Fix ability to choose line plot bigwig coloring (#4385)

GMOD · May 13, 2024 · 1bdf5ce · 1bdf5ce
1 parent 1e131e0
commit 1bdf5ce
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Showing 5 changed files with 201 additions and 287 deletions.
diff --git a/plugins/data-management/src/HierarchicalTrackSelectorWidget/model.ts b/plugins/data-management/src/HierarchicalTrackSelectorWidget/model.ts
@@ -502,42 +502,45 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
           self,
           autorun(() => {
             const { assemblyNames, view } = self
+
             self.setRecentlyUsed(
               localStorageGetJSON<string[]>(recentlyUsedK(assemblyNames), '[]'),
             )
-            const val = localStorageGetItem(
-              collapsedK(assemblyNames, view.type),
-            )
-            if (!val) {
-              self.expandAllCategories()
-              const session = getSession(self)
-              if (
-                getConf(session, [
+            if (view) {
+              const val = localStorageGetItem(
+                collapsedK(assemblyNames, view.type),
+              )
+              if (!val) {
+                self.expandAllCategories()
+                const session = getSession(self)
+                if (
+                  getConf(session, [
+                    'hierarchical',
+                    'defaultCollapsed',
+                    'topLevelCategories',
+                  ])
+                ) {
+                  self.collapseTopLevelCategories()
+                }
+                if (
+                  getConf(session, [
+                    'hierarchical',
+                    'defaultCollapsed',
+                    'subCategories',
+                  ])
+                ) {
+                  self.collapseSubCategories()
+                }
+                for (const entry of getConf(session, [
                   'hierarchical',
                   'defaultCollapsed',
-                  'topLevelCategories',
-                ])
-              ) {
-                self.collapseTopLevelCategories()
+                  'categoryNames',
+                ])) {
+                  self.setCategoryCollapsed(`Tracks-${entry}`, true)
+                }
+              } else {
+                self.setCollapsedCategories(JSON.parse(val))
               }
-              if (
-                getConf(session, [
-                  'hierarchical',
-                  'defaultCollapsed',
-                  'subCategories',
-                ])
-              ) {
-                self.collapseSubCategories()
-              }
-              for (const entry of getConf(session, [
-                'hierarchical',
-                'defaultCollapsed',
-                'categoryNames',
-              ])) {
-                self.setCategoryCollapsed(`Tracks-${entry}`, true)
-              }
-            } else {
-              self.setCollapsedCategories(JSON.parse(val))
             }
           }),
         )
@@ -547,10 +550,15 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
           autorun(() => {
             const { assemblyNames, collapsed, view } = self
             localStorageSetJSON(recentlyUsedK(assemblyNames), self.recentlyUsed)
-            localStorageSetJSON(collapsedK(assemblyNames, view.type), collapsed)
             localStorageSetJSON(favoritesK(), self.favorites)
             localStorageSetJSON(sortTrackNamesK(), self.sortTrackNames)
             localStorageSetJSON(sortCategoriesK(), self.sortCategories)
+            if (view) {
+              localStorageSetJSON(
+                collapsedK(assemblyNames, view.type),
+                collapsed,
+              )
+            }
           }),
         )
       },

diff --git a/plugins/wiggle/src/LinePlotRenderer/LinePlotRenderer.ts b/plugins/wiggle/src/LinePlotRenderer/LinePlotRenderer.ts
@@ -1,3 +1,5 @@
+import { readConfObject } from '@jbrowse/core/configuration'
+import { Feature } from '@jbrowse/core/util'
 import WiggleBaseRenderer, {
   RenderArgsDeserializedWithFeatures,
 } from '../WiggleBaseRenderer'
@@ -10,10 +12,15 @@ export default class LinePlotRenderer extends WiggleBaseRenderer {
     ctx: CanvasRenderingContext2D,
     props: RenderArgsDeserializedWithFeatures,
   ) {
+    const { config } = props
+    const c = readConfObject(config, 'color')
     return drawLine(ctx, {
       ...props,
       offset: YSCALEBAR_LABEL_OFFSET,
-      colorCallback: () => 'grey',
+      colorCallback:
+        c === '#f0f'
+          ? () => 'grey'
+          : (feature: Feature) => readConfObject(config, 'color', { feature }),
     })
   }
 }
diff --git a/plugins/wiggle/src/LinearWiggleDisplay/components/SetColorDialog.tsx b/plugins/wiggle/src/LinearWiggleDisplay/components/SetColorDialog.tsx
@@ -39,13 +39,13 @@ const SetColorDialog = observer(function SetColorDialog({
           checked={!posneg}
           onClick={() => setPosNeg(false)}
           control={<Radio />}
-          label={'Overall color'}
+          label="Overall color"
         />
         <FormControlLabel
           checked={posneg}
           onClick={() => setPosNeg(true)}
           control={<Radio />}
-          label={'Positive/negative color'}
+          label="Positive/negative color"
         />
 
         {posneg ? (

diff --git a/plugins/wiggle/src/WiggleBaseRenderer.tsx b/plugins/wiggle/src/WiggleBaseRenderer.tsx
@@ -4,6 +4,8 @@ import FeatureRendererType, {
 } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
 import { renderToAbstractCanvas, Feature } from '@jbrowse/core/util'
 import { ThemeOptions } from '@mui/material'
+
+// locals
 import { ScaleOpts, Source } from './util'
 
 export interface RenderArgs extends FeatureRenderArgs {