@vitessce/constants-internal 3.4.9 → 3.4.11

package/dist/index.js

@@ -37,6 +37,7 @@ const FileType = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
   ANNDATA_ZARR_ZIP: "anndata.zarr.zip",
+  ANNDATA_H5AD: "anndata.h5ad",
   SPATIALDATA_ZARR: "spatialdata.zarr",
   // Atomic file types
   OBS_EMBEDDING_CSV: "obsEmbedding.csv",
@@ -77,6 +78,18 @@ const FileType = {
   OBS_LABELS_ANNDATA_ZARR_ZIP: "obsLabels.anndata.zarr.zip",
   FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
   SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
+  // AnnData - h5ad via reference spec
+  OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
+  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
+  OBS_SETS_ANNDATA_H5AD: "obsSets.anndata.h5ad",
+  OBS_EMBEDDING_ANNDATA_H5AD: "obsEmbedding.anndata.h5ad",
+  OBS_SPOTS_ANNDATA_H5AD: "obsSpots.anndata.h5ad",
+  OBS_POINTS_ANNDATA_H5AD: "obsPoints.anndata.h5ad",
+  OBS_LOCATIONS_ANNDATA_H5AD: "obsLocations.anndata.h5ad",
+  OBS_SEGMENTATIONS_ANNDATA_H5AD: "obsSegmentations.anndata.h5ad",
+  OBS_LABELS_ANNDATA_H5AD: "obsLabels.anndata.h5ad",
+  FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
+  SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
   LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -266,6 +279,27 @@ const STATUS = {
   SUCCESS: "success",
   ERROR: "error"
 };
+const DescriptionType = {
+  PLAIN: "plain",
+  MARKDOWN: "markdown"
+};
+const ViewHelpMapping = {
+  SCATTERPLOT: "The scatterplot displays two-dimensional (pre-computed) dimensionality reduction results (such as from t-SNE or UMAP). Each point on the scatterplot represents an observation (e.g., cell).",
+  HEATMAP: "The heatmap displays an observation-by-feature (e.g., cell-by-gene) matrix, typically with transformed (e.g., normalized or standardized) values.",
+  SPATIAL: "The spatial view displays (potentially layered) spatially-resolved data including RGB or multiplexed images, segmentations of observations (bitmask- or polygon-based), and/or points (e.g., representing FISH transcripts).",
+  DESCRIPTION: "The description view displays additional information about a dataset. When images are included in a dataset, the description view also includes image metadata (if contained in the image files).",
+  STATUS: "The status view displays debugging messages, including app-wide error messages when datasets fail to load or when schemas fail to validate. Details about the entity under the mouse cursor (cell, gene, and/or molecule) are displayed during hover interactions.",
+  LAYER_CONTROLLER: "The spatial layer controller provides an interface for manipulating the visualization layers displayed in the spatial view.",
+  GENOMIC_PROFILES: "The genomic profiles view displays genome browser tracks (using the genomic-profiles data type) containing bar plots, where the genome is along the x-axis and the value at each genome position is encoded with a bar along the y-axis.",
+  GATING: "The gating scatterplot displays expression data for two genes (along the X and Y axes). Users can select two genes, and the scatterplot is dynamically generated using observation-by-feature matrix data. Gating can then be performed by using the lasso or box select tools.",
+  FEATURE_LIST: "The feature list controller displays an interactive list of features (e.g., genes).",
+  OBS_SETS: "The observation sets controller displays an interactive list of (potentially hierarchical) observation sets (e.g., cell clusters or cell type annotations).",
+  OBS_SET_SIZES: "The observation set sizes view displays a bar plot with the currently-selected observation sets (e.g., cell types) on the x-axis and bars representing their size (e.g., number of cells) on the y-axis.",
+  OBS_SET_FEATURE_VALUE_DISTRIBUTION: "The observation set feature value distribution view displays a violin plot with values (e.g., expression values) per set (e.g., cell type) for the selected feature (e.g., gene).",
+  FEATURE_VALUE_HISTOGRAM: "The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).",
+  DOT_PLOT: "The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).",
+  FEATURE_BAR_PLOT: "The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis."
+};
 const FILE_TYPE_DATA_TYPE_MAPPING = {
   // For new file types
   [FileType.OBS_EMBEDDING_CSV]: DataType.OBS_EMBEDDING,
@@ -376,37 +410,48 @@ const DATA_TYPE_COORDINATION_VALUE_USAGE = {
 };
 const ALT_ZARR_STORE_TYPES = {
   [FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: {
-    zip: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_FEATURE_MATRIX_ANNDATA_H5AD
   },
   [FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR]: {
-    zip: FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_FEATURE_COLUMNS_ANNDATA_H5AD
   },
   [FileType.OBS_SETS_ANNDATA_ZARR]: {
-    zip: FileType.OBS_SETS_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_SETS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_SETS_ANNDATA_H5AD
   },
   [FileType.OBS_EMBEDDING_ANNDATA_ZARR]: {
-    zip: FileType.OBS_EMBEDDING_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_EMBEDDING_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_EMBEDDING_ANNDATA_H5AD
   },
   [FileType.OBS_SPOTS_ANNDATA_ZARR]: {
-    zip: FileType.OBS_SPOTS_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_SPOTS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_SPOTS_ANNDATA_H5AD
   },
   [FileType.OBS_POINTS_ANNDATA_ZARR]: {
-    zip: FileType.OBS_POINTS_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_POINTS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_POINTS_ANNDATA_H5AD
   },
   [FileType.OBS_LOCATIONS_ANNDATA_ZARR]: {
-    zip: FileType.OBS_LOCATIONS_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_LOCATIONS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_LOCATIONS_ANNDATA_H5AD
   },
   [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: {
-    zip: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_SEGMENTATIONS_ANNDATA_H5AD
   },
   [FileType.OBS_LABELS_ANNDATA_ZARR]: {
-    zip: FileType.OBS_LABELS_ANNDATA_ZARR_ZIP
+    zip: FileType.OBS_LABELS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_LABELS_ANNDATA_H5AD
   },
   [FileType.FEATURE_LABELS_ANNDATA_ZARR]: {
-    zip: FileType.FEATURE_LABELS_ANNDATA_ZARR_ZIP
+    zip: FileType.FEATURE_LABELS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.FEATURE_LABELS_ANNDATA_H5AD
   },
   [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: {
-    zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP
+    zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.SAMPLE_EDGES_ANNDATA_H5AD
   }
 };
 const AUTO_INDEPENDENT_COORDINATION_TYPES = [
@@ -842,10 +887,10 @@ const COMPONENT_COORDINATION_TYPES = {
   ]
 };
 const note = "This file is autogenerated by .changeset/post-changelog.mjs.";
-const version = "3.4.9";
-const date = "2024-07-26";
+const version = "3.4.11";
+const date = "2024-09-27";
 const branch = "changeset-release/main";
-const hash = "9582ddcf";
+const hash = "efd7d698";
 const version$1 = {
   note,
   version,
@@ -860,9 +905,11 @@ export {
   CoordinationType,
   DATA_TYPE_COORDINATION_VALUE_USAGE,
   DataType,
+  DescriptionType,
   FILE_TYPE_DATA_TYPE_MAPPING,
   FileType,
   version$1 as META_VERSION,
   STATUS,
+  ViewHelpMapping,
   ViewType
 };

package/dist-tsc/constant-relationships.d.ts

@@ -17,6 +17,7 @@ export declare const DATA_TYPE_COORDINATION_VALUE_USAGE: {
 export declare const ALT_ZARR_STORE_TYPES: {
     [x: string]: {
         zip: string;
+        h5ad: string;
     };
 };
 //# sourceMappingURL=constant-relationships.d.ts.map

package/dist-tsc/constant-relationships.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"constant-relationships.d.ts","sourceRoot":"","sources":["../src/constant-relationships.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,eAAO,MAAM,2BAA2B;;CA+DvC,CAAC;AAEF;;;;GAIG;AACH,eAAO,MAAM,kCAAkC;;CA6C9C,CAAC;AAKF,eAAO,MAAM,oBAAoB;;;;CAkChC,CAAC"}
+{"version":3,"file":"constant-relationships.d.ts","sourceRoot":"","sources":["../src/constant-relationships.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,eAAO,MAAM,2BAA2B;;CA+DvC,CAAC;AAEF;;;;GAIG;AACH,eAAO,MAAM,kCAAkC;;CA6C9C,CAAC;AAKF,eAAO,MAAM,oBAAoB;;;;;CA6ChC,CAAC"}

package/dist-tsc/constant-relationships.js

@@ -123,35 +123,46 @@ export const DATA_TYPE_COORDINATION_VALUE_USAGE = {
 export const ALT_ZARR_STORE_TYPES = {
     [FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: {
         zip: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_FEATURE_MATRIX_ANNDATA_H5AD,
     },
     [FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR]: {
         zip: FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_FEATURE_COLUMNS_ANNDATA_H5AD,
     },
     [FileType.OBS_SETS_ANNDATA_ZARR]: {
         zip: FileType.OBS_SETS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_SETS_ANNDATA_H5AD,
     },
     [FileType.OBS_EMBEDDING_ANNDATA_ZARR]: {
         zip: FileType.OBS_EMBEDDING_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_EMBEDDING_ANNDATA_H5AD,
     },
     [FileType.OBS_SPOTS_ANNDATA_ZARR]: {
         zip: FileType.OBS_SPOTS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_SPOTS_ANNDATA_H5AD,
     },
     [FileType.OBS_POINTS_ANNDATA_ZARR]: {
         zip: FileType.OBS_POINTS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_POINTS_ANNDATA_H5AD,
     },
     [FileType.OBS_LOCATIONS_ANNDATA_ZARR]: {
         zip: FileType.OBS_LOCATIONS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_LOCATIONS_ANNDATA_H5AD,
     },
     [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: {
         zip: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_SEGMENTATIONS_ANNDATA_H5AD,
     },
     [FileType.OBS_LABELS_ANNDATA_ZARR]: {
         zip: FileType.OBS_LABELS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.OBS_LABELS_ANNDATA_H5AD,
     },
     [FileType.FEATURE_LABELS_ANNDATA_ZARR]: {
         zip: FileType.FEATURE_LABELS_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.FEATURE_LABELS_ANNDATA_H5AD,
     },
     [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: {
         zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
+        h5ad: FileType.SAMPLE_EDGES_ANNDATA_H5AD,
     },
 };

package/dist-tsc/constants.d.ts

@@ -48,6 +48,7 @@ export declare const AsyncFunctionType: {
 export declare const FileType: {
     ANNDATA_ZARR: string;
     ANNDATA_ZARR_ZIP: string;
+    ANNDATA_H5AD: string;
     SPATIALDATA_ZARR: string;
     OBS_EMBEDDING_CSV: string;
     OBS_SPOTS_CSV: string;
@@ -84,6 +85,17 @@ export declare const FileType: {
     OBS_LABELS_ANNDATA_ZARR_ZIP: string;
     FEATURE_LABELS_ANNDATA_ZARR_ZIP: string;
     SAMPLE_EDGES_ANNDATA_ZARR_ZIP: string;
+    OBS_FEATURE_MATRIX_ANNDATA_H5AD: string;
+    OBS_FEATURE_COLUMNS_ANNDATA_H5AD: string;
+    OBS_SETS_ANNDATA_H5AD: string;
+    OBS_EMBEDDING_ANNDATA_H5AD: string;
+    OBS_SPOTS_ANNDATA_H5AD: string;
+    OBS_POINTS_ANNDATA_H5AD: string;
+    OBS_LOCATIONS_ANNDATA_H5AD: string;
+    OBS_SEGMENTATIONS_ANNDATA_H5AD: string;
+    OBS_LABELS_ANNDATA_H5AD: string;
+    FEATURE_LABELS_ANNDATA_H5AD: string;
+    SAMPLE_EDGES_ANNDATA_H5AD: string;
     IMAGE_SPATIALDATA_ZARR: string;
     LABELS_SPATIALDATA_ZARR: string;
     SHAPES_SPATIALDATA_ZARR: string;
@@ -249,4 +261,29 @@ export declare const STATUS: {
     SUCCESS: string;
     ERROR: string;
 };
+export declare const DescriptionType: {
+    PLAIN: string;
+    MARKDOWN: string;
+};
+/**
+ * Constants representing the help text for
+ * each view.
+ */
+export declare const ViewHelpMapping: {
+    SCATTERPLOT: string;
+    HEATMAP: string;
+    SPATIAL: string;
+    DESCRIPTION: string;
+    STATUS: string;
+    LAYER_CONTROLLER: string;
+    GENOMIC_PROFILES: string;
+    GATING: string;
+    FEATURE_LIST: string;
+    OBS_SETS: string;
+    OBS_SET_SIZES: string;
+    OBS_SET_FEATURE_VALUE_DISTRIBUTION: string;
+    FEATURE_VALUE_HISTOGRAM: string;
+    DOT_PLOT: string;
+    FEATURE_BAR_PLOT: string;
+};
 //# sourceMappingURL=constants.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;CAkBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;CAM7B,CAAC;AAGF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAwGpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAqH5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC"}
+{"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;CAkBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;CAM7B,CAAC;AAGF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAqHpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAqH5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC;AAEF,eAAO,MAAM,eAAe;;;CAG3B,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;CAgB3B,CAAC"}

package/dist-tsc/constants.js

@@ -49,6 +49,7 @@ export const FileType = {
     // Joint file types
     ANNDATA_ZARR: 'anndata.zarr',
     ANNDATA_ZARR_ZIP: 'anndata.zarr.zip',
+    ANNDATA_H5AD: 'anndata.h5ad',
     SPATIALDATA_ZARR: 'spatialdata.zarr',
     // Atomic file types
     OBS_EMBEDDING_CSV: 'obsEmbedding.csv',
@@ -89,6 +90,18 @@ export const FileType = {
     OBS_LABELS_ANNDATA_ZARR_ZIP: 'obsLabels.anndata.zarr.zip',
     FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
     SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
+    // AnnData - h5ad via reference spec
+    OBS_FEATURE_MATRIX_ANNDATA_H5AD: 'obsFeatureMatrix.anndata.h5ad',
+    OBS_FEATURE_COLUMNS_ANNDATA_H5AD: 'obsFeatureColumns.anndata.h5ad',
+    OBS_SETS_ANNDATA_H5AD: 'obsSets.anndata.h5ad',
+    OBS_EMBEDDING_ANNDATA_H5AD: 'obsEmbedding.anndata.h5ad',
+    OBS_SPOTS_ANNDATA_H5AD: 'obsSpots.anndata.h5ad',
+    OBS_POINTS_ANNDATA_H5AD: 'obsPoints.anndata.h5ad',
+    OBS_LOCATIONS_ANNDATA_H5AD: 'obsLocations.anndata.h5ad',
+    OBS_SEGMENTATIONS_ANNDATA_H5AD: 'obsSegmentations.anndata.h5ad',
+    OBS_LABELS_ANNDATA_H5AD: 'obsLabels.anndata.h5ad',
+    FEATURE_LABELS_ANNDATA_H5AD: 'featureLabels.anndata.h5ad',
+    SAMPLE_EDGES_ANNDATA_H5AD: 'sampleEdges.anndata.h5ad',
     // SpatialData
     IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
     LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -277,3 +290,28 @@ export const STATUS = {
     SUCCESS: 'success',
     ERROR: 'error',
 };
+export const DescriptionType = {
+    PLAIN: 'plain',
+    MARKDOWN: 'markdown',
+};
+/**
+ * Constants representing the help text for
+ * each view.
+ */
+export const ViewHelpMapping = {
+    SCATTERPLOT: 'The scatterplot displays two-dimensional (pre-computed) dimensionality reduction results (such as from t-SNE or UMAP). Each point on the scatterplot represents an observation (e.g., cell).',
+    HEATMAP: 'The heatmap displays an observation-by-feature (e.g., cell-by-gene) matrix, typically with transformed (e.g., normalized or standardized) values.',
+    SPATIAL: 'The spatial view displays (potentially layered) spatially-resolved data including RGB or multiplexed images, segmentations of observations (bitmask- or polygon-based), and/or points (e.g., representing FISH transcripts).',
+    DESCRIPTION: 'The description view displays additional information about a dataset. When images are included in a dataset, the description view also includes image metadata (if contained in the image files).',
+    STATUS: 'The status view displays debugging messages, including app-wide error messages when datasets fail to load or when schemas fail to validate. Details about the entity under the mouse cursor (cell, gene, and/or molecule) are displayed during hover interactions.',
+    LAYER_CONTROLLER: 'The spatial layer controller provides an interface for manipulating the visualization layers displayed in the spatial view.',
+    GENOMIC_PROFILES: 'The genomic profiles view displays genome browser tracks (using the genomic-profiles data type) containing bar plots, where the genome is along the x-axis and the value at each genome position is encoded with a bar along the y-axis.',
+    GATING: 'The gating scatterplot displays expression data for two genes (along the X and Y axes). Users can select two genes, and the scatterplot is dynamically generated using observation-by-feature matrix data. Gating can then be performed by using the lasso or box select tools.',
+    FEATURE_LIST: 'The feature list controller displays an interactive list of features (e.g., genes).',
+    OBS_SETS: 'The observation sets controller displays an interactive list of (potentially hierarchical) observation sets (e.g., cell clusters or cell type annotations).',
+    OBS_SET_SIZES: 'The observation set sizes view displays a bar plot with the currently-selected observation sets (e.g., cell types) on the x-axis and bars representing their size (e.g., number of cells) on the y-axis.',
+    OBS_SET_FEATURE_VALUE_DISTRIBUTION: 'The observation set feature value distribution view displays a violin plot with values (e.g., expression values) per set (e.g., cell type) for the selected feature (e.g., gene).',
+    FEATURE_VALUE_HISTOGRAM: 'The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).',
+    DOT_PLOT: 'The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).',
+    FEATURE_BAR_PLOT: 'The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis.',
+};

package/dist-tsc/index.d.ts

@@ -1,4 +1,4 @@
-export { ViewType, DataType, FileType, CoordinationType, STATUS, } from './constants.js';
+export { ViewType, DataType, FileType, CoordinationType, STATUS, ViewHelpMapping, DescriptionType, } from './constants.js';
 export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE, ALT_ZARR_STORE_TYPES, } from './constant-relationships.js';
 export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
 export { default as META_VERSION } from './version.json';

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,GACvD,MAAM,gBAAgB,CAAC;AACxB,OAAO,EACL,2BAA2B,EAC3B,kCAAkC,EAClC,oBAAoB,GACrB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EAAE,mCAAmC,EAAE,4BAA4B,EAAE,MAAM,mBAAmB,CAAC;AACtG,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,EAAE,eAAe,EAAE,eAAe,GACzF,MAAM,gBAAgB,CAAC;AACxB,OAAO,EACL,2BAA2B,EAC3B,kCAAkC,EAClC,oBAAoB,GACrB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EAAE,mCAAmC,EAAE,4BAA4B,EAAE,MAAM,mBAAmB,CAAC;AACtG,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC"}

package/dist-tsc/index.js

@@ -1,4 +1,4 @@
-export { ViewType, DataType, FileType, CoordinationType, STATUS, } from './constants.js';
+export { ViewType, DataType, FileType, CoordinationType, STATUS, ViewHelpMapping, DescriptionType, } from './constants.js';
 export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE, ALT_ZARR_STORE_TYPES, } from './constant-relationships.js';
 export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
 export { default as META_VERSION } from './version.json';

package/dist-tsc/version.json

@@ -1,7 +1,7 @@
 {
     "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
-    "version": "3.4.9",
-    "date": "2024-07-26",
+    "version": "3.4.11",
+    "date": "2024-09-27",
     "branch": "changeset-release/main",
-    "hash": "9582ddcf"
+    "hash": "efd7d698"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/constants-internal",
-  "version": "3.4.9",
+  "version": "3.4.11",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {

package/src/constant-relationships.ts

@@ -128,35 +128,46 @@ export const DATA_TYPE_COORDINATION_VALUE_USAGE = {
 export const ALT_ZARR_STORE_TYPES = {
   [FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: {
     zip: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_FEATURE_MATRIX_ANNDATA_H5AD,
   },
   [FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR]: {
     zip: FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_FEATURE_COLUMNS_ANNDATA_H5AD,
   },
   [FileType.OBS_SETS_ANNDATA_ZARR]: {
     zip: FileType.OBS_SETS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_SETS_ANNDATA_H5AD,
   },
   [FileType.OBS_EMBEDDING_ANNDATA_ZARR]: {
     zip: FileType.OBS_EMBEDDING_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_EMBEDDING_ANNDATA_H5AD,
   },
   [FileType.OBS_SPOTS_ANNDATA_ZARR]: {
     zip: FileType.OBS_SPOTS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_SPOTS_ANNDATA_H5AD,
   },
   [FileType.OBS_POINTS_ANNDATA_ZARR]: {
     zip: FileType.OBS_POINTS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_POINTS_ANNDATA_H5AD,
   },
   [FileType.OBS_LOCATIONS_ANNDATA_ZARR]: {
     zip: FileType.OBS_LOCATIONS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_LOCATIONS_ANNDATA_H5AD,
   },
   [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: {
     zip: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_SEGMENTATIONS_ANNDATA_H5AD,
   },
   [FileType.OBS_LABELS_ANNDATA_ZARR]: {
     zip: FileType.OBS_LABELS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.OBS_LABELS_ANNDATA_H5AD,
   },
   [FileType.FEATURE_LABELS_ANNDATA_ZARR]: {
     zip: FileType.FEATURE_LABELS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.FEATURE_LABELS_ANNDATA_H5AD,
   },
   [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: {
     zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
+    h5ad: FileType.SAMPLE_EDGES_ANNDATA_H5AD,
   },
 };

package/src/constants.ts

@@ -53,6 +53,7 @@ export const FileType = {
   // Joint file types
   ANNDATA_ZARR: 'anndata.zarr',
   ANNDATA_ZARR_ZIP: 'anndata.zarr.zip',
+  ANNDATA_H5AD: 'anndata.h5ad',
   SPATIALDATA_ZARR: 'spatialdata.zarr',
   // Atomic file types
   OBS_EMBEDDING_CSV: 'obsEmbedding.csv',
@@ -93,6 +94,18 @@ export const FileType = {
   OBS_LABELS_ANNDATA_ZARR_ZIP: 'obsLabels.anndata.zarr.zip',
   FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
   SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
+  // AnnData - h5ad via reference spec
+  OBS_FEATURE_MATRIX_ANNDATA_H5AD: 'obsFeatureMatrix.anndata.h5ad',
+  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: 'obsFeatureColumns.anndata.h5ad',
+  OBS_SETS_ANNDATA_H5AD: 'obsSets.anndata.h5ad',
+  OBS_EMBEDDING_ANNDATA_H5AD: 'obsEmbedding.anndata.h5ad',
+  OBS_SPOTS_ANNDATA_H5AD: 'obsSpots.anndata.h5ad',
+  OBS_POINTS_ANNDATA_H5AD: 'obsPoints.anndata.h5ad',
+  OBS_LOCATIONS_ANNDATA_H5AD: 'obsLocations.anndata.h5ad',
+  OBS_SEGMENTATIONS_ANNDATA_H5AD: 'obsSegmentations.anndata.h5ad',
+  OBS_LABELS_ANNDATA_H5AD: 'obsLabels.anndata.h5ad',
+  FEATURE_LABELS_ANNDATA_H5AD: 'featureLabels.anndata.h5ad',
+  SAMPLE_EDGES_ANNDATA_H5AD: 'sampleEdges.anndata.h5ad',
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
   LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -283,3 +296,30 @@ export const STATUS = {
   SUCCESS: 'success',
   ERROR: 'error',
 };
+
+export const DescriptionType = {
+  PLAIN: 'plain',
+  MARKDOWN: 'markdown',
+};
+
+/**
+ * Constants representing the help text for
+ * each view.
+ */
+export const ViewHelpMapping = {
+  SCATTERPLOT: 'The scatterplot displays two-dimensional (pre-computed) dimensionality reduction results (such as from t-SNE or UMAP). Each point on the scatterplot represents an observation (e.g., cell).',
+  HEATMAP: 'The heatmap displays an observation-by-feature (e.g., cell-by-gene) matrix, typically with transformed (e.g., normalized or standardized) values.',
+  SPATIAL: 'The spatial view displays (potentially layered) spatially-resolved data including RGB or multiplexed images, segmentations of observations (bitmask- or polygon-based), and/or points (e.g., representing FISH transcripts).',
+  DESCRIPTION: 'The description view displays additional information about a dataset. When images are included in a dataset, the description view also includes image metadata (if contained in the image files).',
+  STATUS: 'The status view displays debugging messages, including app-wide error messages when datasets fail to load or when schemas fail to validate. Details about the entity under the mouse cursor (cell, gene, and/or molecule) are displayed during hover interactions.',
+  LAYER_CONTROLLER: 'The spatial layer controller provides an interface for manipulating the visualization layers displayed in the spatial view.',
+  GENOMIC_PROFILES: 'The genomic profiles view displays genome browser tracks (using the genomic-profiles data type) containing bar plots, where the genome is along the x-axis and the value at each genome position is encoded with a bar along the y-axis.',
+  GATING: 'The gating scatterplot displays expression data for two genes (along the X and Y axes). Users can select two genes, and the scatterplot is dynamically generated using observation-by-feature matrix data. Gating can then be performed by using the lasso or box select tools.',
+  FEATURE_LIST: 'The feature list controller displays an interactive list of features (e.g., genes).',
+  OBS_SETS: 'The observation sets controller displays an interactive list of (potentially hierarchical) observation sets (e.g., cell clusters or cell type annotations).',
+  OBS_SET_SIZES: 'The observation set sizes view displays a bar plot with the currently-selected observation sets (e.g., cell types) on the x-axis and bars representing their size (e.g., number of cells) on the y-axis.',
+  OBS_SET_FEATURE_VALUE_DISTRIBUTION: 'The observation set feature value distribution view displays a violin plot with values (e.g., expression values) per set (e.g., cell type) for the selected feature (e.g., gene).',
+  FEATURE_VALUE_HISTOGRAM: 'The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).',
+  DOT_PLOT: 'The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).',
+  FEATURE_BAR_PLOT: 'The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis.',
+};

package/src/index.ts

@@ -1,5 +1,5 @@
 export {
-  ViewType, DataType, FileType, CoordinationType, STATUS,
+  ViewType, DataType, FileType, CoordinationType, STATUS, ViewHelpMapping, DescriptionType,
 } from './constants.js';
 export {
   FILE_TYPE_DATA_TYPE_MAPPING,

package/src/version.json

@@ -1,7 +1,7 @@
 {
   "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
-  "version": "3.4.9",
-  "date": "2024-07-26",
+  "version": "3.4.11",
+  "date": "2024-09-27",
   "branch": "changeset-release/main",
-  "hash": "9582ddcf"
+  "hash": "efd7d698"
 }