@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

package/src/MultiLinearWiggleDisplay/models/renderSvg.tsx

@@ -0,0 +1,26 @@
+import React from 'react'
+import { getContainingView } from '@jbrowse/core/util'
+import { when } from 'mobx'
+import {
+  ExportSvgDisplayOptions,
+  LinearGenomeViewModel,
+} from '@jbrowse/plugin-linear-genome-view'
+import { WiggleDisplayModel } from './model'
+import { StatBars } from '../components/WiggleDisplayComponent'
+
+export async function renderSvg(
+  self: WiggleDisplayModel,
+  opts: ExportSvgDisplayOptions,
+  superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>,
+) {
+  await when(() => !!self.stats && !!self.regionCannotBeRenderedText)
+  const { offsetPx } = getContainingView(self) as LinearGenomeViewModel
+  return (
+    <>
+      <g id="snpcov">{await superRenderSvg(opts)}</g>
+      <g transform={`translate(${Math.max(-offsetPx, 0)})`}>
+        <StatBars model={self} orientation="left" exportSVG />
+      </g>
+    </>
+  )
+}

package/src/MultiRowLineRenderer/MultiRowLineRenderer.ts

@@ -1,5 +1,4 @@
-import { Feature } from '@jbrowse/core/util'
-import { groupBy } from '../util'
+import { groupBy, Feature } from '@jbrowse/core/util'
 import { drawLine } from '../drawxy'
 import WiggleBaseRenderer, {
   MultiRenderArgsDeserialized as MultiArgs,

package/src/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.ts

@@ -1,5 +1,4 @@
-import { Feature } from '@jbrowse/core/util'
-import { groupBy } from '../util'
+import { groupBy, Feature } from '@jbrowse/core/util'
 import { drawXY } from '../drawxy'
 
 import WiggleBaseRenderer, {

package/src/MultiWiggleAdapter/MultiWiggleAdapter.ts

@@ -106,7 +106,7 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
   }
 
   // always render bigwig instead of calculating a feature density for it
-  async estimateRegionsStats(_regions: Region[]) {
+  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
     return { featureDensity: 0 }
   }
 

package/src/MultiWiggleAddTrackWidget/AddTrackWorkflow.tsx

@@ -77,7 +77,7 @@ export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
           const session = getSession(model)
 
           const trackId = [
-            `${trackName.toLowerCase().replace(/ /g, '_')}-${Date.now()}`,
+            `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
             `${session.adminMode ? '' : '-sessionTrack'}`,
           ].join('')
 

package/src/MultiXYPlotRenderer/MultiXYPlotRenderer.ts

@@ -1,6 +1,6 @@
-import { Feature } from '@jbrowse/core/util'
+import { groupBy, Feature } from '@jbrowse/core/util'
 import { drawXY } from '../drawxy'
-import { groupBy, YSCALEBAR_LABEL_OFFSET } from '../util'
+import { YSCALEBAR_LABEL_OFFSET } from '../util'
 
 import WiggleBaseRenderer, {
   MultiRenderArgsDeserialized as MultiArgs,

package/src/WiggleRPC/MultiWiggleGetSources.ts

@@ -0,0 +1,68 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+export class MultiWiggleGetSources extends RpcMethodType {
+  name = 'MultiWiggleGetSources'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async serializeArguments(
+    args: RenderArgs & {
+      signal?: AbortSignal
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      signal?: RemoteAbortSignal
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    return dataAdapter.getSources(regions, deserializedArgs)
+  }
+}

package/src/WiggleRPC/WiggleGetGlobalQuantitativeStats.ts

@@ -0,0 +1,44 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { QuantitativeStats } from '@jbrowse/core/util/stats'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+export class WiggleGetGlobalQuantitativeStats extends RpcMethodType {
+  name = 'WiggleGetGlobalQuantitativeStats'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      signal?: RemoteAbortSignal
+      headers?: Record<string, string>
+      sessionId: string
+    },
+    rpcDriverClassName: string,
+  ): Promise<QuantitativeStats> {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    return dataAdapter.getGlobalStats(deserializedArgs)
+  }
+}

package/src/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.ts

@@ -0,0 +1,73 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { Region, renameRegionsIfNeeded } from '@jbrowse/core/util'
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+
+export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
+  name = 'WiggleGetMultiRegionQuantitativeStats'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async serializeArguments(
+    args: RenderArgs & {
+      signal?: AbortSignal
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: {}
+      signal?: RemoteAbortSignal
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    if (dataAdapter instanceof BaseFeatureDataAdapter) {
+      return dataAdapter.getMultiRegionQuantitativeStats(
+        regions,
+        deserializedArgs,
+      )
+    }
+    throw new Error('Data adapter not found')
+  }
+}

package/src/WiggleRPC/rpcMethods.ts

@@ -1,170 +1,3 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
-import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FeatureStats } from '@jbrowse/core/util/stats'
-
-export class WiggleGetGlobalStats extends RpcMethodType {
-  name = 'WiggleGetGlobalStats'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      sessionId: string
-    },
-    rpcDriverClassName: string,
-  ): Promise<FeatureStats> {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    // @ts-expect-error
-    return dataAdapter.getGlobalStats(deserializedArgs)
-  }
-}
-
-export class WiggleGetMultiRegionStats extends RpcMethodType {
-  name = 'WiggleGetMultiRegionStats'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const assemblyManager = pm.rootModel?.session?.assemblyManager
-    if (!assemblyManager) {
-      return args
-    }
-
-    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-      ...args,
-      filters: args.filters?.toJSON().filters,
-    })
-
-    return super.serializeArguments(renamedArgs, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      sessionId: string
-      headers?: Record<string, string>
-      regions: Region[]
-      bpPerPx: number
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { regions, adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    if (dataAdapter instanceof BaseFeatureDataAdapter) {
-      return dataAdapter.getMultiRegionStats(regions, deserializedArgs)
-    }
-    throw new Error('Data adapter not found')
-  }
-}
-
-export class MultiWiggleGetSources extends RpcMethodType {
-  name = 'MultiWiggleGetSources'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const assemblyManager = pm.rootModel?.session?.assemblyManager
-    if (!assemblyManager) {
-      return args
-    }
-
-    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-      ...args,
-      filters: args.filters?.toJSON().filters,
-    })
-
-    return super.serializeArguments(renamedArgs, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      sessionId: string
-      headers?: Record<string, string>
-      regions: Region[]
-      bpPerPx: number
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { regions, adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    // @ts-expect-error
-    return dataAdapter.getSources(regions, deserializedArgs)
-  }
-}
+export * from './MultiWiggleGetSources'
+export * from './WiggleGetMultiRegionQuantitativeStats'
+export * from './WiggleGetGlobalQuantitativeStats'

package/src/index.ts

@@ -30,8 +30,8 @@ import MultiWiggleAddTrackWidgetF from './MultiWiggleAddTrackWidget'
 import * as utils from './util'
 
 import {
-  WiggleGetGlobalStats,
-  WiggleGetMultiRegionStats,
+  WiggleGetGlobalQuantitativeStats,
+  WiggleGetMultiRegionQuantitativeStats,
   MultiWiggleGetSources,
 } from './WiggleRPC/rpcMethods'
 
@@ -101,8 +101,8 @@ export default class WigglePlugin extends Plugin {
       },
     )
 
-    pm.addRpcMethod(() => new WiggleGetGlobalStats(pm))
-    pm.addRpcMethod(() => new WiggleGetMultiRegionStats(pm))
+    pm.addRpcMethod(() => new WiggleGetGlobalQuantitativeStats(pm))
+    pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm))
     pm.addRpcMethod(() => new MultiWiggleGetSources(pm))
   }
 

package/src/shared/YScaleBar.tsx

@@ -3,11 +3,13 @@ import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import { axisPropsFromTickScale, Axis, LEFT, RIGHT } from 'react-d3-axis-mod'
 
-export default observer(function ({
+type Ticks = ReturnType<typeof axisPropsFromTickScale>
+
+export default observer(function YScaleBar({
   model,
   orientation,
 }: {
-  model: { ticks?: ReturnType<typeof axisPropsFromTickScale> }
+  model: { ticks?: Ticks }
   orientation?: string
 }) {
   const { ticks } = model

package/src/shared/configShared.ts

@@ -0,0 +1,90 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
+import { types } from 'mobx-state-tree'
+
+/**
+ * #config SharedWiggleDisplay
+ */
+export default function sharedWiggleConfigFactory() {
+  return ConfigurationSchema(
+    'MultiLinearWiggleDisplay',
+    {
+      /**
+       * #slot
+       */
+      autoscale: {
+        type: 'stringEnum',
+        defaultValue: 'local',
+        model: types.enumeration('Autoscale type', [
+          'global',
+          'local',
+          'globalsd',
+          'localsd',
+          'zscore',
+        ]),
+        description:
+          'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
+      },
+
+      /**
+       * #slot
+       */
+      minimalTicks: {
+        type: 'boolean',
+        defaultValue: false,
+        description: 'use the minimal amount of ticks',
+      },
+
+      /**
+       * #slot
+       */
+      minScore: {
+        type: 'number',
+        defaultValue: Number.MIN_VALUE,
+        description: 'minimum value for the y-scale',
+      },
+      /**
+       * #slot
+       */
+      maxScore: {
+        type: 'number',
+        description: 'maximum value for the y-scale',
+        defaultValue: Number.MAX_VALUE,
+      },
+      /**
+       * #slot
+       */
+      numStdDev: {
+        type: 'number',
+        description:
+          'number of standard deviations to use for autoscale types globalsd or localsd',
+        defaultValue: 3,
+      },
+      /**
+       * #slot
+       */
+      scaleType: {
+        type: 'stringEnum',
+        model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale
+        description: 'The type of scale to use',
+        defaultValue: 'linear',
+      },
+
+      /**
+       * #slot
+       */
+      inverted: {
+        type: 'boolean',
+        description: 'draw upside down',
+        defaultValue: false,
+      },
+    },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: baseLinearDisplayConfigSchema,
+      explicitlyTyped: true,
+    },
+  )
+}