@vitessce/statistical-plots 3.3.1 → 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()
@@ -86157,6 +86186,8 @@ function CellSetExpressionPlotSubscriber(props) {
   var _a;
   const {
     coordinationScopes,
+    closeButtonVisible,
+    downloadButtonVisible,
     removeGridComponent,
     theme
   } = props;
@@ -86242,6 +86273,8 @@ function CellSetExpressionPlotSubscriber(props) {
     TitleInfo,
     {
       title: `Expression by ${capitalize$2(obsType)} Set${firstGeneSelected ? ` (${firstGeneSelected})` : ""}`,
+      closeButtonVisible,
+      downloadButtonVisible,
       removeGridComponent,
       urls,
       theme,
@@ -86415,6 +86448,8 @@ function CellSetSizesPlot(props) {
 function CellSetSizesPlotSubscriber(props) {
   const {
     coordinationScopes,
+    closeButtonVisible,
+    downloadButtonVisible,
     removeGridComponent,
     theme,
     title: titleOverride
@@ -86500,6 +86535,8 @@ function CellSetSizesPlotSubscriber(props) {
     TitleInfo,
     {
       title: title2,
+      closeButtonVisible,
+      downloadButtonVisible,
       removeGridComponent,
       urls,
       theme,
@@ -86592,6 +86629,8 @@ function ExpressionHistogram(props) {
 function ExpressionHistogramSubscriber(props) {
   const {
     coordinationScopes,
+    closeButtonVisible,
+    downloadButtonVisible,
     removeGridComponent,
     theme
   } = props;
@@ -86690,6 +86729,8 @@ function ExpressionHistogramSubscriber(props) {
     TitleInfo,
     {
       title: `Expression Histogram${firstGeneSelected ? ` (${firstGeneSelected})` : ""}`,
+      closeButtonVisible,
+      downloadButtonVisible,
       removeGridComponent,
       urls,
       theme,

package/dist-tsc/CellSetExpressionPlotSubscriber.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"CellSetExpressionPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotSubscriber.js"],"names":[],"mappings":"AAiGA;;;;;;;;;GASG;AACH;IAL2B,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;gBAsHhB"}
+{"version":3,"file":"CellSetExpressionPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotSubscriber.js"],"names":[],"mappings":"AAiGA;;;;;;;;;GASG;AACH;IAL2B,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;gBA0HhB"}

package/dist-tsc/CellSetExpressionPlotSubscriber.js

@@ -77,7 +77,7 @@ function useExpressionByCellSet(expressionData, obsIndex, cellSets, additionalCe
  * @param {string} props.theme The name of the current Vitessce theme.
  */
 export function CellSetExpressionPlotSubscriber(props) {
-    const { coordinationScopes, removeGridComponent, theme, } = props;
+    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -107,5 +107,5 @@ export function CellSetExpressionPlotSubscriber(props) {
         ? (featureLabelsMap?.get(geneSelection[0]) || geneSelection[0])
         : null;
     const selectedTransformName = transformOptions.find(o => o.value === featureValueTransform)?.name;
-    return (_jsx(TitleInfo, { title: `Expression by ${capitalize(obsType)} Set${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, options: (_jsx(CellSetExpressionPlotOptions, { featureValueTransform: featureValueTransform, setFeatureValueTransform: setFeatureValueTransform, featureValueTransformCoefficient: featureValueTransformCoefficient, setFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, transformOptions: transformOptions })), children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: expressionArr ? (_jsx(CellSetExpressionPlot, { domainMax: expressionMax, colors: setArr, data: expressionArr, theme: theme, width: width, height: height, obsType: obsType, featureValueType: featureValueType, featureValueTransformName: selectedTransformName })) : (_jsxs("span", { children: ["Select a ", featureType, "."] })) }) }));
+    return (_jsx(TitleInfo, { title: `Expression by ${capitalize(obsType)} Set${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, options: (_jsx(CellSetExpressionPlotOptions, { featureValueTransform: featureValueTransform, setFeatureValueTransform: setFeatureValueTransform, featureValueTransformCoefficient: featureValueTransformCoefficient, setFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, transformOptions: transformOptions })), children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: expressionArr ? (_jsx(CellSetExpressionPlot, { domainMax: expressionMax, colors: setArr, data: expressionArr, theme: theme, width: width, height: height, obsType: obsType, featureValueType: featureValueType, featureValueTransformName: selectedTransformName })) : (_jsxs("span", { children: ["Select a ", featureType, "."] })) }) }));
 }

package/dist-tsc/CellSetSizesPlotSubscriber.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"CellSetSizesPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetSizesPlotSubscriber.js"],"names":[],"mappings":"AAgBA;;;;;;;;;;GAUG;AACH;IAN2B,mBAAmB;IACnB,OAAO;IAET,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;gBA2HhB"}
+{"version":3,"file":"CellSetSizesPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetSizesPlotSubscriber.js"],"names":[],"mappings":"AAgBA;;;;;;;;;;GAUG;AACH;IAN2B,mBAAmB;IACnB,OAAO;IAET,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;gBA+HhB"}

package/dist-tsc/CellSetSizesPlotSubscriber.js

@@ -19,7 +19,7 @@ import { useStyles } from './styles.js';
  * @param {string} props.title The component title.
  */
 export function CellSetSizesPlotSubscriber(props) {
-    const { coordinationScopes, removeGridComponent, theme, title: titleOverride, } = props;
+    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, title: titleOverride, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -71,5 +71,5 @@ export function CellSetSizesPlotSubscriber(props) {
             setCellSetSelection([...cellSetSelection, setNamePath]);
         }
     };
-    return (_jsx(TitleInfo, { title: title, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: _jsx(CellSetSizesPlot, { data: data, onBarSelect: onBarSelect, theme: theme, width: width, height: height, obsType: obsType }) }) }));
+    return (_jsx(TitleInfo, { title: title, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: _jsx(CellSetSizesPlot, { data: data, onBarSelect: onBarSelect, theme: theme, width: width, height: height, obsType: obsType }) }) }));
 }

package/dist-tsc/ExpressionHistogramSubscriber.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ExpressionHistogramSubscriber.d.ts","sourceRoot":"","sources":["../src/ExpressionHistogramSubscriber.js"],"names":[],"mappings":"AAcA;;;;;;;;;GASG;AACH;IAL2B,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;gBAqHhB"}
+{"version":3,"file":"ExpressionHistogramSubscriber.d.ts","sourceRoot":"","sources":["../src/ExpressionHistogramSubscriber.js"],"names":[],"mappings":"AAcA;;;;;;;;;GASG;AACH;IAL2B,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;gBAyHhB"}

package/dist-tsc/ExpressionHistogramSubscriber.js

@@ -17,7 +17,7 @@ import { useStyles } from './styles.js';
  * @param {string} props.theme The name of the current Vitessce theme.
  */
 export function ExpressionHistogramSubscriber(props) {
-    const { coordinationScopes, removeGridComponent, theme, } = props;
+    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -68,5 +68,5 @@ export function ExpressionHistogramSubscriber(props) {
     }, [additionalCellSets, cellSetColor, data, setAdditionalCellSets,
         setCellColorEncoding, setCellSetColor, setCellSetSelection, firstGeneSelected,
     ]);
-    return (_jsx(TitleInfo, { title: `Expression Histogram${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: _jsx(ExpressionHistogram, { geneSelection: geneSelection, onSelect: onSelect, data: data, theme: theme, width: width, height: height }) }) }));
+    return (_jsx(TitleInfo, { title: `Expression Histogram${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: _jsx(ExpressionHistogram, { geneSelection: geneSelection, onSelect: onSelect, data: data, theme: theme, width: width, height: height }) }) }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/statistical-plots",
-  "version": "3.3.1",
+  "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": "3.3.1",
-    "@vitessce/sets-utils": "3.3.1",
-    "@vitessce/utils": "3.3.1",
-    "@vitessce/vega": "3.3.1",
-    "@vitessce/vit-s": "3.3.1"
+    "@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",

package/src/CellSetExpressionPlotSubscriber.js

@@ -108,6 +108,8 @@ function useExpressionByCellSet(
 export function CellSetExpressionPlotSubscriber(props) {
   const {
     coordinationScopes,
+    closeButtonVisible,
+    downloadButtonVisible,
     removeGridComponent,
     theme,
   } = props;
@@ -188,6 +190,8 @@ export function CellSetExpressionPlotSubscriber(props) {
   return (
     <TitleInfo
       title={`Expression by ${capitalize(obsType)} Set${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`}
+      closeButtonVisible={closeButtonVisible}
+      downloadButtonVisible={downloadButtonVisible}
       removeGridComponent={removeGridComponent}
       urls={urls}
       theme={theme}

package/src/CellSetSizesPlotSubscriber.js

@@ -28,6 +28,8 @@ import { useStyles } from './styles.js';
 export function CellSetSizesPlotSubscriber(props) {
   const {
     coordinationScopes,
+    closeButtonVisible,
+    downloadButtonVisible,
     removeGridComponent,
     theme,
     title: titleOverride,
@@ -129,6 +131,8 @@ export function CellSetSizesPlotSubscriber(props) {
   return (
     <TitleInfo
       title={title}
+      closeButtonVisible={closeButtonVisible}
+      downloadButtonVisible={downloadButtonVisible}
       removeGridComponent={removeGridComponent}
       urls={urls}
       theme={theme}

package/src/ExpressionHistogramSubscriber.js

@@ -25,6 +25,8 @@ import { useStyles } from './styles.js';
 export function ExpressionHistogramSubscriber(props) {
   const {
     coordinationScopes,
+    closeButtonVisible,
+    downloadButtonVisible,
     removeGridComponent,
     theme,
   } = props;
@@ -120,6 +122,8 @@ export function ExpressionHistogramSubscriber(props) {
   return (
     <TitleInfo
       title={`Expression Histogram${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`}
+      closeButtonVisible={closeButtonVisible}
+      downloadButtonVisible={downloadButtonVisible}
       removeGridComponent={removeGridComponent}
       urls={urls}
       theme={theme}