@vitessce/scatterplot-gating 3.4.12 → 3.5.0

package/dist/{deflate-acef7820.js → deflate-2f9a6f39.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-c5949f9a.js";
+import { B as BaseDecoder } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-c5949f9a.js → index-c5f7bda6.js}

@@ -11017,7 +11017,8 @@ const ViewType$1 = {
   OBS_SET_FEATURE_VALUE_DISTRIBUTION: "obsSetFeatureValueDistribution",
   FEATURE_VALUE_HISTOGRAM: "featureValueHistogram",
   DOT_PLOT: "dotPlot",
-  FEATURE_BAR_PLOT: "featureBarPlot"
+  FEATURE_BAR_PLOT: "featureBarPlot",
+  BIOMARKER_SELECT: "biomarkerSelect"
 };
 const DataType$2 = {
   OBS_LABELS: "obsLabels",
@@ -11056,6 +11057,9 @@ const FileType$1 = {
   // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
   OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
+  // OME-Zarr - Zipped
+  IMAGE_OME_ZARR_ZIP: "image.ome-zarr.zip",
+  OBS_SEGMENTATIONS_OME_ZARR_ZIP: "obsSegmentations.ome-zarr.zip",
   // AnnData
   OBS_FEATURE_MATRIX_ANNDATA_ZARR: "obsFeatureMatrix.anndata.zarr",
   OBS_FEATURE_COLUMNS_ANNDATA_ZARR: "obsFeatureColumns.anndata.zarr",
@@ -11709,6 +11713,11 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.ADDITIONAL_OBS_SETS
+  ],
+  [ViewType$1.BIOMARKER_SELECT]: [
+    CoordinationType$1.FEATURE_SELECTION,
+    CoordinationType$1.SAMPLE_SET_SELECTION
+    // TODO: create coordination types for internal state of the biomarker selection view?
   ]
 };
 const ViewType = {
@@ -12012,24 +12021,29 @@ const imageOmeZarrSchema = z.object({
 imageOmeZarrSchema.extend({
   obsTypesFromChannelNames: z.boolean().optional()
 });
-const imageSpatialdataSchema = imageOmeZarrSchema.extend({
-  path: z.string()
+const imageSpatialdataSchema = z.object({
+  path: z.string(),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 const obsSegmentationsSpatialdataSchema = z.object({
-  // TODO: should this also extend the imageOmeZarrSchema?
   // TODO: should this be renamed labelsSpatialdataSchema?
   // TODO: support obsTypesFromChannelNames?
-  path: z.string()
+  path: z.string(),
+  tablePath: z.string().optional().describe("The path to a table which annotates the labels. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 z.object({
-  path: z.string()
+  path: z.string(),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the coordinates. If not provided, the "global" coordinate system is assumed.')
 });
 const obsSpotsSpatialdataSchema = z.object({
   path: z.string(),
-  tablePath: z.string().optional().describe("The path to a table which annotates the spots. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected.")
+  tablePath: z.string().optional().describe("The path to a table which annotates the spots. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the coordinates and radii. If not provided, the "global" coordinate system is assumed.')
 });
 const obsFeatureMatrixSpatialdataSchema = annDataObsFeatureMatrix.extend({
-  region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional()
+  region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 const obsSetsSpatialdataSchema = z.object({
   region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
@@ -12130,15 +12144,21 @@ anndataZarrSchema.extend({
 z.object({
   // TODO: should `image` be a special schema
   // to allow specifying fileUid (like for embeddingType)?
+  // TODO: allow multiple images
   image: imageSpatialdataSchema,
   // TODO: should this be a special schema
   // to allow specifying fileUid (like for embeddingType)?
+  // TODO: allow multiple labels
   labels: obsSegmentationsSpatialdataSchema,
   obsFeatureMatrix: obsFeatureMatrixSpatialdataSchema,
   obsSpots: obsSpotsSpatialdataSchema,
   // TODO: obsPoints
   // TODO: obsLocations
-  obsSets: obsSetsSpatialdataSchema
+  obsSets: obsSetsSpatialdataSchema,
+  // TODO: obsEmbedding
+  // TODO: obsLabels
+  // TODO: featureLabels
+  coordinateSystem: z.string().optional().describe("The name of a coordinate transformation output used to transform all elements which lack a per-element coordinateSystem property.")
 }).partial();
 z.object({
   obsLabelsTypes: z.array(z.string()).optional(),
@@ -89533,7 +89553,7 @@ keysShim.shim = function shimObjectKeys() {
   return Object.keys || keysShim;
 };
 var objectKeys$1 = keysShim;
-var shams$2 = function hasSymbols() {
+var shams$1 = function hasSymbols() {
   if (typeof Symbol !== "function" || typeof Object.getOwnPropertySymbols !== "function") {
     return false;
   }
@@ -89578,9 +89598,9 @@ var shams$2 = function hasSymbols() {
   }
   return true;
 };
-var hasSymbols$4 = shams$2;
-var shams$1 = function hasToStringTagShams() {
-  return hasSymbols$4() && !!Symbol.toStringTag;
+var hasSymbols$3 = shams$1;
+var shams = function hasToStringTagShams() {
+  return hasSymbols$3() && !!Symbol.toStringTag;
 };
 var esErrors = Error;
 var _eval = EvalError;
@@ -89590,8 +89610,8 @@ var syntax = SyntaxError;
 var type = TypeError;
 var uri = URIError;
 var origSymbol = typeof Symbol !== "undefined" && Symbol;
-var hasSymbolSham = shams$2;
-var hasSymbols$3 = function hasNativeSymbols() {
+var hasSymbolSham = shams$1;
+var hasSymbols$2 = function hasNativeSymbols() {
   if (typeof origSymbol !== "function") {
     return false;
   }
@@ -89607,11 +89627,12 @@ var hasSymbols$3 = function hasNativeSymbols() {
   return hasSymbolSham();
 };
 var test = {
+  __proto__: null,
   foo: {}
 };
 var $Object$1 = Object;
 var hasProto$1 = function hasProto() {
-  return { __proto__: test }.foo === test.foo && !({ __proto__: null } instanceof $Object$1);
+  return { __proto__: test }.foo === test.foo && !(test instanceof $Object$1);
 };
 var ERROR_MESSAGE = "Function.prototype.bind called on incompatible ";
 var toStr$2 = Object.prototype.toString;
@@ -89726,7 +89747,7 @@ var ThrowTypeError = $gOPD$2 ? function() {
     }
   }
 }() : throwTypeError;
-var hasSymbols$2 = hasSymbols$3();
+var hasSymbols$1 = hasSymbols$2();
 var hasProto2 = hasProto$1();
 var getProto$1 = Object.getPrototypeOf || (hasProto2 ? function(x2) {
   return x2.__proto__;
@@ -89738,7 +89759,7 @@ var INTRINSICS = {
   "%AggregateError%": typeof AggregateError === "undefined" ? undefined$1 : AggregateError,
   "%Array%": Array,
   "%ArrayBuffer%": typeof ArrayBuffer === "undefined" ? undefined$1 : ArrayBuffer,
-  "%ArrayIteratorPrototype%": hasSymbols$2 && getProto$1 ? getProto$1([][Symbol.iterator]()) : undefined$1,
+  "%ArrayIteratorPrototype%": hasSymbols$1 && getProto$1 ? getProto$1([][Symbol.iterator]()) : undefined$1,
   "%AsyncFromSyncIteratorPrototype%": undefined$1,
   "%AsyncFunction%": needsEval,
   "%AsyncGenerator%": needsEval,
@@ -89769,10 +89790,10 @@ var INTRINSICS = {
   "%Int32Array%": typeof Int32Array === "undefined" ? undefined$1 : Int32Array,
   "%isFinite%": isFinite,
   "%isNaN%": isNaN,
-  "%IteratorPrototype%": hasSymbols$2 && getProto$1 ? getProto$1(getProto$1([][Symbol.iterator]())) : undefined$1,
+  "%IteratorPrototype%": hasSymbols$1 && getProto$1 ? getProto$1(getProto$1([][Symbol.iterator]())) : undefined$1,
   "%JSON%": typeof JSON === "object" ? JSON : undefined$1,
   "%Map%": typeof Map === "undefined" ? undefined$1 : Map,
-  "%MapIteratorPrototype%": typeof Map === "undefined" || !hasSymbols$2 || !getProto$1 ? undefined$1 : getProto$1((/* @__PURE__ */ new Map())[Symbol.iterator]()),
+  "%MapIteratorPrototype%": typeof Map === "undefined" || !hasSymbols$1 || !getProto$1 ? undefined$1 : getProto$1((/* @__PURE__ */ new Map())[Symbol.iterator]()),
   "%Math%": Math,
   "%Number%": Number,
   "%Object%": Object,
@@ -89785,11 +89806,11 @@ var INTRINSICS = {
   "%Reflect%": typeof Reflect === "undefined" ? undefined$1 : Reflect,
   "%RegExp%": RegExp,
   "%Set%": typeof Set === "undefined" ? undefined$1 : Set,
-  "%SetIteratorPrototype%": typeof Set === "undefined" || !hasSymbols$2 || !getProto$1 ? undefined$1 : getProto$1((/* @__PURE__ */ new Set())[Symbol.iterator]()),
+  "%SetIteratorPrototype%": typeof Set === "undefined" || !hasSymbols$1 || !getProto$1 ? undefined$1 : getProto$1((/* @__PURE__ */ new Set())[Symbol.iterator]()),
   "%SharedArrayBuffer%": typeof SharedArrayBuffer === "undefined" ? undefined$1 : SharedArrayBuffer,
   "%String%": String,
-  "%StringIteratorPrototype%": hasSymbols$2 && getProto$1 ? getProto$1(""[Symbol.iterator]()) : undefined$1,
-  "%Symbol%": hasSymbols$2 ? Symbol : undefined$1,
+  "%StringIteratorPrototype%": hasSymbols$1 && getProto$1 ? getProto$1(""[Symbol.iterator]()) : undefined$1,
+  "%Symbol%": hasSymbols$1 ? Symbol : undefined$1,
   "%SyntaxError%": $SyntaxError$1,
   "%ThrowTypeError%": ThrowTypeError,
   "%TypedArray%": TypedArray,
@@ -90158,7 +90179,7 @@ var callBound$2 = function callBoundIntrinsic(name2, allowMissing) {
   }
   return intrinsic;
 };
-var hasToStringTag$2 = shams$1();
+var hasToStringTag$2 = shams();
 var callBound$1 = callBound$2;
 var $toString$1 = callBound$1("Object.prototype.toString");
 var isStandardArguments = function isArguments2(value) {
@@ -90203,7 +90224,7 @@ hasPropertyDescriptors2.hasArrayLengthDefineBug = function hasArrayLengthDefineB
 };
 var hasPropertyDescriptors_1 = hasPropertyDescriptors2;
 var keys$1 = objectKeys$1;
-var hasSymbols$1 = typeof Symbol === "function" && typeof Symbol("foo") === "symbol";
+var hasSymbols2 = typeof Symbol === "function" && typeof Symbol("foo") === "symbol";
 var toStr$1 = Object.prototype.toString;
 var concat = Array.prototype.concat;
 var defineDataProperty2 = defineDataProperty$1;
@@ -90230,7 +90251,7 @@ var defineProperty$3 = function(object2, name2, value, predicate) {
 var defineProperties = function(object2, map2) {
   var predicates = arguments.length > 2 ? arguments[2] : {};
   var props = keys$1(map2);
-  if (hasSymbols$1) {
+  if (hasSymbols2) {
     props = concat.call(props, Object.getOwnPropertySymbols(map2));
   }
   for (var i2 = 0; i2 < props.length; i2 += 1) {
@@ -90281,10 +90302,6 @@ define$2(polyfill$1, {
   shim: shim$2
 });
 var objectIs = polyfill$1;
-var hasSymbols2 = shams$2;
-var shams = function hasToStringTagShams2() {
-  return hasSymbols2() && !!Symbol.toStringTag;
-};
 var callBound = callBound$2;
 var hasToStringTag$1 = shams();
 var has$3;
@@ -90491,7 +90508,7 @@ var tryDateObject = function tryDateGetDayCall(value) {
 };
 var toStr = Object.prototype.toString;
 var dateClass = "[object Date]";
-var hasToStringTag = shams$1();
+var hasToStringTag = shams();
 var isDateObject = function isDateObject2(value) {
   if (typeof value !== "object" || value === null) {
     return false;
@@ -123811,16 +123828,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-61e39bd3.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-857aa477.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-76bd4a80.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-f1763f1b.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-7e5e6ad5.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-acef7820.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-f7f733c7.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-94ffa556.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-a60dfc27.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-16205d41.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-2f9a6f39.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-dba200ba.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-88582bf6.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-89fabb16.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -150257,6 +150274,7 @@ const CELLS_LAYER_ID = "scatterplot";
 const LABEL_FONT_FAMILY = "-apple-system, 'Helvetica Neue', Arial, sans-serif";
 const NUM_FORCE_SIMULATION_TICKS = 100;
 const LABEL_UPDATE_ZOOM_DELTA = 0.25;
+const POINT_LAYER_Z_INDEX = 0;
 const makeDefaultGetCellColors = (cellColors, obsIndex, theme) => (object2, { index: index2 }) => {
   const [r2, g2, b, a2] = cellColors && obsIndex && cellColors.get(obsIndex[index2]) || getDefaultColor(theme);
   return [r2, g2, b, 255 * (a2 || 1)];
@@ -150274,7 +150292,7 @@ const makeFlippedGetObsCoords = (obsEmbedding) => (i2) => [
 const getPosition = (object2, { index: index2, data, target }) => {
   target[0] = data.src.obsEmbedding.data[0][index2];
   target[1] = -data.src.obsEmbedding.data[1][index2];
-  target[2] = 0;
+  target[2] = POINT_LAYER_Z_INDEX;
   return target;
 };
 const contourGetWeight = (object2, { index: index2, data }) => data.src.featureValues[index2];
@@ -150284,7 +150302,6 @@ const contourGetPosition = (object2, { index: index2, data, target }) => {
   target[2] = 0;
   return target;
 };
-const contourGetPolygonOffset = () => [0, 20];
 class Scatterplot extends AbstractSpatialOrScatterplot {
   constructor(props) {
     super(props);
@@ -150324,7 +150341,6 @@ class Scatterplot extends AbstractSpatialOrScatterplot {
         data: deckData,
         getWeight: contourGetWeight,
         getPosition: contourGetPosition,
-        getPolygonOffset: contourGetPolygonOffset,
         contours: contourThresholds.map((threshold, i2) => ({
           threshold: contoursFilled ? [threshold, threshold[i2 + 1] || Infinity] : threshold,
           // TODO: should the opacity steps be uniform? Should align with human perception.
@@ -150335,7 +150351,10 @@ class Scatterplot extends AbstractSpatialOrScatterplot {
             // a
             contoursFilled ? (i2 + 0.5) / contourThresholds.length * 255 : (i2 + 1) / contourThresholds.length * 255
           ],
-          strokeWidth: 2
+          strokeWidth: 2,
+          // We need to specify a greater z-index so that the contour layers
+          // will render on top of the point layer.
+          zIndex: POINT_LAYER_Z_INDEX + 1 + i2
         })),
         aggregation: "MEAN",
         gpuAggregation: true,
@@ -151356,7 +151375,7 @@ function GatingSubscriber(props) {
   const getCellIsSelected = useCallback((object2, { index: index2 }) => (cellSelectionSet || /* @__PURE__ */ new Set([])).has(obsIndex[index2]) ? 1 : 0, [cellSelectionSet, obsIndex]);
   const cellRadius = cellRadiusMode === "manual" ? cellRadiusFixed : dynamicCellRadius;
   const cellOpacity = cellOpacityMode === "manual" ? cellOpacityFixed : dynamicCellOpacity;
-  const [uint8ExpressionData] = useUint8FeatureSelection(expressionDataColor);
+  const { normData: uint8ExpressionData } = useUint8FeatureSelection(expressionDataColor);
   const getExpressionValue = useExpressionValueGetter({
     instanceObsIndex: obsIndex,
     matrixObsIndex: obsIndex,

package/dist/index.js

@@ -1,4 +1,4 @@
-import { G } from "./index-c5949f9a.js";
+import { G } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-7e5e6ad5.js → jpeg-16205d41.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-c5949f9a.js";
+import { B as BaseDecoder } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-94ffa556.js → lerc-88582bf6.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-c5949f9a.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-857aa477.js → lzw-f1763f1b.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-c5949f9a.js";
+import { B as BaseDecoder } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-f7f733c7.js → packbits-dba200ba.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-c5949f9a.js";
+import { B as BaseDecoder } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-61e39bd3.js → raw-76bd4a80.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-c5949f9a.js";
+import { B as BaseDecoder } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-a60dfc27.js → webimage-89fabb16.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-c5949f9a.js";
+import { B as BaseDecoder } from "./index-c5f7bda6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist-tsc/GatingSubscriber.js

@@ -170,7 +170,7 @@ export function GatingSubscriber(props) {
     const getCellIsSelected = useCallback((object, { index }) => ((cellSelectionSet || new Set([])).has(obsIndex[index]) ? 1.0 : 0.0), [cellSelectionSet, obsIndex]);
     const cellRadius = (cellRadiusMode === 'manual' ? cellRadiusFixed : dynamicCellRadius);
     const cellOpacity = (cellOpacityMode === 'manual' ? cellOpacityFixed : dynamicCellOpacity);
-    const [uint8ExpressionData] = useUint8FeatureSelection(expressionDataColor);
+    const { normData: uint8ExpressionData } = useUint8FeatureSelection(expressionDataColor);
     // Set up a getter function for gene expression values, to be used
     // by the DeckGL layer to obtain values for instanced attributes.
     const getExpressionValue = useExpressionValueGetter({

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@vitessce/scatterplot-gating",
-  "version": "3.4.12",
-  "author": "Gehlenborg Lab",
+  "version": "3.5.0",
+  "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
     "type": "git",
@@ -20,11 +20,11 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.4.12",
-    "@vitessce/scatterplot": "3.4.12",
-    "@vitessce/sets-utils": "3.4.12",
-    "@vitessce/utils": "3.4.12",
-    "@vitessce/vit-s": "3.4.12"
+    "@vitessce/constants-internal": "3.5.0",
+    "@vitessce/scatterplot": "3.5.0",
+    "@vitessce/sets-utils": "3.5.0",
+    "@vitessce/utils": "3.5.0",
+    "@vitessce/vit-s": "3.5.0"
   },
   "devDependencies": {
     "react": "^18.0.0",

package/src/GatingSubscriber.js

@@ -325,7 +325,7 @@ export function GatingSubscriber(props) {
   const cellRadius = (cellRadiusMode === 'manual' ? cellRadiusFixed : dynamicCellRadius);
   const cellOpacity = (cellOpacityMode === 'manual' ? cellOpacityFixed : dynamicCellOpacity);
 
-  const [uint8ExpressionData] = useUint8FeatureSelection(expressionDataColor);
+  const { normData: uint8ExpressionData } = useUint8FeatureSelection(expressionDataColor);
 
   // Set up a getter function for gene expression values, to be used
   // by the DeckGL layer to obtain values for instanced attributes.