@sjcrh/proteinpaint-client 2.93.0 → 2.94.0

package/dist/{AppHeader-SQHECA7Z.js → AppHeader-LG4672GF.js}

@@ -4,7 +4,7 @@ import {
 } from "./chunk-R2GU73LD.js";
 import {
   InputSearch
-} from "./chunk-KPOHA2ND.js";
+} from "./chunk-VJ467ESZ.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-4WBP22U2.js";
@@ -20,8 +20,8 @@ import "./chunk-PBT5AMVE.js";
 import "./chunk-WTM3GD2X.js";
 import {
   get_tklst
-} from "./chunk-CR2HON7H.js";
-import "./chunk-EV3U4BV7.js";
+} from "./chunk-BXDSVZIH.js";
+import "./chunk-Y4CIIEAJ.js";
 import "./chunk-MYPTC6HX.js";
 import "./chunk-MKAF2BHB.js";
 import {
@@ -36,7 +36,7 @@ import "./chunk-NAEANGSC.js";
 import "./chunk-ALPXXDQD.js";
 import {
   block_init_default
-} from "./chunk-NMKS6EU2.js";
+} from "./chunk-AI5IUCP3.js";
 import {
   throwMsgWithFilePathAndFnName
 } from "./chunk-RKJGIOIF.js";
@@ -235,7 +235,7 @@ async function findgene2paint(str, app, genomename, jwt) {
       debugmode: app.debugmode
     };
     first_genetrack_tolist(g, par2.tklst);
-    import("./block-WJLKUYKL.js").then((b) => new b.Block(par2)).catch((err) => {
+    import("./block-2TYUPQPC.js").then((b) => new b.Block(par2)).catch((err) => {
       app.error0(err);
     });
     return;
@@ -841,7 +841,7 @@ var AppHeader = class _AppHeader {
         debugmode: app.debugmode
       };
       first_genetrack_tolist(g, par.tklst);
-      import("./block-WJLKUYKL.js").then((b) => new b.Block(par));
+      import("./block-2TYUPQPC.js").then((b) => new b.Block(par));
       app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
     });
     return g_browser_btn;
@@ -854,4 +854,4 @@ var AppHeader = class _AppHeader {
 export {
   AppHeader
 };
-//# sourceMappingURL=AppHeader-SQHECA7Z.js.map
+//# sourceMappingURL=AppHeader-LG4672GF.js.map

package/dist/{DEanalysis-6YEXM5OP.js → DEanalysis-EQUCIHAI.js}

@@ -4,7 +4,7 @@ import {
   controlsInit,
   downloadTable,
   renderTable
-} from "./chunk-KPOHA2ND.js";
+} from "./chunk-VJ467ESZ.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-4WBP22U2.js";
@@ -642,4 +642,4 @@ export {
   makeChartBtnMenu,
   openHiercluster
 };
-//# sourceMappingURL=DEanalysis-6YEXM5OP.js.map
+//# sourceMappingURL=DEanalysis-EQUCIHAI.js.map

package/dist/{Disco-23C3FNA4.js → Disco-KEJNY7UJ.js}

@@ -1,7 +1,7 @@
 import {
   configUiInit,
   svgLegend
-} from "./chunk-KPOHA2ND.js";
+} from "./chunk-VJ467ESZ.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-4WBP22U2.js";
@@ -223,9 +223,36 @@ var DiscoInteractions = class {
           }
         ]
       };
-      const _ = await import("./block.init-4G7UJWQC.js");
+      const _ = await import("./block.init-RWNEBD2U.js");
       await _.default(arg);
     };
+    this.colorScaleNumericInputsCallback = async (obj) => {
+      const callAppDispatch = (settings) => {
+        this.discoApp.app.dispatch({
+          type: "plot_edit",
+          id: this.discoApp.id,
+          config: { settings: { Disco: Object.assign({ cnvCutoffMode: obj.cutoffMode }, settings) } }
+        });
+      };
+      if (obj.cutoffMode == "auto") {
+        if (obj.min == null || obj.max == null)
+          throw new Error('Color scale must return min and max if cutoffMode "auto"');
+        callAppDispatch({
+          cnvCapping: this.discoApp.state.settings.cnv.capping,
+          cnvPercentile: this.discoApp.state.settings.cnv.percentile
+        });
+      } else if (obj.cutoffMode == "fixed") {
+        if (obj.min == null || obj.max == null)
+          throw new Error('Color scale must return min and max if cutoffMode "fixed"');
+        const diffValue = obj.max !== this.discoApp.state.settings.cnv.capping ? obj.max : Math.abs(obj.min);
+        callAppDispatch({
+          cnvCapping: diffValue
+        });
+      } else if (obj.cutoffMode == "percentile")
+        callAppDispatch({ cnvPercentile: obj.percentile });
+      else
+        throw new Error("Unknown cutoff mode returned from dom/ColorScale");
+    };
   }
 };
 
@@ -601,16 +628,19 @@ var DataMapper = class _DataMapper {
 
 // plots/disco/legend/Legend.ts
 var Legend = class {
-  constructor(snvTitle, cnvTitle, lohTitle, fusionTitle, snvClassMap, cnvClassMap, cnvRenderingType, fusionLegend, lohLegend) {
+  constructor(snvTitle, cnvTitle, lohTitle, fusionTitle, cnvPercentile, cnvCutoffmode, snvClassMap, cnvClassMap, cnvRenderingType, fusionLegend, discoInteractions, lohLegend) {
     this.snvTitle = snvTitle;
     this.cnvTitle = cnvTitle;
     this.lohTitle = lohTitle;
     this.fusionTitle = fusionTitle;
+    this.cnvPercentile = cnvPercentile;
+    this.cnvCutoffMode = cnvCutoffmode;
     this.snvClassMap = snvClassMap;
     this.cnvClassMap = cnvClassMap;
     this.cnvRenderingType = cnvRenderingType;
     this.lohLegend = lohLegend;
     this.fusionLegend = fusionLegend;
+    this.discoInteractions = discoInteractions;
   }
   legendCount() {
     return (this.snvClassMap.size > 0 ? 1 : 0) + (this.cnvClassMap.size > 0 ? 1 : 0) + (this.lohLegend ? 1 : 0) + (this.fusionLegend ? 1 : 0);
@@ -1550,13 +1580,14 @@ var Rings = class {
 
 // plots/disco/viewmodel/ViewModelProvider.ts
 var ViewModelProvider = class {
-  constructor(settings, dataMapper, reference, sampleName, genesetName) {
+  constructor(settings, dataMapper, reference, sampleName, genesetName, discoInteractions) {
     this.nonExonicArcRing = void 0;
     this.settings = settings;
     this.dataMapper = dataMapper;
     this.reference = reference;
     this.sampleName = sampleName;
     this.genesetName = genesetName;
+    this.discoInteractions = discoInteractions;
   }
   map(data) {
     const dataHolder = this.dataMapper.map(data);
@@ -1635,10 +1666,13 @@ var ViewModelProvider = class {
       this.settings.legend.cnvTitle,
       this.settings.legend.lohTitle,
       this.settings.legend.fusionTitle,
+      this.settings.Disco.cnvPercentile,
+      this.settings.Disco.cnvCutoffMode,
       this.snvArcsMapper ? this.snvArcsMapper.snvClassMap : /* @__PURE__ */ new Map(),
       this.cnvArcsMapper ? this.cnvArcsMapper.cnvClassMap : /* @__PURE__ */ new Map(),
       this.settings.Disco.cnvRenderingType,
       fusions.length > 0,
+      this.discoInteractions,
       lohLegend
     );
     const rings = new Rings(
@@ -1686,8 +1720,9 @@ var ViewModelMapper = class {
       noncoding: "non-exonic"
     };
   }
-  constructor(settings) {
+  constructor(settings, discoInteractions) {
     this.settings = settings;
+    this.discoInteractions = discoInteractions;
   }
   map(opts) {
     const chromosomesOverride = opts.args.chromosomes;
@@ -1699,7 +1734,14 @@ var ViewModelMapper = class {
     const data = opts.args.data;
     const reference = new Reference(this.settings, chrSizes, chromosomesOverride);
     const dataMapper = new DataMapper(this.settings, reference, sampleName, prioritizedGenes);
-    return new ViewModelProvider(this.settings, dataMapper, reference, sampleName, genesetName).map(data);
+    return new ViewModelProvider(
+      this.settings,
+      dataMapper,
+      reference,
+      sampleName,
+      genesetName,
+      this.discoInteractions
+    ).map(data);
   }
 };
 
@@ -1812,13 +1854,19 @@ var LegendJSONMapper = class {
       };
       if (gain.value > 0 && loss.value < 0) {
         const maxValue = Math.max(Math.abs(loss.value), gain.value);
-        const domain = maxValue < 1 ? [-1, 0, 1] : [-maxValue, 0, maxValue];
+        const domain = [-maxValue, 0, maxValue];
         cnvItems.push(
           Object.assign(
             {
               key: 3 /* LossGain */,
               domain,
-              scale: linear([-1, 0, 1], [loss.color, "white", gain.color])
+              scale: linear([-1, 0, 1], [loss.color, "white", gain.color]),
+              labels: { left: "Loss", right: "Gain" },
+              numericInputs: {
+                cutoffMode: legend.cnvCutoffMode,
+                defaultPercentile: legend.cnvPercentile,
+                callback: (obj) => legend.discoInteractions.colorScaleNumericInputsCallback(obj)
+              }
             },
             base
           )
@@ -2059,7 +2107,8 @@ function discoDefaults(overrides = {}) {
       prioritizeGeneLabelsByGeneSets: false,
       showPrioritizeGeneLabelsByGeneSets: false,
       cnvRenderingType: "heatmap" /* heatmap */,
-      cnvPercentile: 80
+      cnvPercentile: 80,
+      cnvCutoffMode: "auto"
     },
     rings: {
       nonExonicRingWidth: 20,
@@ -2089,6 +2138,7 @@ function discoDefaults(overrides = {}) {
     },
     cnv: {
       capping: 5,
+      percentile: 80,
       ampColor: "#D6683C",
       lossColor: "#67a9cf",
       cappedAmpColor: "#8B0000",
@@ -2331,7 +2381,7 @@ var Disco = class {
   async init() {
     const state = this.app.getState();
     const settings = state.plots.find((p) => p.id === this.id).settings;
-    this.stateViewModelMapper = new ViewModelMapper(settings);
+    this.stateViewModelMapper = new ViewModelMapper(settings, this.discoInteractions);
     this.viewModel = this.stateViewModelMapper.map(state);
     const holder = this.opts.holder;
     const controlsHolder = holder.append("div").style("display", "inline-block").style("vertical-align", "top");
@@ -2373,14 +2423,6 @@ var Disco = class {
       configInputsOptions.push(...filterMutationsGenesCheckbox);
     }
     const cnvConfigInputOptions = [
-      {
-        label: "CNV capping",
-        type: "number",
-        chartType: "Disco",
-        settingsKey: "cnvCapping",
-        title: "Cnv capping",
-        min: 0
-      },
       {
         boxLabel: "",
         label: "CNV rendering type",
@@ -2392,15 +2434,6 @@ var Disco = class {
           { label: "Heatmap", value: "heatmap" /* heatmap */ },
           { label: "Bar", value: "bar" /* bar */ }
         ]
-      },
-      {
-        label: "CNV percentile",
-        type: "number",
-        chartType: "Disco",
-        settingsKey: "cnvPercentile",
-        title: "Cnv percentile",
-        min: 1,
-        max: 100
       }
     ];
     if (viewModel.cnvMaxValue !== 0 || viewModel.cnvMinValue !== 0)
@@ -2411,7 +2444,7 @@ var Disco = class {
     const settings = this.state.settings;
     this.isOpen = settings.Disco.isOpen;
     if (this.recreateViewModel) {
-      this.stateViewModelMapper = new ViewModelMapper(settings);
+      this.stateViewModelMapper = new ViewModelMapper(settings, this.discoInteractions);
       this.viewModel = this.stateViewModelMapper.map(this.app.getState());
     }
     this.recreateViewModel = true;
@@ -2481,4 +2514,4 @@ export {
   discoInit,
   getPlotConfig
 };
-//# sourceMappingURL=Disco-23C3FNA4.js.map
+//# sourceMappingURL=Disco-KEJNY7UJ.js.map