Merge pull request #332 from vgteam/highlightReferencePaths

Highlight reference paths
vgteam · Aug 31, 2023 · dbbdf1e · dbbdf1e
2 parents 586b044 + c739059
commit dbbdf1e
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Showing 3 changed files with 11 additions and 10 deletions.
diff --git a/src/components/TrackSettings.js b/src/components/TrackSettings.js
@@ -38,7 +38,6 @@ export const TrackSettings = ({
 
     function colorRenderSwitch(fileType) {
         switch(fileType) {
-            case "graph":
             case "haplotype":
                 return(
                     <Form>
@@ -64,13 +63,14 @@ export const TrackSettings = ({
                         </Row>
                     </Form>
                 );
+            case "graph":
             case  "read":
                 return(
                     <Form>
                         <Row>
                             <Col className="radio-row">
                                 <RadioRow
-                                    rowHeading="Forward Reads"
+                                    rowHeading={fileType === "read" ? "Forward Reads" : "Reference Path"}
                                     color={trackColorSettings.mainPalette}
                                     setting="mainPalette"
                                     setColorSetting={setTrackColorSetting}
@@ -90,7 +90,7 @@ export const TrackSettings = ({
                         <Row>
                             <Col className="radio-row">
                                 <RadioRow
-                                    rowHeading="Reverse Reads"
+                                    rowHeading={fileType === "read" ? "Reverse Reads" : "Non-Reference Path"}
                                     color={trackColorSettings.auxPalette}
                                     setting="auxPalette"
                                     setColorSetting={setTrackColorSetting}

diff --git a/src/config.json b/src/config.json
@@ -61,8 +61,8 @@
   },
 
   "defaultReadColorPalette" : {
-    "mainPalette": "reds", 
-    "auxPalette": "blues", 
+    "mainPalette": "blues", 
+    "auxPalette": "reds", 
     "colorReadsByMappingQuality": false
   },
 

diff --git a/src/util/tubemap.js b/src/util/tubemap.js
@@ -2480,18 +2480,19 @@ function generateTrackColor(track, highlight) {
       // Don't repeat the color of the first track (reference) to highilight is better.
       // TODO: Allow using color 0 for other schemes not the same as the one for the reference path.
       // TODO: Stop reads from taking this color?
-
-      const colorSet = getColorSet(config.colorSchemes[sourceID].mainPalette);
-      if (track.id === 0 || colorSet.length === 1) {
-        trackColor = colorSet[0];
+      const auxColorSet = getColorSet(config.colorSchemes[sourceID].auxPalette);
+      const primaryColorSet = getColorSet(config.colorSchemes[sourceID].mainPalette);
+      if (track.id === 0) {
+        trackColor = primaryColorSet[0];
       } else {
-        trackColor = colorSet[((track.id - 1) % (colorSet.length - 1)) + 1];
+        trackColor = auxColorSet[((track.id - 1) % (auxColorSet.length))];
       }
     } else {
       const colorSet = getColorSet(config.exonColors);
       trackColor = colorSet[track.id % colorSet.length];
     }
   }
+  console.log("trackColor:", trackColor)
   return trackColor;
 }