@vitessce/all 2.0.3 → 3.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (48) hide show
  1. package/dist/{deflate.8ace1ac4.mjs → deflate-f57b3163.js} +2 -2
  2. package/dist/hglib-1422f224.js +138925 -0
  3. package/dist/{index.7dac8670.mjs → index-3f1c1764.js} +67100 -52955
  4. package/dist/index.js +12 -0
  5. package/dist/{jpeg.c8011e3a.mjs → jpeg-e740c9a5.js} +1 -1
  6. package/dist/{lerc.ccda5eb2.mjs → lerc-01e6c4d8.js} +76 -5
  7. package/dist/{lzw.39876143.mjs → lzw-865bd058.js} +1 -1
  8. package/dist/{packbits.9e95d117.mjs → packbits-d4191efd.js} +1 -1
  9. package/dist/{pako.esm.4b234125.mjs → pako.esm-68f84e2a.js} +97 -15
  10. package/dist/{raw.0279d74b.mjs → raw-3c693341.js} +1 -1
  11. package/dist/{webimage.5ac7ce95.mjs → webimage-83da2258.js} +1 -1
  12. package/dist-tsc/Vitessce.d.ts +2 -0
  13. package/dist-tsc/Vitessce.d.ts.map +1 -0
  14. package/dist-tsc/Vitessce.js +41 -0
  15. package/dist-tsc/base-plugins.d.ts +854 -0
  16. package/dist-tsc/base-plugins.d.ts.map +1 -0
  17. package/dist-tsc/base-plugins.js +191 -0
  18. package/dist-tsc/index.d.ts +4 -0
  19. package/dist-tsc/index.d.ts.map +1 -0
  20. package/dist-tsc/index.js +3 -2
  21. package/dist-tsc/joint-file-types-legacy.d.ts +226 -0
  22. package/dist-tsc/joint-file-types-legacy.d.ts.map +1 -0
  23. package/dist-tsc/joint-file-types-legacy.js +266 -0
  24. package/dist-tsc/joint-file-types-legacy.test.d.ts +2 -0
  25. package/dist-tsc/joint-file-types-legacy.test.d.ts.map +1 -0
  26. package/dist-tsc/joint-file-types-legacy.test.js +401 -0
  27. package/dist-tsc/joint-file-types.d.ts +4 -0
  28. package/dist-tsc/joint-file-types.d.ts.map +1 -0
  29. package/dist-tsc/joint-file-types.js +127 -0
  30. package/dist-tsc/joint-file-types.test.d.ts +2 -0
  31. package/dist-tsc/joint-file-types.test.d.ts.map +1 -0
  32. package/dist-tsc/joint-file-types.test.js +128 -0
  33. package/dist-tsc/latest-config-schema.test.d.ts +2 -0
  34. package/dist-tsc/latest-config-schema.test.d.ts.map +1 -0
  35. package/dist-tsc/latest-config-schema.test.js +19 -0
  36. package/package.json +37 -21
  37. package/src/Vitessce.tsx +74 -0
  38. package/src/base-plugins.ts +362 -0
  39. package/src/index.ts +8 -0
  40. package/src/joint-file-types-legacy.test.ts +413 -0
  41. package/src/joint-file-types-legacy.ts +284 -0
  42. package/src/joint-file-types.test.ts +132 -0
  43. package/src/joint-file-types.ts +142 -0
  44. package/src/latest-config-schema.test.ts +26 -0
  45. package/dist/hglib.1f1ea875.mjs +0 -130303
  46. package/dist/index.mjs +0 -11
  47. package/src/index.js +0 -7
  48. package/src/setup.js +0 -143
@@ -0,0 +1 @@
1
+ {"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AASA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACvB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EA4BF,MAAM,mBAAmB,CAAC;AAoG3B,eAAO,MAAM,aAAa,kBAezB,CAAC;AAEF,eAAO,MAAM,aAAa,wDA8CzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;OAc9B,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;OAkIjC,CAAC"}
@@ -0,0 +1,191 @@
1
+ import { FileType, DataType, ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, } from '@vitessce/constants-internal';
2
+ import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, } from '@vitessce/plugins';
3
+ import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, } from '@vitessce/schemas';
4
+ // Register view type plugins
5
+ import { DescriptionSubscriber } from '@vitessce/description';
6
+ import { ObsSetsManagerSubscriber } from '@vitessce/obs-sets-manager';
7
+ import { EmbeddingScatterplotSubscriber } from '@vitessce/scatterplot-embedding';
8
+ import { GatingSubscriber } from '@vitessce/scatterplot-gating';
9
+ import { SpatialSubscriber } from '@vitessce/spatial';
10
+ import { HeatmapSubscriber } from '@vitessce/heatmap';
11
+ import { FeatureListSubscriber } from '@vitessce/feature-list';
12
+ import { LayerControllerSubscriber } from '@vitessce/layer-controller';
13
+ import { StatusSubscriber } from '@vitessce/status';
14
+ import { HiGlassSubscriber, GenomicProfilesSubscriber } from '@vitessce/genomic-profiles';
15
+ import { CellSetExpressionPlotSubscriber, CellSetSizesPlotSubscriber, ExpressionHistogramSubscriber, } from '@vitessce/statistical-plots';
16
+ // Register file type plugins
17
+ import {
18
+ // CSV
19
+ CsvSource, ObsSetsCsvLoader, ObsEmbeddingCsvLoader, ObsLocationsCsvLoader, ObsLabelsCsvLoader, ObsFeatureMatrixCsvLoader, FeatureLabelsCsvLoader, } from '@vitessce/csv';
20
+ import {
21
+ // JSON
22
+ JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader,
23
+ // Legacy
24
+ RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
25
+ import {
26
+ // AnnData
27
+ AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader,
28
+ // MuData
29
+ MuDataSource,
30
+ // OME
31
+ OmeZarrLoader,
32
+ // Legacy
33
+ ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
34
+ import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
35
+ // Joint file types
36
+ import { expandAnndataZarr, } from './joint-file-types.js';
37
+ import { expandAnndataCellSetsZarr, expandAnndataCellsZarr, expandAnndataExpressionMatrixZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandExpressionMatrixZarr, expandGenesJson, expandMoleculesJson, expandRasterJson, expandRasterOmeZarr, } from './joint-file-types-legacy.js';
38
+ // Helper function to use COMPONENT_COORDINATION_TYPES.
39
+ function makeViewType(name, component) {
40
+ return new PluginViewType(name, component, COMPONENT_COORDINATION_TYPES[name]);
41
+ }
42
+ function makeFileType(name, dataType, dataLoaderClass, dataSourceClass, optionsSchema) {
43
+ return new PluginFileType(name, dataType, dataLoaderClass, dataSourceClass, optionsSchema);
44
+ }
45
+ export const baseViewTypes = [
46
+ makeViewType(ViewType.DESCRIPTION, DescriptionSubscriber),
47
+ makeViewType(ViewType.OBS_SETS, ObsSetsManagerSubscriber),
48
+ makeViewType(ViewType.SCATTERPLOT, EmbeddingScatterplotSubscriber),
49
+ makeViewType(ViewType.GATING, GatingSubscriber),
50
+ makeViewType(ViewType.SPATIAL, SpatialSubscriber),
51
+ makeViewType(ViewType.HEATMAP, HeatmapSubscriber),
52
+ makeViewType(ViewType.FEATURE_LIST, FeatureListSubscriber),
53
+ makeViewType(ViewType.LAYER_CONTROLLER, LayerControllerSubscriber),
54
+ makeViewType(ViewType.STATUS, StatusSubscriber),
55
+ makeViewType(ViewType.OBS_SET_FEATURE_VALUE_DISTRIBUTION, CellSetExpressionPlotSubscriber),
56
+ makeViewType(ViewType.OBS_SET_SIZES, CellSetSizesPlotSubscriber),
57
+ makeViewType(ViewType.FEATURE_VALUE_HISTOGRAM, ExpressionHistogramSubscriber),
58
+ makeViewType('higlass', HiGlassSubscriber),
59
+ makeViewType(ViewType.GENOMIC_PROFILES, GenomicProfilesSubscriber),
60
+ ];
61
+ export const baseFileTypes = [
62
+ // All CSV file types
63
+ makeFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource, obsSetsCsvSchema),
64
+ makeFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource, obsEmbeddingCsvSchema),
65
+ makeFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource, obsLocationsCsvSchema),
66
+ makeFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource, obsLabelsCsvSchema),
67
+ makeFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource, z.null()),
68
+ makeFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource, featureLabelsCsvSchema),
69
+ // All JSON file types
70
+ makeFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource, z.null()),
71
+ makeFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
72
+ // All AnnData file types
73
+ makeFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource, obsSetsAnndataSchema),
74
+ makeFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource, obsEmbeddingAnndataSchema),
75
+ makeFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource, obsLocationsAnndataSchema),
76
+ makeFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource, obsLabelsAnndataSchema),
77
+ makeFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource, obsFeatureMatrixAnndataSchema),
78
+ makeFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource, obsSegmentationsAnndataSchema),
79
+ makeFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource, featureLabelsAnndataSchema),
80
+ // All MuData file types
81
+ makeFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource, obsSetsAnndataSchema),
82
+ makeFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource, obsEmbeddingAnndataSchema),
83
+ makeFileType(FileType.OBS_LOCATIONS_MUDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, MuDataSource, obsLocationsAnndataSchema),
84
+ makeFileType(FileType.OBS_LABELS_MUDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, MuDataSource, obsLabelsAnndataSchema),
85
+ makeFileType(FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, MuDataSource, obsFeatureMatrixAnndataSchema),
86
+ makeFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource, obsSegmentationsAnndataSchema),
87
+ makeFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource, featureLabelsAnndataSchema),
88
+ // All OME file types
89
+ makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
90
+ makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
91
+ makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, imageOmeZarrSchema),
92
+ // All legacy file types
93
+ makeFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource, z.null()),
94
+ makeFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource, rasterJsonSchema),
95
+ makeFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource, rasterJsonSchema),
96
+ makeFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
97
+ makeFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource, z.null()),
98
+ makeFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource, z.null()),
99
+ makeFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource, z.null()),
100
+ makeFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource, z.null()),
101
+ makeFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource, z.null()),
102
+ makeFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource, z.null()),
103
+ makeFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource, z.null()),
104
+ makeFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource, z.null()),
105
+ makeFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource, z.null()),
106
+ makeFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource, z.null()),
107
+ ];
108
+ export const baseJointFileTypes = [
109
+ new PluginJointFileType(FileType.ANNDATA_ZARR, expandAnndataZarr, anndataZarrSchema),
110
+ // For legacy file types:
111
+ new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
112
+ new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),
113
+ new PluginJointFileType(FileType.ANNDATA_EXPRESSION_MATRIX_ZARR, expandAnndataExpressionMatrixZarr, anndataExpressionMatrixZarrSchema),
114
+ new PluginJointFileType(FileType.EXPRESSION_MATRIX_ZARR, expandExpressionMatrixZarr, z.null()),
115
+ new PluginJointFileType(FileType.RASTER_JSON, expandRasterJson, rasterJsonSchema),
116
+ new PluginJointFileType(FileType.RASTER_OME_ZARR, expandRasterOmeZarr, z.null()),
117
+ new PluginJointFileType(FileType.CELL_SETS_JSON, expandCellSetsJson, z.null()),
118
+ new PluginJointFileType(FileType.CLUSTERS_JSON, expandClustersJson, z.null()),
119
+ new PluginJointFileType(FileType.GENES_JSON, expandGenesJson, z.null()),
120
+ new PluginJointFileType(FileType.CELLS_JSON, expandCellsJson, cellsJsonSchema),
121
+ new PluginJointFileType(FileType.MOLECULES_JSON, expandMoleculesJson, z.null()),
122
+ ];
123
+ // TODO: should these schemas be imported from a common location in package/ rather than here in packages/main/?
124
+ // That would allow view implementations to depend on them for type checking and their default values.
125
+ export const baseCoordinationTypes = [
126
+ new PluginCoordinationType(CoordinationType.DATASET, null, z.string().nullable()),
127
+ new PluginCoordinationType(CoordinationType.OBS_TYPE, 'cell', z.string()),
128
+ new PluginCoordinationType(CoordinationType.FEATURE_TYPE, 'gene', z.string()),
129
+ new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TYPE, 'expression', z.string()),
130
+ new PluginCoordinationType(CoordinationType.OBS_LABELS_TYPE, null, z.string().nullable()),
131
+ new PluginCoordinationType(CoordinationType.EMBEDDING_ZOOM, null, z.number().nullable()),
132
+ new PluginCoordinationType(CoordinationType.EMBEDDING_ROTATION, 0, z.number().nullable()),
133
+ new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_X, null, z.number().nullable()),
134
+ new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_Y, null, z.number().nullable()),
135
+ new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_Z, 0, z.number().nullable()),
136
+ new PluginCoordinationType(CoordinationType.EMBEDDING_TYPE, null, z.string().nullable()),
137
+ new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE, false, z.boolean()),
138
+ new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE, false, z.boolean()),
139
+ new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE, 14, z.number()),
140
+ new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_RADIUS, 1, z.number()),
141
+ new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_OPACITY, 1, z.number()),
142
+ new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_RADIUS_MODE, 'auto', z.enum(['manual', 'auto'])),
143
+ new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_OPACITY_MODE, 'auto', z.enum(['manual', 'auto'])),
144
+ new PluginCoordinationType(CoordinationType.SPATIAL_ZOOM, null, z.number().nullable()),
145
+ new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION, 0, z.number().nullable()),
146
+ new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_X, null, z.number().nullable()),
147
+ new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_Y, null, z.number().nullable()),
148
+ new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_Z, null, z.number().nullable()),
149
+ new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_X, null, z.number().nullable()),
150
+ new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_Y, null, z.number().nullable()),
151
+ new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_Z, null, z.number().nullable()),
152
+ new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_ORBIT, 0, z.number().nullable()),
153
+ new PluginCoordinationType(CoordinationType.SPATIAL_ORBIT_AXIS, 'Y', z.string().nullable()),
154
+ new PluginCoordinationType(CoordinationType.SPATIAL_AXIS_FIXED, false, z.boolean().nullable()),
155
+ new PluginCoordinationType(CoordinationType.SPATIAL_IMAGE_LAYER, null, imageLayerObj.nullable()),
156
+ new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_LAYER, null, z.union([
157
+ cellsLayerObj, imageLayerObj,
158
+ ]).nullable()),
159
+ new PluginCoordinationType(CoordinationType.SPATIAL_NEIGHBORHOOD_LAYER, null, neighborhoodsLayerObj.nullable()),
160
+ new PluginCoordinationType(CoordinationType.SPATIAL_POINT_LAYER, null, moleculesLayerObj.nullable()),
161
+ new PluginCoordinationType(CoordinationType.HEATMAP_ZOOM_X, 0, z.number()),
162
+ new PluginCoordinationType(CoordinationType.HEATMAP_ZOOM_Y, 0, z.number()),
163
+ new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_X, 0, z.number()),
164
+ new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_Y, 0, z.number()),
165
+ new PluginCoordinationType(CoordinationType.OBS_FILTER, null, z.array(z.string()).nullable()),
166
+ new PluginCoordinationType(CoordinationType.OBS_HIGHLIGHT, null, z.string().nullable()),
167
+ new PluginCoordinationType(CoordinationType.OBS_SET_SELECTION, null, z.array(obsSetPath).nullable()),
168
+ new PluginCoordinationType(CoordinationType.OBS_SET_EXPANSION, null, z.array(obsSetPath).nullable()),
169
+ new PluginCoordinationType(CoordinationType.OBS_SET_HIGHLIGHT, null, obsSetPath.nullable()),
170
+ new PluginCoordinationType(CoordinationType.OBS_SET_COLOR, null, z.array(z.object({
171
+ path: obsSetPath,
172
+ color: rgbArray,
173
+ })).nullable()),
174
+ new PluginCoordinationType(CoordinationType.OBS_COLOR_ENCODING, 'cellSetSelection', z.enum(['geneSelection', 'cellSetSelection'])),
175
+ new PluginCoordinationType(CoordinationType.FEATURE_FILTER, null, z.array(z.string()).nullable()),
176
+ new PluginCoordinationType(CoordinationType.FEATURE_HIGHLIGHT, null, z.string().nullable()),
177
+ new PluginCoordinationType(CoordinationType.FEATURE_SELECTION, null, z.array(z.string()).nullable()),
178
+ new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM, null, z.enum(['log1p', 'arcsinh']).nullable()),
179
+ new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT, 1, z.number()),
180
+ new PluginCoordinationType(CoordinationType.TOOLTIPS_VISIBLE, true, z.boolean()),
181
+ new PluginCoordinationType(CoordinationType.FEATURE_VALUE_COLORMAP, 'plasma', z.string().nullable()),
182
+ new PluginCoordinationType(CoordinationType.FEATURE_VALUE_COLORMAP_RANGE, [0.0, 1.0], z.array(z.number()).length(2)),
183
+ new PluginCoordinationType(CoordinationType.GATING_FEATURE_SELECTION_X, null, z.string().nullable()),
184
+ new PluginCoordinationType(CoordinationType.GATING_FEATURE_SELECTION_Y, null, z.string().nullable()),
185
+ new PluginCoordinationType(CoordinationType.GENOMIC_ZOOM_X, 0, z.number()),
186
+ new PluginCoordinationType(CoordinationType.GENOMIC_ZOOM_Y, 0, z.number()),
187
+ new PluginCoordinationType(CoordinationType.GENOMIC_TARGET_X, 1549999999.5, z.number()),
188
+ new PluginCoordinationType(CoordinationType.GENOMIC_TARGET_Y, 1549999999.5, z.number()),
189
+ new PluginCoordinationType(CoordinationType.ADDITIONAL_OBS_SETS, null, obsSetsSchema.nullable()),
190
+ new PluginCoordinationType(CoordinationType.MOLECULE_HIGHLIGHT, null, z.string().nullable()),
191
+ ];
@@ -0,0 +1,4 @@
1
+ export { Vitessce } from './Vitessce.js';
2
+ export { PluginFileType, PluginViewType, PluginCoordinationType, PluginJointFileType, } from '@vitessce/plugins';
3
+ export { z } from '@vitessce/schemas';
4
+ //# sourceMappingURL=index.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AACzC,OAAO,EACL,cAAc,EACd,cAAc,EACd,sBAAsB,EACtB,mBAAmB,GACpB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAAE,CAAC,EAAE,MAAM,mBAAmB,CAAC"}
package/dist-tsc/index.js CHANGED
@@ -1,2 +1,3 @@
1
- export { Vitessce } from './setup';
2
- export { registerPluginFileType, registerPluginViewType, registerPluginCoordinationType, registerPluginJointFileType, } from '@vitessce/vit-s';
1
+ export { Vitessce } from './Vitessce.js';
2
+ export { PluginFileType, PluginViewType, PluginCoordinationType, PluginJointFileType, } from '@vitessce/plugins';
3
+ export { z } from '@vitessce/schemas';
@@ -0,0 +1,226 @@
1
+ import type { z } from 'zod';
2
+ import type { latestFileDefSchema } from '@vitessce/schemas';
3
+ declare type legacyFileDefSchema = z.infer<typeof latestFileDefSchema> & {
4
+ type?: string;
5
+ };
6
+ export declare function expandMoleculesJson(fileDef: legacyFileDefSchema): {
7
+ fileType: string;
8
+ coordinationValues: {
9
+ obsType: string;
10
+ };
11
+ name?: string | undefined;
12
+ url?: string | undefined;
13
+ options?: any;
14
+ requestInit?: {
15
+ method?: string | undefined;
16
+ headers?: Record<string, any> | undefined;
17
+ body?: string | undefined;
18
+ mode?: string | undefined;
19
+ credentials?: string | undefined;
20
+ cache?: string | undefined;
21
+ redirect?: string | undefined;
22
+ referrer?: string | undefined;
23
+ integrity?: string | undefined;
24
+ } | undefined;
25
+ type?: string | undefined;
26
+ }[];
27
+ export declare function expandExpressionMatrixZarr(fileDef: legacyFileDefSchema): {
28
+ fileType: string;
29
+ coordinationValues: {
30
+ obsType: string;
31
+ featureType: string;
32
+ featureValueType: string;
33
+ };
34
+ name?: string | undefined;
35
+ url?: string | undefined;
36
+ options?: any;
37
+ requestInit?: {
38
+ method?: string | undefined;
39
+ headers?: Record<string, any> | undefined;
40
+ body?: string | undefined;
41
+ mode?: string | undefined;
42
+ credentials?: string | undefined;
43
+ cache?: string | undefined;
44
+ redirect?: string | undefined;
45
+ referrer?: string | undefined;
46
+ integrity?: string | undefined;
47
+ } | undefined;
48
+ type?: string | undefined;
49
+ }[];
50
+ export declare function expandRasterJson(fileDef: legacyFileDefSchema): {
51
+ fileType: string;
52
+ name?: string | undefined;
53
+ url?: string | undefined;
54
+ options?: any;
55
+ requestInit?: {
56
+ method?: string | undefined;
57
+ headers?: Record<string, any> | undefined;
58
+ body?: string | undefined;
59
+ mode?: string | undefined;
60
+ credentials?: string | undefined;
61
+ cache?: string | undefined;
62
+ redirect?: string | undefined;
63
+ referrer?: string | undefined;
64
+ integrity?: string | undefined;
65
+ } | undefined;
66
+ coordinationValues?: Record<string, string> | undefined;
67
+ type?: string | undefined;
68
+ }[];
69
+ export declare function expandRasterOmeZarr(fileDef: legacyFileDefSchema): {
70
+ fileType: string;
71
+ name?: string | undefined;
72
+ url?: string | undefined;
73
+ options?: any;
74
+ requestInit?: {
75
+ method?: string | undefined;
76
+ headers?: Record<string, any> | undefined;
77
+ body?: string | undefined;
78
+ mode?: string | undefined;
79
+ credentials?: string | undefined;
80
+ cache?: string | undefined;
81
+ redirect?: string | undefined;
82
+ referrer?: string | undefined;
83
+ integrity?: string | undefined;
84
+ } | undefined;
85
+ coordinationValues?: Record<string, string> | undefined;
86
+ type?: string | undefined;
87
+ }[];
88
+ export declare function expandCellSetsJson(fileDef: legacyFileDefSchema): {
89
+ fileType: string;
90
+ coordinationValues: {
91
+ obsType: string;
92
+ };
93
+ name?: string | undefined;
94
+ url?: string | undefined;
95
+ options?: any;
96
+ requestInit?: {
97
+ method?: string | undefined;
98
+ headers?: Record<string, any> | undefined;
99
+ body?: string | undefined;
100
+ mode?: string | undefined;
101
+ credentials?: string | undefined;
102
+ cache?: string | undefined;
103
+ redirect?: string | undefined;
104
+ referrer?: string | undefined;
105
+ integrity?: string | undefined;
106
+ } | undefined;
107
+ type?: string | undefined;
108
+ }[];
109
+ export declare function expandCellsJson(fileDef: legacyFileDefSchema): any[];
110
+ export declare function expandClustersJson(fileDef: legacyFileDefSchema): {
111
+ fileType: string;
112
+ coordinationValues: {
113
+ obsType: string;
114
+ featureType: string;
115
+ featureValueType: string;
116
+ };
117
+ name?: string | undefined;
118
+ url?: string | undefined;
119
+ options?: any;
120
+ requestInit?: {
121
+ method?: string | undefined;
122
+ headers?: Record<string, any> | undefined;
123
+ body?: string | undefined;
124
+ mode?: string | undefined;
125
+ credentials?: string | undefined;
126
+ cache?: string | undefined;
127
+ redirect?: string | undefined;
128
+ referrer?: string | undefined;
129
+ integrity?: string | undefined;
130
+ } | undefined;
131
+ type?: string | undefined;
132
+ }[];
133
+ export declare function expandGenesJson(fileDef: legacyFileDefSchema): {
134
+ fileType: string;
135
+ coordinationValues: {
136
+ obsType: string;
137
+ featureType: string;
138
+ featureValueType: string;
139
+ };
140
+ name?: string | undefined;
141
+ url?: string | undefined;
142
+ options?: any;
143
+ requestInit?: {
144
+ method?: string | undefined;
145
+ headers?: Record<string, any> | undefined;
146
+ body?: string | undefined;
147
+ mode?: string | undefined;
148
+ credentials?: string | undefined;
149
+ cache?: string | undefined;
150
+ redirect?: string | undefined;
151
+ referrer?: string | undefined;
152
+ integrity?: string | undefined;
153
+ } | undefined;
154
+ type?: string | undefined;
155
+ }[];
156
+ export declare function expandAnndataCellsZarr(fileDef: legacyFileDefSchema): any[];
157
+ export declare function expandAnndataCellSetsZarr(fileDef: legacyFileDefSchema): {
158
+ fileType: string;
159
+ options: any;
160
+ coordinationValues: {
161
+ obsType: string;
162
+ };
163
+ url: string | undefined;
164
+ requestInit: {
165
+ method?: string | undefined;
166
+ headers?: Record<string, any> | undefined;
167
+ body?: string | undefined;
168
+ mode?: string | undefined;
169
+ credentials?: string | undefined;
170
+ cache?: string | undefined;
171
+ redirect?: string | undefined;
172
+ referrer?: string | undefined;
173
+ integrity?: string | undefined;
174
+ } | undefined;
175
+ }[];
176
+ export declare function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDefSchema): ({
177
+ fileType: string;
178
+ options: {
179
+ path: any;
180
+ featureFilterPath?: undefined;
181
+ initialFeatureFilterPath?: undefined;
182
+ };
183
+ coordinationValues: {
184
+ featureType: string;
185
+ obsType?: undefined;
186
+ featureValueType?: undefined;
187
+ };
188
+ url: string | undefined;
189
+ requestInit: {
190
+ method?: string | undefined;
191
+ headers?: Record<string, any> | undefined;
192
+ body?: string | undefined;
193
+ mode?: string | undefined;
194
+ credentials?: string | undefined;
195
+ cache?: string | undefined;
196
+ redirect?: string | undefined;
197
+ referrer?: string | undefined;
198
+ integrity?: string | undefined;
199
+ } | undefined;
200
+ } | {
201
+ fileType: string;
202
+ options: {
203
+ path: any;
204
+ featureFilterPath: any;
205
+ initialFeatureFilterPath: any;
206
+ };
207
+ coordinationValues: {
208
+ obsType: string;
209
+ featureType: string;
210
+ featureValueType: string;
211
+ };
212
+ url: string | undefined;
213
+ requestInit: {
214
+ method?: string | undefined;
215
+ headers?: Record<string, any> | undefined;
216
+ body?: string | undefined;
217
+ mode?: string | undefined;
218
+ credentials?: string | undefined;
219
+ cache?: string | undefined;
220
+ redirect?: string | undefined;
221
+ referrer?: string | undefined;
222
+ integrity?: string | undefined;
223
+ } | undefined;
224
+ })[];
225
+ export {};
226
+ //# sourceMappingURL=joint-file-types-legacy.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"joint-file-types-legacy.d.ts","sourceRoot":"","sources":["../src/joint-file-types-legacy.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAG7D,aAAK,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,GAAG;IAC/D,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,CAAC;AAEF,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;IAkB/D;AAED,wBAAgB,0BAA0B,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;IAgBtE;AAED,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAiB5D;AAED,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAS/D;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;IAY9D;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB,SA0C3D;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;IAgB9D;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;IAgB3D;AAeD,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,mBAAmB,SAkDlE;AAED,wBAAgB,yBAAyB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAiBrE;AAED,wBAAgB,iCAAiC,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KA6B7E"}