@jbrowse/plugin-wiggle 4.1.3 → 4.1.5

package/esm/d3-hierarchy2/treemap/squarify.js

@@ -0,0 +1,46 @@
+import treemapDice from "./dice.js";
+import treemapSlice from "./slice.js";
+export var phi = (1 + Math.sqrt(5)) / 2;
+export function squarifyRatio(ratio, parent, x0, y0, x1, y1) {
+    var rows = [], nodes = parent.children, row, nodeValue, i0 = 0, i1 = 0, n = nodes.length, dx, dy, value = parent.value, sumValue, minValue, maxValue, newRatio, minRatio, alpha, beta;
+    while (i0 < n) {
+        dx = x1 - x0, dy = y1 - y0;
+        do
+            sumValue = nodes[i1++].value;
+        while (!sumValue && i1 < n);
+        minValue = maxValue = sumValue;
+        alpha = Math.max(dy / dx, dx / dy) / (value * ratio);
+        beta = sumValue * sumValue * alpha;
+        minRatio = Math.max(maxValue / beta, beta / minValue);
+        for (; i1 < n; ++i1) {
+            sumValue += nodeValue = nodes[i1].value;
+            if (nodeValue < minValue)
+                minValue = nodeValue;
+            if (nodeValue > maxValue)
+                maxValue = nodeValue;
+            beta = sumValue * sumValue * alpha;
+            newRatio = Math.max(maxValue / beta, beta / minValue);
+            if (newRatio > minRatio) {
+                sumValue -= nodeValue;
+                break;
+            }
+            minRatio = newRatio;
+        }
+        rows.push(row = { value: sumValue, dice: dx < dy, children: nodes.slice(i0, i1) });
+        if (row.dice)
+            treemapDice(row, x0, y0, x1, value ? y0 += dy * sumValue / value : y1);
+        else
+            treemapSlice(row, x0, y0, value ? x0 += dx * sumValue / value : x1, y1);
+        value -= sumValue, i0 = i1;
+    }
+    return rows;
+}
+export default (function custom(ratio) {
+    function squarify(parent, x0, y0, x1, y1) {
+        squarifyRatio(ratio, parent, x0, y0, x1, y1);
+    }
+    squarify.ratio = function (x) {
+        return custom((x = +x) > 1 ? x : 1);
+    };
+    return squarify;
+})(phi);

package/esm/index.d.ts

@@ -21,7 +21,7 @@ export default class WigglePlugin extends Plugin {
         }) => import("react/jsx-runtime").JSX.Element;
         XYPlotRenderer: typeof XYPlotRenderer;
         linearWiggleDisplayModelFactory: typeof linearWiggleDisplayModelFactory;
-        xyPlotRendererConfigSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+        xyPlotRendererConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             filled: {
                 type: string;
                 defaultValue: boolean;
@@ -41,7 +41,7 @@ export default class WigglePlugin extends Plugin {
                 type: string;
                 defaultValue: number;
             };
-        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             color: {
                 type: string;
                 description: string;
@@ -76,7 +76,7 @@ export default class WigglePlugin extends Plugin {
                 defaultValue: number;
                 description: string;
             };
-        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
         utils: typeof utils;
     };
 }

package/esm/shared/SharedWiggleConfigSchema.d.ts

@@ -1,4 +1,4 @@
-export default function sharedWiggleConfigFactory(): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function sharedWiggleConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     autoscale: {
         type: string;
         defaultValue: string;
@@ -36,7 +36,7 @@ export default function sharedWiggleConfigFactory(): import("node_modules/@jbrow
         description: string;
         defaultValue: boolean;
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
         description: string;
@@ -63,4 +63,4 @@ export default function sharedWiggleConfigFactory(): import("node_modules/@jbrow
         description: string;
         defaultValue: never[];
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/shared/SharedWiggleMixin.d.ts

@@ -35,6 +35,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 statusMessage?: string;
                 reactElement?: React.ReactElement;
                 isRenderingPending?: boolean;
+                displayHeight?: number;
             };
         }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
@@ -53,10 +54,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         beforeDestroy(): void;
     } & {
         readonly statusMessage: any;
+        readonly displayHeight: number | undefined;
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -83,7 +85,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {
@@ -392,6 +394,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -410,6 +413,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -436,6 +440,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -454,6 +459,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -467,7 +473,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                         [x: string]: any;
                     } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -494,7 +500,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
             showLegend: boolean | undefined;
             showTooltips: boolean | undefined;
         } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -784,6 +790,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -802,10 +809,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -832,7 +840,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         }, {
@@ -1103,6 +1111,8 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
+        scoreMeanMin?: number;
+        scoreMeanMax?: number;
         statsRegion?: string;
     } | undefined;
     statsFetchInProgress: undefined | StopToken;
@@ -1111,6 +1121,8 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
+        scoreMeanMin?: number;
+        scoreMeanMax?: number;
     }, statsRegion?: string): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
@@ -1159,6 +1171,8 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
+            scoreMeanMin?: number;
+            scoreMeanMax?: number;
             statsRegion?: string;
         } | undefined;
         autoscaleType: string;
@@ -1229,6 +1243,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 statusMessage?: string;
                 reactElement?: React.ReactElement;
                 isRenderingPending?: boolean;
+                displayHeight?: number;
             };
         }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
@@ -1247,10 +1262,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         beforeDestroy(): void;
     } & {
         readonly statusMessage: any;
+        readonly displayHeight: number | undefined;
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -1277,7 +1293,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
@@ -1314,6 +1330,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
                 statusMessage?: string;
                 reactElement?: React.ReactElement;
                 isRenderingPending?: boolean;
+                displayHeight?: number;
             };
         }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
@@ -1332,10 +1349,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
         beforeDestroy(): void;
     } & {
         readonly statusMessage: any;
+        readonly displayHeight: number | undefined;
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -1362,7 +1380,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {

package/esm/shared/SharedWiggleMixin.js

@@ -34,7 +34,7 @@ export default function SharedWiggleMixin(configSchema) {
     }))
         .actions(self => ({
         updateQuantitativeStats(stats, statsRegion) {
-            const { currStatsBpPerPx, scoreMin, scoreMax } = stats;
+            const { currStatsBpPerPx, scoreMin, scoreMax, scoreMeanMin, scoreMeanMax, } = stats;
             const EPSILON = 0.000001;
             if (!self.stats ||
                 Math.abs(self.stats.scoreMax - scoreMax) > EPSILON ||
@@ -44,6 +44,8 @@ export default function SharedWiggleMixin(configSchema) {
                     currStatsBpPerPx,
                     scoreMin,
                     scoreMax,
+                    scoreMeanMin,
+                    scoreMeanMax,
                     statsRegion,
                 };
             }
@@ -163,12 +165,20 @@ export default function SharedWiggleMixin(configSchema) {
         let oldDomain = [0, 0];
         return {
             get domain() {
-                const { stats, scaleType, minScore, maxScore } = self;
+                const { stats, scaleType, minScore, maxScore, rendererConfig } = self;
                 if (!stats) {
                     return undefined;
                 }
+                const { summaryScoreMode } = rendererConfig;
+                const useMeanStats = summaryScoreMode === 'mean' || summaryScoreMode === 'avg';
+                const domainMin = useMeanStats
+                    ? (stats.scoreMeanMin ?? stats.scoreMin)
+                    : stats.scoreMin;
+                const domainMax = useMeanStats
+                    ? (stats.scoreMeanMax ?? stats.scoreMax)
+                    : stats.scoreMax;
                 const ret = getNiceDomain({
-                    domain: [stats.scoreMin, stats.scoreMax],
+                    domain: [domainMin, domainMax],
                     bounds: [minScore, maxScore],
                     scaleType,
                 });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "4.1.3",
+  "version": "4.1.5",
   "type": "module",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
@@ -24,10 +24,10 @@
     "@gmod/bbi": "^8.1.1",
     "@gmod/hclust": "^1.0.7",
     "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/icons-material": "^7.3.7",
-    "@mui/material": "^7.3.7",
+    "@mui/icons-material": "^7.3.8",
+    "@mui/material": "^7.3.8",
     "@mui/x-charts-vendor": "^8.26.0",
-    "@mui/x-data-grid": "^8.26.0",
+    "@mui/x-data-grid": "^8.27.1",
     "@types/file-saver-es": "^2.0.3",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.3",
@@ -36,9 +36,9 @@
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.1.3",
-    "@jbrowse/plugin-data-management": "^4.1.3",
-    "@jbrowse/plugin-linear-genome-view": "^4.1.3"
+    "@jbrowse/core": "^4.1.5",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.5",
+    "@jbrowse/plugin-data-management": "^4.1.5"
   },
   "peerDependencies": {
     "react": ">=18.0.0"