object') throw 'arg.filter0 not object'\n\n\t\tconst vocabApi = await vocabInit({\n\t\t\tstate: { vocab: { genome: toolGenome, dslabel: toolDslabel } }\n\t\t})\n\t\tvocabApi.getTermdbConfig()\n\n\t\tconst plotAppApi = await appInit({\n\t\t\tholder: select(arg.holder).select('.sja_root_holder'),\n\t\t\tgenome,\n\t\t\tstate: copyMerge(\n\t\t\t\t{\n\t\t\t\t\tgenome: toolGenome,\n\t\t\t\t\tdslabel: toolDslabel,\n\t\t\t\t\ttermfilter: { filter0: arg.filter0 },\n\t\t\t\t\tplots: [\n\t\t\t\t\t\t// initialize with a geneset component, in case the genes lst is empty.\n\t\t\t\t\t\t// This will be replaced with the actual matrix/hierCluster app once\n\t\t\t\t\t\t// a valid geneset is selected.\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tchartType: 'geneset',\n\t\t\t\t\t\t\ttoolName: 'OncoMatrix',\n\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\tmaxGenes: settings.matrix.maxGenes,\n\t\t\t\t\t\t\t\tgeneFilter: settings.matrix.geneFilter\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t},\n\t\t\t\targ.state || {}\n\t\t\t),\n\t\t\tapp: arg.opts?.app || {},\n\t\t\tgeneset: {\n\t\t\t\tmode: 'geneVariant', // consistent mode value as GeneSetEdit\n\t\t\t\tgenome,\n\t\t\t\tgenes: arg.genes,\n\t\t\t\treactsTo(action) {\n\t\t\t\t\tif (action.type.startsWith('plot_')) return action.id === this.id\n\t\t\t\t\tif (action.type.startsWith('filter')) return true\n\t\t\t\t\tif (action.type == 'app_refresh') return true\n\t\t\t\t},\n\t\t\t\tshowWaitMessage(div) {\n\t\t\t\t\tdiv.style('margin', '20px')\n\t\t\t\t\tdiv.append('div').text('Loading the top mutated genes in the current cohort...')\n\t\t\t\t\t// can delete cgc line when new api is online\n\t\t\t\t\t// div.append('div').style('font-size', '.8em').html(`\n\t\t\t\t\t// \tGenes are selected from 738 Cancer Gene Census genes.<br>\n\t\t\t\t\t// \tOnly up to 1000 cases with gene expression data will be used to select genes.\n\t\t\t\t\t// `)\n\t\t\t\t},\n\t\t\t\tasync callback(_genesetCompApi, twlst) {\n\t\t\t\t\t// exit early if the geneset api is already gone,\n\t\t\t\t\t// as caused by race condition from quick changes to the filter0\n\t\t\t\t\tif (!_genesetCompApi) return\n\t\t\t\t\tgenesetCompApi = _genesetCompApi\n\t\t\t\t\tif (!matrixApi) {\n\t\t\t\t\t\tconst plotConfig = plotAppApi.getState().plots.find(p => p.chartType == 'matrix')\n\t\t\t\t\t\tif (plotConfig) matrixApi = plotAppApi.getComponents(`plots.${plotConfig.id}`)\n\t\t\t\t\t}\n\n\t\t\t\t\tconst termgroups = [\n\t\t\t\t\t\t...(arg.termgroups || []),\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\t//name: 'Gene Expression',\n\t\t\t\t\t\t\tlst: twlst\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\n\t\t\t\t\tif (matrixApi) {\n\t\t\t\t\t\tplotAppApi.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: matrixApi.id,\n\t\t\t\t\t\t\tconfig: { termgroups }\n\t\t\t\t\t\t})\n\t\t\t\t\t} else {\n\t\t\t\t\t\tplotAppApi.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\t\tchartType: 'matrix',\n\t\t\t\t\t\t\t\t// avoid making a dictionary request when there is no gene data;\n\t\t\t\t\t\t\t\t// if there is gene data, then the arg.termgroups can be submitted and rehydrated on app/store.init()\n\t\t\t\t\t\t\t\ttermgroups,\n\t\t\t\t\t\t\t\tdivideBy: arg.divideBy || undefined,\n\t\t\t\t\t\t\t\t// moved default settings to gdc.hg38.js termdb[chartType].settings\n\t\t\t\t\t\t\t\t// but can still override in the runpp() argument\n\t\t\t\t\t\t\t\tsettings\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t},\n\t\t\trecover: {\n\t\t\t\tundoHtml: 'Undo',\n\t\t\t\tredoHtml: 'Redo',\n\t\t\t\tresetHtml: 'Restore',\n\t\t\t\thide(state) {\n\t\t\t\t\treturn state.plots[0]?.chartType != 'matrix'\n\t\t\t\t},\n\t\t\t\tadjustTrackedState: state => {\n\t\t\t\t\tconst s = structuredClone(state)\n\t\t\t\t\tdelete s.termfilter.filter0\n\t\t\t\t\tif (s.plots) {\n\t\t\t\t\t\t// don't track plot configuration that are not specific to the plot config/settings\n\t\t\t\t\t\tfor (const plot of s.plots) {\n\t\t\t\t\t\t\tif (!plot.termgroups) continue\n\t\t\t\t\t\t\tfor (const grp of plot.termgroups) {\n\t\t\t\t\t\t\t\tif (!grp.lst) continue\n\t\t\t\t\t\t\t\tfor (const tw of grp.lst) {\n\t\t\t\t\t\t\t\t\tif (!tw?.term) continue\n\t\t\t\t\t\t\t\t\t// this is cohort-dependent and should be ignored like termfilter.filter0\n\t\t\t\t\t\t\t\t\tdelete tw.term.category2samplecount\n\t\t\t\t\t\t\t\t\t// for GDC, the term.values may not be known ahead of time\n\t\t\t\t\t\t\t\t\t// and only filled in as data comes in, should ignore this\n\t\t\t\t\t\t\t\t\t// computed value as to avoid affecting tracked state\n\t\t\t\t\t\t\t\t\tdelete tw.term.values\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\treturn s\n\t\t\t\t}\n\t\t\t},\n\t\t\tmatrix: copyMerge(\n\t\t\t\t{\n\t\t\t\t\treactsTo(action) {\n\t\t\t\t\t\tif (action.type.startsWith('plot_')) return action.id === this.id\n\t\t\t\t\t\tif (action.type.startsWith('filter')) return true\n\t\t\t\t\t\tif (action.type == 'app_refresh') return true\n\t\t\t\t\t},\n\t\t\t\t\t// these will display the inputs together in the Genes menu,\n\t\t\t\t\t// instead of being rendered outside of the matrix holder\n\t\t\t\t\tcustomInputs: {\n\t\t\t\t\t\tgenes: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tlabel: `Maximum # Genes`,\n\t\t\t\t\t\t\t\ttitle: 'Limit the number of displayed genes',\n\t\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\t\tchartType: 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Promise.all(\n\t\t\t\t\t\t\t\t\t\targ.genes.map(async g => {\n\t\t\t\t\t\t\t\t\t\t\treturn await fillTermWrapper(\n\t\t\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\t\t\tterm: { gene: g.gene, type: 'geneVariant', name: g.gene }\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvocabApi\n\t\t\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t} else if ('filter0' in arg) {\n\t\t\t\t\tplotAppApi.dispatch({\n\t\t\t\t\t\ttype: 'filter_replace',\n\t\t\t\t\t\tfilter0: arg.filter0\n\t\t\t\t\t})\n\t\t\t\t} else if (matrixApi) {\n\t\t\t\t\tplotAppApi.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: matrixApi.id,\n\t\t\t\t\t\tconfig: arg\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t},\n\t\t\ttriggerAbort: _ => plotAppApi.triggerAbort(_)\n\t\t}\n\t\treturn api\n\t} catch (e) {\n\t\tthrow e\n\t}\n}\n\nasync function getGenes(arg, settings, vocabApi) {\n\t// genes are not predefined. query to get top genes using 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+}