@jbrowse/plugin-wiggle 2.0.0 → 2.1.2

package/esm/LinearWiggleDisplay/components/SetColorDialog.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SetColorDialog.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/components/SetColorDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,UAAU,EACV,KAAK,EACL,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AACjD,OAAO,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAA;AAE1D,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,WAAW,GAWZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAE3C,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAGV,oBAAC,UAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,OAAO,EAAE,CAAC,MAAM,EAChB,OAAO,EAAE,GAAG,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,EAC/B,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAE,eAAe,GACtB;YACF,oBAAC,gBAAgB,IACf,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,GAAG,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,EAC9B,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAE,yBAAyB,GAChC;YAED,MAAM,CAAC,CAAC,CAAC,CACR;gBACE,oBAAC,UAAU,yBAA4B;gBACvC,oBAAC,WAAW,IACV,KAAK,EAAE,KAAK,CAAC,QAAQ,IAAI,OAAO,EAChC,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;wBACxB,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;oBAC3B,CAAC,GACD;gBACF,oBAAC,UAAU,yBAA4B;gBAEvC,oBAAC,WAAW,IACV,KAAK,EAAE,KAAK,CAAC,QAAQ,IAAI,OAAO,EAChC,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;wBACxB,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;oBAC3B,CAAC,GACD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;gBACE,oBAAC,UAAU,wBAA2B;gBACtC,oBAAC,WAAW,IACV,KAAK,EAAE,KAAK,CAAC,KAAK,IAAI,OAAO,EAC7B,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,GACxC,CACD,CACJ,CACa;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;oBAC5B,KAAK,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;oBAC5B,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBAC3B,CAAC,EACD,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,sBAGZ;YAET,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,cAAc,CAAC,CAAA"}

package/esm/LinearWiggleDisplay/components/Tooltip.d.ts

@@ -1,16 +1,10 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
+import Tooltip, { TooltipContentsComponent } from '../../Tooltip';
+declare const TooltipContents: React.ForwardRefExoticComponent<{
+    feature: Feature;
+} & React.RefAttributes<HTMLDivElement>>;
 declare type Coord = [number, number];
-declare const Tooltip: ({ model, height, clientMouseCoord, offsetMouseCoord, clientRect, TooltipContents, }: {
-    model: {
-        featureUnderMouse: Feature;
-    };
-    height: number;
-    clientMouseCoord: Coord;
-    offsetMouseCoord: Coord;
-    clientRect?: DOMRect | undefined;
-    TooltipContents: React.FC<any>;
-}) => JSX.Element | null;
 declare const WiggleTooltip: (props: {
     model: {
         featureUnderMouse: Feature;
@@ -19,6 +13,7 @@ declare const WiggleTooltip: (props: {
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
     clientRect?: DOMRect;
+    TooltipContents?: TooltipContentsComponent;
 }) => JSX.Element;
 export default WiggleTooltip;
 export { Tooltip };

package/esm/LinearWiggleDisplay/components/Tooltip.js

@@ -1,45 +1,9 @@
-import React, { useMemo, useState } from 'react';
+import React from 'react';
 import { observer } from 'mobx-react';
-import { alpha, Portal } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 // locals
-import { YSCALEBAR_LABEL_OFFSET } from '../models/model';
-import { usePopper } from 'react-popper';
-// convert to number, apply shortened precision, and render
-function toP(s = 0) {
-    return +(+s).toPrecision(6);
-}
-function round(value) {
-    return Math.round(value * 1e5) / 1e5;
-}
+import Tooltip from '../../Tooltip';
+import { toP } from '../../util';
 const en = (n) => n.toLocaleString('en-US');
-const useStyles = makeStyles()(theme => ({
-    // these styles come from
-    // https://github.com/mui-org/material-ui/blob/master/packages/material-ui/src/Tooltip/Tooltip.js
-    tooltip: {
-        position: 'absolute',
-        pointerEvents: 'none',
-        backgroundColor: alpha(theme.palette.grey[700], 0.9),
-        borderRadius: theme.shape.borderRadius,
-        color: theme.palette.common.white,
-        fontFamily: theme.typography.fontFamily,
-        padding: '4px 8px',
-        fontSize: theme.typography.pxToRem(12),
-        lineHeight: `${round(14 / 10)}em`,
-        maxWidth: 300,
-        wordWrap: 'break-word',
-    },
-    hoverVertical: {
-        background: '#333',
-        border: 'none',
-        width: 1,
-        height: '100%',
-        top: YSCALEBAR_LABEL_OFFSET,
-        cursor: 'default',
-        position: 'absolute',
-        pointerEvents: 'none',
-    },
-}));
 const TooltipContents = React.forwardRef(({ feature }, ref) => {
     const start = feature.get('start');
     const end = feature.get('end');
@@ -62,43 +26,6 @@ const TooltipContents = React.forwardRef(({ feature }, ref) => {
         React.createElement("br", null),
         `${toP(feature.get('score'))}`));
 });
-const Tooltip = observer(({ model, height, clientMouseCoord, offsetMouseCoord, clientRect, TooltipContents, }) => {
-    const { featureUnderMouse } = model;
-    const [width, setWidth] = useState(0);
-    const [anchorEl, setAnchorEl] = useState(null);
-    const { classes } = useStyles();
-    // must be memoized a la https://github.com/popperjs/react-popper/issues/391
-    const virtElement = useMemo(() => ({
-        getBoundingClientRect: () => {
-            const x = clientMouseCoord[0] + width / 2 + 20;
-            const y = (clientRect === null || clientRect === void 0 ? void 0 : clientRect.top) || 0;
-            return {
-                top: y,
-                left: x,
-                bottom: y,
-                right: x,
-                width: 0,
-                height: 0,
-                x,
-                y,
-                toJSON() { },
-            };
-        },
-    }), [clientRect === null || clientRect === void 0 ? void 0 : clientRect.top, clientMouseCoord, width]);
-    const { styles, attributes } = usePopper(virtElement, anchorEl);
-    return featureUnderMouse ? (React.createElement(React.Fragment, null,
-        React.createElement(Portal, null,
-            React.createElement("div", { ref: setAnchorEl, className: classes.tooltip, 
-                // zIndex needed to go over widget drawer
-                style: { ...styles.popper, zIndex: 100000 }, ...attributes.popper },
-                React.createElement(TooltipContents, { ref: (elt) => {
-                        setWidth((elt === null || elt === void 0 ? void 0 : elt.getBoundingClientRect().width) || 0);
-                    }, feature: featureUnderMouse }))),
-        React.createElement("div", { className: classes.hoverVertical, style: {
-                left: offsetMouseCoord[0],
-                height: height - YSCALEBAR_LABEL_OFFSET * 2,
-            } }))) : null;
-});
 const WiggleTooltip = observer((props) => {
     return React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props });
 });

package/esm/LinearWiggleDisplay/components/Tooltip.js.map

@@ -1 +1 @@
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package/esm/LinearWiggleDisplay/index.d.ts

@@ -1,3 +1,7 @@
-export { default as configSchemaFactory } from './models/configSchema';
-export { default as modelFactory, YSCALEBAR_LABEL_OFFSET } from './models/model';
-export { default as ReactComponent } from './components/WiggleDisplayComponent';
+import PluginManager from '@jbrowse/core/PluginManager';
+import modelFactory from './models/model';
+import ReactComponent from './components/WiggleDisplayComponent';
+import Tooltip from './components/Tooltip';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { ReactComponent, modelFactory, Tooltip };

package/esm/LinearWiggleDisplay/index.js

@@ -1,4 +1,21 @@
-export { default as configSchemaFactory } from './models/configSchema';
-export { default as modelFactory, YSCALEBAR_LABEL_OFFSET } from './models/model';
-export { default as ReactComponent } from './components/WiggleDisplayComponent';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import configSchemaFactory from './models/configSchema';
+import modelFactory from './models/model';
+import ReactComponent from './components/WiggleDisplayComponent';
+import Tooltip from './components/Tooltip';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        const stateModel = modelFactory(pluginManager, configSchema);
+        return new DisplayType({
+            name: 'LinearWiggleDisplay',
+            configSchema,
+            stateModel,
+            trackType: 'QuantitativeTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent,
+        });
+    });
+};
+export { ReactComponent, modelFactory, Tooltip };
 //# sourceMappingURL=index.js.map

package/esm/LinearWiggleDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearWiggleDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,qCAAqC,CAAA;AAChE,OAAO,OAAO,MAAM,sBAAsB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,MAAM,UAAU,GAAG,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;QAC5D,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,mBAAmB;YAC9B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,OAAO,EAAE,CAAA"}

package/esm/LinearWiggleDisplay/models/model.d.ts

@@ -3,7 +3,6 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-export declare const YSCALEBAR_LABEL_OFFSET = 5;
 declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -64,6 +63,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -209,7 +209,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     };
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats({ scoreMin, scoreMax, }: {
+    updateStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -219,7 +219,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     setLoading(aborter: AbortController): void;
     selectFeature(feature: Feature): void;
     setResolution(res: number): void;
-    setFill(fill: boolean): void;
+    setFill(fill: number): void;
     toggleLogScale(): void;
     setScaleType(scale?: string): void;
     setSummaryScoreMode(val: string): void;
@@ -232,6 +232,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
 } & {
     readonly TooltipComponent: React.FC<{}>;
     readonly adapterTypeName: any;
+    readonly rendererTypeNameSimple: any;
     readonly rendererTypeName: string;
     readonly filters: undefined;
     readonly scaleType: any;
@@ -258,18 +259,36 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly autoscaleType: any;
     readonly displayCrossHatchesSetting: any;
 } & {
-    readonly ticks: any;
+    readonly ticks: {
+        range: number[];
+        values: number[];
+        format: (d: import("d3-scale").NumberValue) => string;
+        position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
+    };
+    readonly adapterCapabilities: string[];
 } & {
     renderProps(): any;
-    readonly adapterCapabilities: string[];
     readonly hasResolution: boolean;
     readonly hasGlobalStats: boolean;
+    readonly fillSetting: 2 | 1 | 0;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
         type: string;
         label: string;
         checked: any;
         onClick: () => void;
+        subMenu?: undefined;
     })[];
 } & {
     reload(): Promise<void>;

package/esm/LinearWiggleDisplay/models/model.js

@@ -1,18 +1,15 @@
 import React, { lazy } from 'react';
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { isAbortException, getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { getSession, getContainingView, isSelectionContainer, } from '@jbrowse/core/util';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
-import { autorun, when } from 'mobx';
-import { addDisposer, isAlive, types, getEnv } from 'mobx-state-tree';
+import { when } from 'mobx';
+import { isAlive, types, getEnv } from 'mobx-state-tree';
 import { axisPropsFromTickScale } from 'react-d3-axis-mod';
-import { getNiceDomain, getScale } from '../../util';
+import { getNiceDomain, getScale, getStats, statsAutorun, YSCALEBAR_LABEL_OFFSET, } from '../../util';
 import Tooltip from '../components/Tooltip';
 import { YScaleBar } from '../components/WiggleDisplayComponent';
 const SetMinMaxDlg = lazy(() => import('../components/SetMinMaxDialog'));
 const SetColorDlg = lazy(() => import('../components/SetColorDialog'));
-// fudge factor for making all labels on the YScalebar visible
-export const YSCALEBAR_LABEL_OFFSET = 5;
 // using a map because it preserves order
 const rendererTypes = new Map([
     ['xyplot', 'XYPlotRenderer'],
@@ -26,6 +23,7 @@ const stateModelFactory = (pluginManager, configSchema) => types
     selectedRendering: types.optional(types.string, ''),
     resolution: types.optional(types.number, 1),
     fill: types.maybe(types.boolean),
+    minSize: types.maybe(types.number),
     color: types.maybe(types.string),
     posColor: types.maybe(types.string),
     negColor: types.maybe(types.string),
@@ -46,12 +44,14 @@ const stateModelFactory = (pluginManager, configSchema) => types
     statsFetchInProgress: undefined,
 }))
     .actions(self => ({
-    updateStats({ scoreMin, scoreMax, }) {
-        if (self.stats.scoreMin !== scoreMin ||
-            self.stats.scoreMax !== scoreMax) {
+    updateStats(stats) {
+        const { scoreMin, scoreMax } = stats;
+        const EPSILON = 0.000001;
+        if (Math.abs(self.stats.scoreMax - scoreMax) > EPSILON ||
+            Math.abs(self.stats.scoreMin - scoreMin) > EPSILON) {
             self.stats = { scoreMin, scoreMax };
+            self.statsReady = true;
         }
-        self.statsReady = true;
     },
     setColor(color) {
         self.color = color;
@@ -82,7 +82,18 @@ const stateModelFactory = (pluginManager, configSchema) => types
         self.resolution = res;
     },
     setFill(fill) {
-        self.fill = fill;
+        if (fill === 0) {
+            self.fill = true;
+            self.minSize = 0;
+        }
+        else if (fill === 1) {
+            self.fill = false;
+            self.minSize = 1;
+        }
+        else if (fill === 2) {
+            self.fill = false;
+            self.minSize = 2;
+        }
     },
     toggleLogScale() {
         if (self.scale !== 'log') {
@@ -124,11 +135,14 @@ const stateModelFactory = (pluginManager, configSchema) => types
     get adapterTypeName() {
         return self.adapterConfig.type;
     },
+    get rendererTypeNameSimple() {
+        return self.rendererTypeNameState || getConf(self, 'defaultRendering');
+    },
     get rendererTypeName() {
-        const viewName = self.rendererTypeNameState || getConf(self, 'defaultRendering');
-        const rendererType = rendererTypes.get(viewName);
+        const name = this.rendererTypeNameSimple;
+        const rendererType = rendererTypes.get(name);
         if (!rendererType) {
-            throw new Error(`unknown alignments view name ${viewName}`);
+            throw new Error(`unknown renderer ${name}`);
         }
         return rendererType;
     },
@@ -140,27 +154,30 @@ const stateModelFactory = (pluginManager, configSchema) => types
         return self.scale || getConf(self, 'scaleType');
     },
     get maxScore() {
-        const { max } = self.constraints;
-        return max !== null && max !== void 0 ? max : getConf(self, 'maxScore');
+        var _a;
+        return (_a = self.constraints.max) !== null && _a !== void 0 ? _a : getConf(self, 'maxScore');
     },
     get minScore() {
-        const { min } = self.constraints;
-        return min !== null && min !== void 0 ? min : getConf(self, 'minScore');
+        var _a;
+        return (_a = self.constraints.min) !== null && _a !== void 0 ? _a : getConf(self, 'minScore');
     },
 }))
     .views(self => ({
     get rendererConfig() {
         const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
-        const { color, posColor, negColor, summaryScoreMode, scaleType, displayCrossHatches, fill, } = self;
+        const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, } = self;
         return self.rendererType.configSchema.create({
             ...configBlob,
             ...(scaleType ? { scaleType } : {}),
-            ...(fill ? { filled: fill } : {}),
-            ...(displayCrossHatches ? { displayCrossHatches } : {}),
-            ...(summaryScoreMode ? { summaryScoreMode } : {}),
-            ...(color ? { color } : {}),
-            ...(negColor ? { negColor } : {}),
-            ...(posColor ? { posColor } : {}),
+            ...(fill !== undefined ? { filled: fill } : {}),
+            ...(displayCrossHatches !== undefined
+                ? { displayCrossHatches }
+                : {}),
+            ...(summaryScoreMode !== undefined ? { summaryScoreMode } : {}),
+            ...(color !== undefined ? { color } : {}),
+            ...(negColor !== undefined ? { negColor } : {}),
+            ...(posColor !== undefined ? { posColor } : {}),
+            ...(minSize !== undefined ? { minSize } : {}),
         }, getEnv(self));
     },
 }))
@@ -222,18 +239,23 @@ const stateModelFactory = (pluginManager, configSchema) => types
     get ticks() {
         const { scaleType, domain, height } = self;
         const minimalTicks = getConf(self, 'minimalTicks');
+        const inverted = getConf(self, 'inverted');
         const range = [height - YSCALEBAR_LABEL_OFFSET, YSCALEBAR_LABEL_OFFSET];
         const scale = getScale({
             scaleType,
             domain,
             range,
-            inverted: getConf(self, 'inverted'),
+            inverted,
         });
         const ticks = axisPropsFromTickScale(scale, 4);
         return height < 100 || minimalTicks
             ? { ...ticks, values: domain }
             : ticks;
     },
+    get adapterCapabilities() {
+        return pluginManager.getAdapterType(self.adapterTypeName)
+            .adapterCapabilities;
+    },
 }))
     .views(self => {
     const { renderProps: superRenderProps } = self;
@@ -255,15 +277,22 @@ const stateModelFactory = (pluginManager, configSchema) => types
                 filters,
             };
         },
-        get adapterCapabilities() {
-            return pluginManager.getAdapterType(self.adapterTypeName)
-                .adapterCapabilities;
-        },
         get hasResolution() {
-            return this.adapterCapabilities.includes('hasResolution');
+            return self.adapterCapabilities.includes('hasResolution');
         },
         get hasGlobalStats() {
-            return this.adapterCapabilities.includes('hasGlobalStats');
+            return self.adapterCapabilities.includes('hasGlobalStats');
+        },
+        get fillSetting() {
+            if (self.filled) {
+                return 0;
+            }
+            else if (!self.filled && self.minSize === 1) {
+                return 1;
+            }
+            else {
+                return 2;
+            }
         },
     };
 })
@@ -293,6 +322,8 @@ const stateModelFactory = (pluginManager, configSchema) => types
                             label: 'Summary score mode',
                             subMenu: ['min', 'max', 'avg', 'whiskers'].map(elt => ({
                                 label: elt,
+                                type: 'radio',
+                                checked: self.summaryScoreModeSetting === elt,
                                 onClick: () => self.setSummaryScoreMode(elt),
                             })),
                         },
@@ -301,10 +332,13 @@ const stateModelFactory = (pluginManager, configSchema) => types
                 ...(self.canHaveFill
                     ? [
                         {
-                            label: self.filled
-                                ? 'Turn off histogram fill'
-                                : 'Turn on histogram fill',
-                            onClick: () => self.setFill(!self.filled),
+                            label: 'Fill mode',
+                            subMenu: ['filled', 'no fill', 'no fill w/ emphasis'].map((elt, idx) => ({
+                                label: elt,
+                                type: 'radio',
+                                checked: self.fillSetting === idx,
+                                onClick: () => self.setFill(idx),
+                            })),
                         },
                     ]
                     : []),
@@ -312,18 +346,24 @@ const stateModelFactory = (pluginManager, configSchema) => types
                     label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
                     onClick: () => self.toggleLogScale(),
                 },
-                {
-                    type: 'checkbox',
-                    label: 'Draw cross hatches',
-                    checked: self.displayCrossHatchesSetting,
-                    onClick: () => self.toggleCrossHatches(),
-                },
+                ...(self.needsScalebar
+                    ? [
+                        {
+                            type: 'checkbox',
+                            label: 'Draw cross hatches',
+                            checked: self.displayCrossHatchesSetting,
+                            onClick: () => self.toggleCrossHatches(),
+                        },
+                    ]
+                    : []),
                 ...(hasRenderings
                     ? [
                         {
                             label: 'Renderer type',
                             subMenu: ['xyplot', 'density', 'line'].map(key => ({
                                 label: key,
+                                type: 'radio',
+                                checked: self.rendererTypeNameSimple === key,
                                 onClick: () => self.setRendererType(key),
                             })),
                         },
@@ -342,6 +382,8 @@ const stateModelFactory = (pluginManager, configSchema) => types
                         ['localsd', 'Local ± 3σ'],
                     ].map(([val, label]) => ({
                         label,
+                        type: 'radio',
+                        checked: self.autoscaleType === val,
                         onClick: () => self.setAutoscale(val),
                     })),
                 },
@@ -369,66 +411,6 @@ const stateModelFactory = (pluginManager, configSchema) => types
 })
     .actions(self => {
     const { reload: superReload, renderSvg: superRenderSvg } = self;
-    async function getStats(opts) {
-        const { rpcManager } = getSession(self);
-        const nd = getConf(self, 'numStdDev') || 3;
-        const { adapterConfig, autoscaleType } = self;
-        const sessionId = getRpcSessionId(self);
-        const params = {
-            sessionId,
-            adapterConfig,
-            statusCallback: (message) => {
-                if (isAlive(self)) {
-                    self.setMessage(message);
-                }
-            },
-            ...opts,
-        };
-        if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
-            const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalStats', params));
-            const { scoreMin, scoreMean, scoreStdDev } = results;
-            // globalsd uses heuristic to avoid unnecessary scoreMin<0
-            // if the scoreMin is never less than 0
-            // helps with most coverage bigwigs just being >0
-            return autoscaleType === 'globalsd'
-                ? {
-                    ...results,
-                    scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
-                    scoreMax: scoreMean + nd * scoreStdDev,
-                }
-                : results;
-        }
-        if (autoscaleType === 'local' || autoscaleType === 'localsd') {
-            const { dynamicBlocks, bpPerPx } = getContainingView(self);
-            const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionStats', {
-                ...params,
-                regions: dynamicBlocks.contentBlocks.map(region => {
-                    const { start, end } = region;
-                    return {
-                        ...JSON.parse(JSON.stringify(region)),
-                        start: Math.floor(start),
-                        end: Math.ceil(end),
-                    };
-                }),
-                bpPerPx,
-            }));
-            const { scoreMin, scoreMean, scoreStdDev } = results;
-            // localsd uses heuristic to avoid unnecessary scoreMin<0 if the
-            // scoreMin is never less than 0 helps with most coverage bigwigs
-            // just being >0
-            return autoscaleType === 'localsd'
-                ? {
-                    ...results,
-                    scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
-                    scoreMax: scoreMean + nd * scoreStdDev,
-                }
-                : results;
-        }
-        if (autoscaleType === 'zscale') {
-            return rpcManager.call(sessionId, 'WiggleGetGlobalStats', params);
-        }
-        throw new Error(`invalid autoscaleType '${autoscaleType}'`);
-    }
     return {
         // re-runs stats and refresh whole display on reload
         async reload() {
@@ -436,7 +418,7 @@ const stateModelFactory = (pluginManager, configSchema) => types
             const aborter = new AbortController();
             self.setLoading(aborter);
             try {
-                const stats = await getStats({
+                const stats = await getStats(self, {
                     signal: aborter.signal,
                     ...self.renderProps(),
                 });
@@ -450,35 +432,7 @@ const stateModelFactory = (pluginManager, configSchema) => types
             }
         },
         afterAttach() {
-            addDisposer(self, autorun(async () => {
-                try {
-                    const view = getContainingView(self);
-                    if (!view.initialized) {
-                        return;
-                    }
-                    if (!self.estimatedStatsReady) {
-                        return;
-                    }
-                    if (self.regionTooLarge) {
-                        return;
-                    }
-                    const aborter = new AbortController();
-                    self.setLoading(aborter);
-                    const wiggleStats = await getStats({
-                        signal: aborter.signal,
-                        ...self.renderProps(),
-                    });
-                    if (isAlive(self)) {
-                        self.updateStats(wiggleStats);
-                    }
-                }
-                catch (e) {
-                    if (!isAbortException(e) && isAlive(self)) {
-                        console.error(e);
-                        self.setError(e);
-                    }
-                }
-            }, { delay: 1000 }));
+            statsAutorun(self);
         },
         async renderSvg(opts) {
             await when(() => self.statsReady && !!self.regionCannotBeRenderedText);