@vitessce/statistical-plots 3.3.2 → 3.3.3

package/dist/index.js

@@ -967,7 +967,9 @@ const FileType$1 = {
   OBS_SEGMENTATIONS_JSON: "obsSegmentations.json",
   OBS_SETS_CSV: "obsSets.csv",
   OBS_SETS_JSON: "obsSets.json",
+  // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
+  OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
   // AnnData
   OBS_FEATURE_MATRIX_ANNDATA_ZARR: "obsFeatureMatrix.anndata.zarr",
   OBS_SETS_ANNDATA_ZARR: "obsSets.anndata.zarr",
@@ -1451,7 +1453,9 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_SEGMENTATION_FILLED,
     CoordinationType$1.SPATIAL_SEGMENTATION_STROKE_WIDTH,
     CoordinationType$1.IMAGE_CHANNEL,
+    CoordinationType$1.IMAGE_LAYER,
     CoordinationType$1.SEGMENTATION_CHANNEL,
+    CoordinationType$1.SEGMENTATION_LAYER,
     CoordinationType$1.SPATIAL_CHANNEL_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_OPACITY,
     CoordinationType$1.SPATIAL_CHANNEL_WINDOW,
@@ -1469,6 +1473,9 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_SPOT_STROKE_WIDTH,
     CoordinationType$1.SPATIAL_LAYER_COLOR,
     CoordinationType$1.OBS_COLOR_ENCODING,
+    CoordinationType$1.FEATURE_VALUE_COLORMAP,
+    CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.TOOLTIPS_VISIBLE,
     CoordinationType$1.TOOLTIP_CROSSHAIRS_VISIBLE,
     CoordinationType$1.LEGEND_VISIBLE,
@@ -10660,30 +10667,39 @@ const omeCoordinateTransformations = z.array(z.union([
     scale: z.array(z.number())
   })
 ]));
-z.object({
+const imageOmeTiffSchema = z.object({
   offsetsUrl: z.string().optional(),
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
+imageOmeTiffSchema.extend({
+  obsTypesFromChannelNames: z.boolean().optional()
+});
 const imageOmeZarrSchema = z.object({
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
 imageOmeZarrSchema.extend({
+  obsTypesFromChannelNames: z.boolean().optional()
+});
+const imageSpatialdataSchema = imageOmeZarrSchema.extend({
   path: z.string()
 });
-z.object({
+const obsSegmentationsSpatialdataSchema = z.object({
+  // TODO: should this also extend the imageOmeZarrSchema?
+  // TODO: should this be renamed labelsSpatialdataSchema?
+  // TODO: support obsTypesFromChannelNames?
   path: z.string()
 });
 z.object({
   path: z.string()
 });
-z.object({
+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.")
 });
-annDataObsFeatureMatrix.extend({
+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()
 });
-z.object({
+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(),
   tablePath: z.string().optional().describe("The path to a table which contains the index for the set values."),
   obsSets: annDataObsSets
@@ -10746,6 +10762,19 @@ z.object({
     z.array(annDataConvenienceObsEmbeddingItem)
   ])
 }).partial();
+z.object({
+  // TODO: should `image` be a special schema
+  // to allow specifying fileUid (like for embeddingType)?
+  image: imageSpatialdataSchema,
+  // TODO: should this be a special schema
+  // to allow specifying fileUid (like for embeddingType)?
+  labels: obsSegmentationsSpatialdataSchema,
+  obsFeatureMatrix: obsFeatureMatrixSpatialdataSchema,
+  obsSpots: obsSpotsSpatialdataSchema,
+  // TODO: obsPoints
+  // TODO: obsLocations
+  obsSets: obsSetsSpatialdataSchema
+}).partial();
 z.object({
   obsLabelsTypes: z.array(z.string()).optional(),
   embeddingTypes: z.array(z.string()).optional()

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/statistical-plots",
-  "version": "3.3.2",
+  "version": "3.3.3",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,11 +20,11 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.3.2",
-    "@vitessce/vega": "3.3.2",
-    "@vitessce/utils": "3.3.2",
-    "@vitessce/vit-s": "3.3.2",
-    "@vitessce/sets-utils": "3.3.2"
+    "@vitessce/constants-internal": "3.3.3",
+    "@vitessce/sets-utils": "3.3.3",
+    "@vitessce/utils": "3.3.3",
+    "@vitessce/vega": "3.3.3",
+    "@vitessce/vit-s": "3.3.3"
   },
   "devDependencies": {
     "react": "^18.0.0",