Phased

GMOD · Jan 28, 2025 · f1a427c · f1a427c
1 parent e832413
commit f1a427c
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Showing 6 changed files with 23 additions and 18 deletions.
diff --git a/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts b/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts
@@ -59,7 +59,7 @@ export default function stateModelFactory(
           ...superProps,
           notReady:
             superProps.notReady || !self.sources || !self.featuresVolatile,
-          phasedMode: self.phasedMode,
+          renderingMode: self.renderingMode,
           minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
           height: self.totalHeight,
           sources: self.sources,

diff --git a/plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts b/plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts
@@ -74,8 +74,12 @@ export function makeImageData({
   canvasHeight: number
   renderArgs: RenderArgsDeserializedWithFeaturesAndLayout
 }) {
-  const { phasedMode, minorAlleleFrequencyFilter, sources, features } =
-    renderArgs
+  const {
+    renderingMode: renderingMode,
+    minorAlleleFrequencyFilter,
+    sources,
+    features,
+  } = renderArgs
   const h = canvasHeight / sources.length
   const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(
     features.values(),
@@ -95,7 +99,7 @@ export function makeImageData({
       const genotype = samp[name]
       if (genotype) {
         const isPhased = genotype.includes('|')
-        if (phasedMode === 'phasedOnly') {
+        if (renderingMode === 'phased') {
           if (isPhased) {
             const alleles = genotype.split('|')
             drawPhased(alleles, ctx, x, y, w, h, HP!)

diff --git a/plugins/variants/src/MultiLinearVariantMatrixRenderer/types.ts b/plugins/variants/src/MultiLinearVariantMatrixRenderer/types.ts
@@ -7,12 +7,12 @@ export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
   minorAlleleFrequencyFilter: number
   highResolutionScaling: number
   height: number
-  phasedMode: string
+  renderingMode: string
 }
 
 export interface RenderArgsDeserializedWithFeaturesAndLayout
   extends RenderArgsDeserialized {
   sources: Source[]
   features: Map<string, Feature>
-  phasedMode: string
+  renderingMode: string
 }
diff --git a/plugins/variants/src/VariantRPC/MultiVariantGetSimplifiedFeatures.ts b/plugins/variants/src/VariantRPC/MultiVariantGetSimplifiedFeatures.ts
@@ -53,7 +53,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         sampleInfo[key] = {
           maxPloidy: Math.max(
             sampleInfo[key]?.maxPloidy || 0,
-            val.split(/|/).length,
+            val.split('|').length,
           ),
           isPhased: sampleInfo[key]?.isPhased || isPhased,
         }

diff --git a/plugins/variants/src/shared/ClusterDialog.tsx b/plugins/variants/src/shared/ClusterDialog.tsx
@@ -34,7 +34,7 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
-export default function HierarchicalCluster({
+export default function ClusterDialog({
   model,
   handleClose,
 }: {

diff --git a/plugins/variants/src/shared/MultiVariantBaseModel.tsx b/plugins/variants/src/shared/MultiVariantBaseModel.tsx
@@ -58,7 +58,7 @@ export default function MultiVariantBaseModelF(
         /**
          * #property
          */
-        phasedMode: types.optional(types.string, 'none'),
+        renderingMode: types.optional(types.string, 'none'),
       }),
     )
     .volatile(() => ({
@@ -144,7 +144,7 @@ export default function MultiVariantBaseModelF(
        * #action
        */
       setPhasedMode(arg: string) {
-        self.phasedMode = arg
+        self.renderingMode = arg
       },
       /**
        * #action
@@ -179,7 +179,7 @@ export default function MultiVariantBaseModelF(
           )
           for (const row of this.preSources) {
             // make separate rows for each haplotype in phased mode
-            if (self.phasedMode === 'phasedOnly') {
+            if (self.renderingMode === 'phased') {
               const info = self.sampleInfo?.[row.name]
               if (info?.isPhased) {
                 const ploidy = info.maxPloidy
@@ -240,34 +240,35 @@ export default function MultiVariantBaseModelF(
                 self.setShowSidebarLabels(!self.showSidebarLabelsSetting)
               },
             },
+
             ...(self.hasPhased
               ? [
                   {
-                    label: 'Phased mode',
+                    label: 'Rendering mode',
                     type: 'subMenu',
                     subMenu: [
                       {
-                        label: 'Draw unphased (maps allele count to color)',
+                        label: 'Allele count mode',
                         type: 'radio',
-                        checked: self.phasedMode === 'none',
+                        checked: self.renderingMode === 'none',
                         onClick: () => {
                           self.setPhasedMode('none')
                         },
                       },
                       {
-                        label: 'Draw phased (split into haplotype rows)',
-                        checked: self.phasedMode === 'phasedOnly',
+                        label: 'Phased mode',
+                        checked: self.renderingMode === 'phased',
                         type: 'radio',
                         onClick: () => {
-                          self.setPhasedMode('phasedOnly')
+                          self.setPhasedMode('phased')
                         },
                       },
                     ],
                   },
                 ]
               : []),
             {
-              label: 'Set minor allele frequency filter',
+              label: 'Filter by minor allele frequency',
               onClick: () => {
                 getSession(self).queueDialog(handleClose => [
                   MAFFilterDialog,
-Original file line number
+Diff line change
@@ Expand Up / @@ -34,7 +34,7 @@ const useStyles = makeStyles()(theme => ({ @@
       },
     }))
-    export default function HierarchicalCluster({
+    export default function ClusterDialog({
       model,
       handleClose,
     }: {
@@ Expand Down @@