@sjcrh/proteinpaint-client 2.192.0 → 2.193.0

package/dist/oncomatrix-A3IE47HV.js

@@ -0,0 +1,295 @@
+import {
+  appInit
+} from "./chunk-LLX3NKB4.js";
+import "./chunk-BO47H3VP.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-4KY4XKJV.js";
+import {
+  fillTermWrapper,
+  vocabInit
+} from "./chunk-L7VDSIM7.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-UXDVUCXU.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-KM4JBR26.js";
+import "./chunk-COYULNJF.js";
+import {
+  dofetch3
+} from "./chunk-6G4YOMWW.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-IVXCWCKS.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.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-A3IE47HV.js.map