@vitessce/vega 4.0.7 → 4.0.9

package/dist/index.js

@@ -49012,7 +49012,7 @@ const latestFileDefSchema = z.object({
   options: fileOptionsSchema.optional(),
   requestInit: requestInit.optional(),
   // New: file def can have coordinationValues.
-  coordinationValues: z.record(z.string()).optional()
+  coordinationValues: z.record(z.any()).optional()
 });
 const datasetsSchema1_0_13 = z.array(z.object({
   uid: z.string(),
@@ -49043,7 +49043,8 @@ const configSchema1_0_16 = configSchema1_0_13.extend({
     h: z.number().int().optional(),
     // Updates coordinationScopes and coordinationScopesBy
     coordinationScopes: componentCoordinationScopes.optional(),
-    coordinationScopesBy: componentCoordinationScopesBy.optional()
+    coordinationScopesBy: componentCoordinationScopesBy.optional(),
+    coordinationValues: z.record(z.any()).optional()
   }))
 });
 const configSchema1_0_17 = configSchema1_0_16.extend({
@@ -51549,7 +51550,9 @@ const ViewType$1 = {
   DUAL_SCATTERPLOT: "dualScatterplot",
   TREEMAP: "treemap",
   SAMPLE_SET_PAIR_MANAGER: "sampleSetPairManager",
-  FEATURE_STATS_TABLE: "featureStatsTable"
+  FEATURE_STATS_TABLE: "featureStatsTable",
+  SINGLE_OBS_SET_SELECTOR: "singleObsSetSelector",
+  ANNOTATION_CONTROLLER: "annotationController"
 };
 const DataType$1 = {
   OBS_LABELS: "obsLabels",
@@ -51570,7 +51573,8 @@ const DataType$1 = {
   COMPARISON_METADATA: "comparisonMetadata",
   FEATURE_STATS: "featureStats",
   FEATURE_SET_STATS: "featureSetStats",
-  OBS_SET_STATS: "obsSetStats"
+  OBS_SET_STATS: "obsSetStats",
+  ANNOTATION_STORY: "annotationStory"
 };
 const FileType$1 = {
   // Joint file types
@@ -51592,6 +51596,7 @@ const FileType$1 = {
   OBS_SETS_CSV: "obsSets.csv",
   OBS_SETS_JSON: "obsSets.json",
   SAMPLE_SETS_CSV: "sampleSets.csv",
+  ANNOTATION_STORY_JSON: "annotationStory.json",
   // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
   OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
@@ -51876,7 +51881,15 @@ const CoordinationType$1 = {
   FEATURE_POINT_FOLD_CHANGE_THRESHOLD: "featurePointFoldChangeThreshold",
   FEATURE_LABEL_FOLD_CHANGE_THRESHOLD: "featureLabelFoldChangeThreshold",
   // Treemap
-  HIERARCHY_LEVELS: "hierarchyLevels"
+  HIERARCHY_LEVELS: "hierarchyLevels",
+  // Annotation frames
+  ANNOTATION_STORY: "annotationStory",
+  ANNOTATION_FRAME_INDEX: "annotationFrameIndex",
+  ANNOTATION_SHAPES: "annotationShapes",
+  ANNOTATION_OVERLAY_VISIBLE: "annotationOverlayVisible",
+  ANNOTATION_TRANSITION_DURATION: "annotationTransitionDuration",
+  ANNOTATION_SEMANTIC_ZOOM: "annotationSemanticZoom",
+  ANNOTATION_EDITABLE: "annotationEditable"
 };
 ({
   // For new file types
@@ -51892,6 +51905,7 @@ const CoordinationType$1 = {
   [FileType$1.OBS_SEGMENTATIONS_JSON]: DataType$1.OBS_SEGMENTATIONS,
   [FileType$1.OBS_SETS_CSV]: DataType$1.OBS_SETS,
   [FileType$1.OBS_SETS_JSON]: DataType$1.OBS_SETS,
+  [FileType$1.ANNOTATION_STORY_JSON]: DataType$1.ANNOTATION_STORY,
   [FileType$1.IMAGE_OME_ZARR]: DataType$1.IMAGE,
   [FileType$1.OBS_SEGMENTATIONS_OME_ZARR]: DataType$1.OBS_SEGMENTATIONS,
   [FileType$1.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: DataType$1.OBS_FEATURE_MATRIX,
@@ -52014,7 +52028,8 @@ const CoordinationType$1 = {
   [DataType$1.OBS_SET_STATS]: [
     CoordinationType$1.OBS_TYPE
     // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
-  ]
+  ],
+  [DataType$1.ANNOTATION_STORY]: []
 });
 ({
   // For AnnData:
@@ -52147,7 +52162,9 @@ const CoordinationType$1 = {
   CoordinationType$1.SPATIAL_TARGET_Z,
   CoordinationType$1.SPATIAL_AXIS_FIXED,
   CoordinationType$1.SPATIAL_ORBIT_AXIS,
-  CoordinationType$1.FEATURE_AGGREGATION_STRATEGY
+  CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
+  // Annotation shapes are specific to a view's coordinate system.
+  CoordinationType$1.ANNOTATION_SHAPES
 ];
 ({
   [ViewType$1.NEUROGLANCER]: [
@@ -52239,7 +52256,14 @@ const CoordinationType$1 = {
     CoordinationType$1.EMBEDDING_CONTOURS_FILLED,
     CoordinationType$1.EMBEDDING_CONTOUR_PERCENTILES,
     CoordinationType$1.CONTOUR_COLOR_ENCODING,
-    CoordinationType$1.CONTOUR_COLOR
+    CoordinationType$1.CONTOUR_COLOR,
+    CoordinationType$1.ANNOTATION_STORY,
+    CoordinationType$1.ANNOTATION_SHAPES,
+    CoordinationType$1.ANNOTATION_FRAME_INDEX,
+    CoordinationType$1.ANNOTATION_OVERLAY_VISIBLE,
+    CoordinationType$1.ANNOTATION_TRANSITION_DURATION,
+    CoordinationType$1.ANNOTATION_EDITABLE,
+    CoordinationType$1.ANNOTATION_SEMANTIC_ZOOM
   ],
   [ViewType$1.DUAL_SCATTERPLOT]: [
     CoordinationType$1.DATASET,
@@ -52355,7 +52379,14 @@ const CoordinationType$1 = {
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.MOLECULE_HIGHLIGHT,
     CoordinationType$1.TOOLTIPS_VISIBLE,
-    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION,
+    CoordinationType$1.ANNOTATION_STORY,
+    CoordinationType$1.ANNOTATION_SHAPES,
+    CoordinationType$1.ANNOTATION_FRAME_INDEX,
+    CoordinationType$1.ANNOTATION_OVERLAY_VISIBLE,
+    CoordinationType$1.ANNOTATION_TRANSITION_DURATION,
+    CoordinationType$1.ANNOTATION_EDITABLE,
+    CoordinationType$1.ANNOTATION_SEMANTIC_ZOOM
   ],
   [ViewType$1.SPATIAL_BETA]: [
     CoordinationType$1.META_COORDINATION_SCOPES,
@@ -52433,7 +52464,27 @@ const CoordinationType$1 = {
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_ORIENTATION,
     CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE,
     CoordinationType$1.SPATIAL_CHANNELS_SORT_ORDER,
-    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION,
+    CoordinationType$1.ANNOTATION_STORY,
+    CoordinationType$1.ANNOTATION_SHAPES,
+    CoordinationType$1.ANNOTATION_FRAME_INDEX,
+    CoordinationType$1.ANNOTATION_OVERLAY_VISIBLE,
+    CoordinationType$1.ANNOTATION_TRANSITION_DURATION,
+    CoordinationType$1.ANNOTATION_EDITABLE,
+    CoordinationType$1.ANNOTATION_SEMANTIC_ZOOM
+  ],
+  [ViewType$1.ANNOTATION_CONTROLLER]: [
+    CoordinationType$1.DATASET,
+    CoordinationType$1.ANNOTATION_STORY,
+    CoordinationType$1.ANNOTATION_FRAME_INDEX,
+    CoordinationType$1.ANNOTATION_OVERLAY_VISIBLE,
+    CoordinationType$1.ANNOTATION_TRANSITION_DURATION,
+    CoordinationType$1.ANNOTATION_EDITABLE,
+    CoordinationType$1.ANNOTATION_SEMANTIC_ZOOM
+    // Note: the annotation controller also needs to read the coordination state
+    // of all other views/coordination types via the full config.
+    // Note: we get/set the CoordinationType.ANNOTATION_SHAPES from the full config,
+    // as this info is view-specific rather than global to the story.
   ],
   [ViewType$1.HEATMAP]: [
     CoordinationType$1.DATASET,
@@ -52743,6 +52794,11 @@ const CoordinationType$1 = {
     CoordinationType$1.FEATURE_POINT_FOLD_CHANGE_THRESHOLD,
     CoordinationType$1.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD
   ],
+  [ViewType$1.SINGLE_OBS_SET_SELECTOR]: [
+    CoordinationType$1.OBS_TYPE,
+    CoordinationType$1.OBS_SET_COLOR,
+    CoordinationType$1.OBS_SET_SELECTION
+  ],
   [ViewType$1.OBS_SET_COMPOSITION_BAR_PLOT]: [
     CoordinationType$1.DATASET,
     CoordinationType$1.OBS_TYPE,
@@ -53446,6 +53502,124 @@ z.object({
   radius: z.number(),
   opacity: z.number()
 });
+const shapeBaseObj = z.object({
+  uid: z.string(),
+  text: z.string().optional(),
+  strokeColor: z.array(z.number()).length(3).optional(),
+  strokeWidth: z.number().optional(),
+  // SVG-style dash pattern, e.g. "10 5" or "10 20 30 10". "none" or omitted = solid.
+  strokeDashArray: z.string().optional(),
+  visible: z.boolean().optional()
+  // TODO: define unit modes for x and y axes
+  // ("pixels" vs "normalized" vs "physical" etc.)
+  // TODO: a coordinate system identifier (e.g., "DeckGL" for now,
+  // but a coordinate system from OME-NGFF/SpatialData eventually?)
+});
+const rectangleShapeObj = shapeBaseObj.extend({
+  type: z.literal("rectangle"),
+  // OME-XML field names verbatim (upper-left origin)
+  x: z.number(),
+  y: z.number(),
+  width: z.number(),
+  height: z.number(),
+  fillColor: z.array(z.number()).length(3).optional(),
+  fillOpacity: z.number().optional()
+});
+const lineShapeObj = shapeBaseObj.extend({
+  type: z.literal("line"),
+  // OME-XML field names verbatim
+  x1: z.number(),
+  y1: z.number(),
+  x2: z.number(),
+  y2: z.number(),
+  markerStart: z.enum(["Arrow", "Tick"]).nullable().optional(),
+  markerEnd: z.enum(["Arrow", "Tick"]).nullable().optional(),
+  textPosition: z.enum(["start", "middle", "end"]).optional(),
+  textBufferPx: z.number().optional()
+});
+const ellipseShapeObj = shapeBaseObj.extend({
+  type: z.literal("ellipse"),
+  // OME-XML field names verbatim (centre point + radii)
+  x1: z.number(),
+  y1: z.number(),
+  radiusX: z.number(),
+  radiusY: z.number(),
+  fillColor: z.array(z.number()).length(3).optional(),
+  fillOpacity: z.number().optional()
+});
+const polygonShapeObj = shapeBaseObj.extend({
+  type: z.literal("polygon"),
+  // OME-XML: array of [x, y] coordinate pairs, closed automatically
+  points: z.array(z.tuple([z.number(), z.number()])),
+  fillColor: z.array(z.number()).length(3).optional(),
+  fillOpacity: z.number().optional()
+});
+const polylineShapeObj = shapeBaseObj.extend({
+  type: z.literal("polyline"),
+  // OME-XML: array of [x, y] coordinate pairs, open (not closed)
+  points: z.array(z.tuple([z.number(), z.number()])),
+  markerStart: z.enum(["Arrow", "Tick"]).nullable().optional(),
+  markerEnd: z.enum(["Arrow", "Tick"]).nullable().optional()
+});
+const annotationShapeObj = z.discriminatedUnion("type", [
+  rectangleShapeObj,
+  lineShapeObj,
+  ellipseShapeObj,
+  polygonShapeObj,
+  polylineShapeObj
+]);
+z.array(annotationShapeObj);
+const annotationFrameObj = z.object({
+  uid: z.string(),
+  title: z.string().optional(),
+  description: z.string().optional(),
+  descriptionType: z.enum(["text", "markdown"]).optional(),
+  // A frame can define per-view: coordinationValues
+  // (if the view's state should not be coordinated with other views)
+  // or per-view coordinationScopes/coordinationScopesBy
+  // (if at this frame, the view should be coordinated with other views).
+  // We can also define a frame-level coordination space,
+  // which will be merged with the global coordination space.
+  // TODO: datasets
+  // TODO: coordinationSpace
+  layout: z.array(
+    // Note: for now, we will infer view objects which have a uid
+    // that is present in the global layout, and do NOT have x/y/w/h defined,
+    // to mean that in this frame, the layout and set of views is unchanged
+    // from the global layout.
+    // This will allow each frame to omit the full list of views from the layout,
+    // and only specify the views whose coordination state is changing in this frame.
+    // If a frame includes a view with a uid that is not present
+    // in the global layout, then that view will be added to the layout at this frame.
+    // This frame should also define x/y/w/h for all views,
+    // since it will otherwise be ambiguous how to layout the updated set of views
+    // for this frame.
+    z.object({
+      // The view UID. If this view uid is not present in the global layout,
+      // it will be added to the layout at this frame,
+      // and will need to have its coordination values initialized to their defaults
+      // for any that were not fully specified.
+      uid: z.string(),
+      coordinationValues: z.record(
+        z.string(),
+        // The coordination type name, e.g. "embeddingType"
+        z.any()
+      ).optional()
+      // TODO: support coordinationScopes/coordinationScopesBy for per-view coordination
+      // at this frame.
+      // TODO: view x/y/w/h once we support view layout changes per-frame.
+    })
+  ).optional()
+});
+z.object({
+  // TODO: schema version for the story schema?
+  // Same as current Vitessce schema version?
+  uid: z.string(),
+  title: z.string().optional(),
+  description: z.string().optional(),
+  descriptionType: z.enum(["text", "markdown"]).optional(),
+  frames: z.array(annotationFrameObj)
+});
 var tinycolor = { exports: {} };
 var hasRequiredTinycolor;
 function requireTinycolor() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vega",
-  "version": "4.0.7",
+  "version": "4.0.9",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -21,9 +21,9 @@
     "vega": "^5.21.0",
     "vega-lite": "^5.1.1",
     "vega-tooltip": "^0.27.0",
-    "@vitessce/tooltip": "4.0.7",
-    "@vitessce/styles": "4.0.7",
-    "@vitessce/legend": "4.0.7"
+    "@vitessce/styles": "4.0.9",
+    "@vitessce/legend": "4.0.9",
+    "@vitessce/tooltip": "4.0.9"
   },
   "devDependencies": {
     "react": "19.2.6",