diff --git a/src/App.js b/src/App.js
index 24d25228..beea0316 100644
--- a/src/App.js
+++ b/src/App.js
@@ -68,6 +68,7 @@ class App extends Component {
         alphaReadsByMappingQuality: false,
         colorSchemes: getColorSchemesFromTracks(this.defaultViewTarget.tracks),
         mappingQualityCutoff: 0,
+        hiddenTracks: [],
       },
       APIInterface: new ServerAPI(props.apiUrl)
     };
@@ -95,6 +96,7 @@ class App extends Component {
             visOptions: {
               ...state.visOptions,
               colorSchemes: [],
+              hiddenTracks: [],
             },
           };
         } else if (mode === "server") {
@@ -107,6 +109,7 @@ class App extends Component {
             visOptions: {
               ...state.visOptions,
               colorSchemes: getColorSchemesFromTracks(this.defaultViewTarget.tracks),
+              hiddenTracks: [],
             },
           };
         } else {
@@ -199,6 +202,15 @@ class App extends Component {
     }));
   };
 
+  handleTrackVisibilityChanged = (hiddenTrackIds) => {
+    this.setState((state) => ({
+      visOptions: {
+        ...state.visOptions,
+        hiddenTracks: hiddenTrackIds,
+      },
+    }));
+  };
+
   // Set a color scheme setting for a particular track.
   //
   // key is the name of the setting to set, and may be "mainPalette", "auxPalette", or "colorByMappingQuality".
@@ -251,6 +263,7 @@ class App extends Component {
           dataOrigin={this.state.dataOrigin}
           visOptions={this.state.visOptions}
           APIInterface={this.state.APIInterface}
+          onTrackVisibilityChanged={this.handleTrackVisibilityChanged}
         />
         <CustomizationAccordion
           enableCompressedNodes={this.state.viewTarget.removeSequences}
diff --git a/src/components/TubeMap.js b/src/components/TubeMap.js
index 3204f779..909e914c 100644
--- a/src/components/TubeMap.js
+++ b/src/components/TubeMap.js
@@ -5,6 +5,7 @@ import isEqual from "react-fast-compare";
 
 class TubeMap extends Component {
   componentDidMount() {
+    this.setupCallback();
     this.updateVisOptions();
     this.createTubeMap();
   }
@@ -16,6 +17,7 @@ class TubeMap extends Component {
     console.log("Old read count:", (prevProps.reads || []).length);
     if (!isEqual(this.props, prevProps)) {
       console.log("Props have changed so re-creating tube map");
+      this.setupCallback();
       this.updateVisOptions();
       this.createTubeMap();
     } else {
@@ -23,6 +25,12 @@ class TubeMap extends Component {
     }
   }
 
+  setupCallback() {
+    if (this.props.onTrackVisibilityChanged) {
+      tubeMap.setVisibilityChangedCallback(this.props.onTrackVisibilityChanged);
+    }
+  }
+
   createTubeMap = () => {
     tubeMap.create({
       svgID: "#svg",
@@ -50,6 +58,7 @@ class TubeMap extends Component {
     tubeMap.setShowReadsFlag(visOptions.showReads);
     tubeMap.setSoftClipsFlag(visOptions.showSoftClips);
     tubeMap.setColoredNodes(visOptions.coloredNodes);
+    tubeMap.setHiddenTrackIds(visOptions.hiddenTracks || []);
 
     for (let key of Object.keys(visOptions.colorSchemes)) {
       // Apply color-by-mapping-quality parameter to all the schemes.
@@ -76,7 +85,8 @@ TubeMap.propTypes = {
   reads: PropTypes.array.isRequired,
   region: PropTypes.array.isRequired,
   visOptions: PropTypes.object.isRequired,
-  nodeSequences: PropTypes.bool
+  nodeSequences: PropTypes.bool,
+  onTrackVisibilityChanged: PropTypes.func,
 };
 
 TubeMap.defaultProps = {
diff --git a/src/components/TubeMapContainer.js b/src/components/TubeMapContainer.js
index f3478f64..530b44db 100644
--- a/src/components/TubeMapContainer.js
+++ b/src/components/TubeMapContainer.js
@@ -126,6 +126,7 @@ class TubeMapContainer extends Component {
               ...this.props.visOptions,
             }}
             nodeSequences={!this.props.viewTarget.removeSequences}
+            onTrackVisibilityChanged={this.props.onTrackVisibilityChanged}
           />
         </div>
       </div>
@@ -326,6 +327,7 @@ TubeMapContainer.propTypes = {
   viewTarget: PropTypes.object.isRequired,
   visOptions: PropTypes.object.isRequired,
   APIInterface: PropTypes.object.isRequired,
+  onTrackVisibilityChanged: PropTypes.func,
 };
 
 export default TubeMapContainer;
diff --git a/src/util/tubemap.js b/src/util/tubemap.js
index 062938d8..5efb45dc 100644
--- a/src/util/tubemap.js
+++ b/src/util/tubemap.js
@@ -159,6 +159,8 @@ const config = {
   showInfoCallback: function (info) {
     alert(info);
   },
+  hiddenTrackIds: new Set(),
+  visibilityChangedCallback: null,
 };
 
 // variables for storing info which can be directly translated into drawing instructions
@@ -191,6 +193,13 @@ export function create(params) {
   // And then leave a hole in the array at 0 which we won't iterate over.
   delete inputNodes[0];
   inputTracks = deepCopy(params.tracks); // deep copy
+  inputTracks.forEach((t) => {
+    if (!t.type) t.type = "haplotype";
+  });
+  config.hiddenTrackIds.forEach((id) => {
+    const track = inputTracks.find((t) => t.id === id);
+    if (track) track.hidden = true;
+  });
   inputReads = params.reads || null;
   inputRegion = params.region;
   bed = params.bed || null;
@@ -311,6 +320,14 @@ export function changeTrackVisibility(trackID) {
     } else {
       inputTracks[i].hidden = true;
     }
+    if (inputTracks[i].hidden) {
+      config.hiddenTrackIds.add(trackID);
+    } else {
+      config.hiddenTrackIds.delete(trackID);
+    }
+    if (config.visibilityChangedCallback) {
+      config.visibilityChangedCallback(Array.from(config.hiddenTrackIds));
+    }
   }
   createTubeMap();
 }
@@ -318,12 +335,19 @@ export function changeTrackVisibility(trackID) {
 // to select/deselect all
 export function changeAllTracksVisibility(value) {
   let i = 0;
+  config.hiddenTrackIds.clear();
   while (i < inputTracks.length) {
     inputTracks[i].hidden = !value;
+    if (!value) {
+      config.hiddenTrackIds.add(inputTracks[i].id);
+    }
     var checkbox = document.getElementById(`showTrack${inputTracks[i].id}`);
     checkbox.checked = value;
     i += 1;
   }
+  if (config.visibilityChangedCallback) {
+    config.visibilityChangedCallback(Array.from(config.hiddenTrackIds));
+  }
   createTubeMap();
 }
 
@@ -418,6 +442,18 @@ export function setMappingQualityCutoff(value) {
   }
 }
 
+export function setHiddenTrackIds(ids) {
+  config.hiddenTrackIds = new Set(ids || []);
+}
+
+export function setVisibilityChangedCallback(callback) {
+  config.visibilityChangedCallback = callback;
+}
+
+export function getHiddenTrackIds() {
+  return Array.from(config.hiddenTrackIds);
+}
+
 // main
 function createTubeMap() {
   console.log("Recreating tube map in", svgID);
@@ -4224,24 +4260,23 @@ function drawLegend() {
   content +=
     '<table class="table-sm table-condensed table-nonfluid"><thead><tr><th>Color</th><th>Trackname</th><th>Show Track</th></tr></thead>';
   const listeners = [];
-  // This is in terms of tracks, but when we change visibility we need to touch inputTracks, so we need to set up listeners by track ID.
-  for (let i = 0; i < tracks.length; i += 1) {
-    if (tracks[i].type === "haplotype") {
+  for (let i = 0; i < inputTracks.length; i += 1) {
+    if (inputTracks[i].type === "haplotype") {
       content += `<tr><td style="text-align:right"><div class="color-box" style="background-color: ${generateTrackColor(
-        tracks[i],
+        inputTracks[i],
         "exon"
       )};"></div></td>`;
-      if (tracks[i].hasOwnProperty("name")) {
-        content += `<td>${tracks[i].name}</td>`;
+      if (inputTracks[i].hasOwnProperty("name")) {
+        content += `<td>${inputTracks[i].name}</td>`;
       } else {
-        content += `<td>${tracks[i].id}</td>`;
+        content += `<td>${inputTracks[i].id}</td>`;
       }
-      content += `<td><input type="checkbox" checked=true id="showTrack${tracks[i].id}"></td>`;
-      listeners.push(tracks[i].id);
+      const isChecked = !config.hiddenTrackIds.has(inputTracks[i].id);
+      content += `<td><input type="checkbox" ${isChecked ? 'checked=true' : ''} id="showTrack${inputTracks[i].id}"></td>`;
+      listeners.push(inputTracks[i].id);
     }
   }
   content += "</table";
-  // $('#legendDiv').html(content);
   document.getElementById("legendDiv").innerHTML = content;
   listeners.forEach((id) => {
     document
diff --git a/src/util/tubemap.test.js b/src/util/tubemap.test.js
index 80d10c20..cb97a30c 100644
--- a/src/util/tubemap.test.js
+++ b/src/util/tubemap.test.js
@@ -1,4 +1,11 @@
-import { cigar_string, coverage, axisIntervals } from "./tubemap";
+import {
+  cigar_string,
+  coverage,
+  axisIntervals,
+  setHiddenTrackIds,
+  getHiddenTrackIds,
+  setVisibilityChangedCallback,
+} from "./tubemap";
 
 // cigar string test
 describe("cigar_string", () => {
@@ -865,6 +872,54 @@ describe("coverage", () => {
 });
 
 
+describe("hiddenTrackIds", () => {
+  it("starts empty", async () => {
+    expect(getHiddenTrackIds()).toStrictEqual([]);
+  });
+
+  it("can set and get hidden track IDs", async () => {
+    setHiddenTrackIds([1, 3, 5]);
+    expect(getHiddenTrackIds()).toStrictEqual([1, 3, 5]);
+  });
+
+  it("can set empty list", async () => {
+    setHiddenTrackIds([]);
+    expect(getHiddenTrackIds()).toStrictEqual([]);
+  });
+
+  it("can set null/undefined to empty", async () => {
+    setHiddenTrackIds(null);
+    expect(getHiddenTrackIds()).toStrictEqual([]);
+    setHiddenTrackIds(undefined);
+    expect(getHiddenTrackIds()).toStrictEqual([]);
+  });
+
+  it("deduplicates IDs via Set", async () => {
+    setHiddenTrackIds([1, 1, 2, 2, 3]);
+    const result = getHiddenTrackIds();
+    expect(result.sort((a, b) => a - b)).toStrictEqual([1, 2, 3]);
+  });
+
+  it("replaces previous values on set", async () => {
+    setHiddenTrackIds([1, 2]);
+    setHiddenTrackIds([3, 4]);
+    expect(getHiddenTrackIds()).toStrictEqual([3, 4]);
+  });
+});
+
+describe("visibilityChangedCallback", () => {
+  it("can set callback", async () => {
+    const cb = () => {};
+    setVisibilityChangedCallback(cb);
+    // No error thrown
+  });
+
+  it("can clear callback with null", async () => {
+    setVisibilityChangedCallback(null);
+    // No error thrown
+  });
+});
+
 describe("axisIntervals", () => {
   // TEST 1
   it("can handle an empty array", async () => {