@vitessce/constants-internal 3.5.5 → 3.5.7

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 (14) hide show
  1. package/dist/index.js +120 -10
  2. package/dist-tsc/constant-relationships.d.ts.map +1 -1
  3. package/dist-tsc/constant-relationships.js +5 -0
  4. package/dist-tsc/constants.d.ts +23 -2
  5. package/dist-tsc/constants.d.ts.map +1 -1
  6. package/dist-tsc/constants.js +24 -2
  7. package/dist-tsc/coordination.d.ts.map +1 -1
  8. package/dist-tsc/coordination.js +83 -0
  9. package/dist-tsc/version.json +3 -3
  10. package/package.json +1 -1
  11. package/src/constant-relationships.ts +5 -0
  12. package/src/constants.ts +24 -2
  13. package/src/coordination.ts +83 -0
  14. package/src/version.json +3 -3
package/dist/index.js CHANGED
@@ -17,7 +17,9 @@ const ViewType = {
17
17
  DOT_PLOT: "dotPlot",
18
18
  FEATURE_BAR_PLOT: "featureBarPlot",
19
19
  BIOMARKER_SELECT: "biomarkerSelect",
20
- LINK_CONTROLLER: "linkController"
20
+ LINK_CONTROLLER: "linkController",
21
+ DUAL_SCATTERPLOT: "dualScatterplot",
22
+ TREEMAP: "treemap"
21
23
  };
22
24
  const DataType = {
23
25
  OBS_LABELS: "obsLabels",
@@ -93,6 +95,7 @@ const FileType = {
93
95
  OBS_LABELS_ANNDATA_ZARR: "obsLabels.anndata.zarr",
94
96
  FEATURE_LABELS_ANNDATA_ZARR: "featureLabels.anndata.zarr",
95
97
  SAMPLE_EDGES_ANNDATA_ZARR: "sampleEdges.anndata.zarr",
98
+ SAMPLE_SETS_ANNDATA_ZARR: "sampleSets.anndata.zarr",
96
99
  // AnnData - zipped
97
100
  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: "obsFeatureMatrix.anndata.zarr.zip",
98
101
  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: "obsFeatureColumns.anndata.zarr.zip",
@@ -105,6 +108,7 @@ const FileType = {
105
108
  OBS_LABELS_ANNDATA_ZARR_ZIP: "obsLabels.anndata.zarr.zip",
106
109
  FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
107
110
  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
111
+ SAMPLE_SETS_ANNDATA_ZARR_ZIP: "sampleSets.anndata.zarr.zip",
108
112
  // AnnData - h5ad via reference spec
109
113
  OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
110
114
  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
@@ -117,6 +121,7 @@ const FileType = {
117
121
  OBS_LABELS_ANNDATA_H5AD: "obsLabels.anndata.h5ad",
118
122
  FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
119
123
  SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
124
+ SAMPLE_SETS_ANNDATA_H5AD: "sampleSets.anndata.h5ad",
120
125
  // SpatialData
121
126
  IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
122
127
  LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -218,15 +223,23 @@ const CoordinationType = {
218
223
  HEATMAP_ZOOM_Y: "heatmapZoomY",
219
224
  HEATMAP_TARGET_X: "heatmapTargetX",
220
225
  HEATMAP_TARGET_Y: "heatmapTargetY",
221
- OBS_FILTER: "obsFilter",
222
226
  OBS_HIGHLIGHT: "obsHighlight",
227
+ OBS_SELECTION: "obsSelection",
223
228
  OBS_SET_SELECTION: "obsSetSelection",
229
+ OBS_SELECTION_MODE: "obsSelectionMode",
230
+ OBS_FILTER: "obsFilter",
231
+ OBS_SET_FILTER: "obsSetFilter",
232
+ OBS_FILTER_MODE: "obsFilterMode",
224
233
  OBS_SET_HIGHLIGHT: "obsSetHighlight",
225
234
  OBS_SET_EXPANSION: "obsSetExpansion",
226
235
  OBS_SET_COLOR: "obsSetColor",
227
- FEATURE_FILTER: "featureFilter",
228
236
  FEATURE_HIGHLIGHT: "featureHighlight",
229
237
  FEATURE_SELECTION: "featureSelection",
238
+ FEATURE_SET_SELECTION: "featureSetSelection",
239
+ FEATURE_SELECTION_MODE: "featureSelectionMode",
240
+ FEATURE_FILTER: "featureFilter",
241
+ FEATURE_SET_FILTER: "featureSetFilter",
242
+ FEATURE_FILTER_MODE: "featureFilterMode",
230
243
  FEATURE_VALUE_COLORMAP: "featureValueColormap",
231
244
  FEATURE_VALUE_TRANSFORM: "featureValueTransform",
232
245
  FEATURE_VALUE_COLORMAP_RANGE: "featureValueColormapRange",
@@ -293,14 +306,22 @@ const CoordinationType = {
293
306
  SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize",
294
307
  // Multi-sample / comparative
295
308
  SAMPLE_TYPE: "sampleType",
309
+ SAMPLE_SELECTION: "sampleSelection",
296
310
  SAMPLE_SET_SELECTION: "sampleSetSelection",
311
+ SAMPLE_SELECTION_MODE: "sampleSelectionMode",
312
+ SAMPLE_FILTER: "sampleFilter",
313
+ SAMPLE_SET_FILTER: "sampleSetFilter",
314
+ SAMPLE_FILTER_MODE: "sampleFilterMode",
297
315
  SAMPLE_SET_COLOR: "sampleSetColor",
316
+ SAMPLE_HIGHLIGHT: "sampleHighlight",
298
317
  EMBEDDING_POINTS_VISIBLE: "embeddingPointsVisible",
299
318
  EMBEDDING_CONTOURS_VISIBLE: "embeddingContoursVisible",
300
319
  EMBEDDING_CONTOURS_FILLED: "embeddingContoursFilled",
301
320
  EMBEDDING_CONTOUR_PERCENTILES: "embeddingContourPercentiles",
302
321
  CONTOUR_COLOR_ENCODING: "contourColorEncoding",
303
- CONTOUR_COLOR: "contourColor"
322
+ CONTOUR_COLOR: "contourColor",
323
+ // Treemap
324
+ HIERARCHY_LEVELS: "hierarchyLevels"
304
325
  };
305
326
  const STATUS = {
306
327
  LOADING: "loading",
@@ -326,7 +347,8 @@ const ViewHelpMapping = {
326
347
  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).",
327
348
  FEATURE_VALUE_HISTOGRAM: "The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).",
328
349
  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).",
329
- 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."
350
+ 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.",
351
+ TREEMAP: "The treemap provides an overview of the current state of sample-level or cell-level selection and filtering."
330
352
  };
331
353
  const FILE_TYPE_DATA_TYPE_MAPPING = {
332
354
  // For new file types
@@ -354,6 +376,7 @@ const FILE_TYPE_DATA_TYPE_MAPPING = {
354
376
  [FileType.OBS_LABELS_ANNDATA_ZARR]: DataType.OBS_LABELS,
355
377
  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
356
378
  [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
379
+ [FileType.SAMPLE_SETS_ANNDATA_ZARR]: DataType.SAMPLE_SETS,
357
380
  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
358
381
  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
359
382
  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -482,6 +505,10 @@ const ALT_ZARR_STORE_TYPES = {
482
505
  zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
483
506
  h5ad: FileType.SAMPLE_EDGES_ANNDATA_H5AD
484
507
  },
508
+ [FileType.SAMPLE_SETS_ANNDATA_ZARR]: {
509
+ zip: FileType.SAMPLE_SETS_ANNDATA_ZARR_ZIP,
510
+ h5ad: FileType.SAMPLE_SETS_ANNDATA_H5AD
511
+ },
485
512
  // For OME-Zarr:
486
513
  [FileType.IMAGE_OME_ZARR]: {
487
514
  zip: FileType.IMAGE_OME_ZARR_ZIP
@@ -528,6 +555,50 @@ const COMPONENT_COORDINATION_TYPES = {
528
555
  CoordinationType.OBS_FILTER,
529
556
  CoordinationType.OBS_HIGHLIGHT,
530
557
  CoordinationType.OBS_SET_SELECTION,
558
+ CoordinationType.OBS_SET_FILTER,
559
+ CoordinationType.OBS_SET_HIGHLIGHT,
560
+ CoordinationType.OBS_SET_COLOR,
561
+ CoordinationType.FEATURE_HIGHLIGHT,
562
+ CoordinationType.FEATURE_SELECTION,
563
+ CoordinationType.FEATURE_VALUE_COLORMAP,
564
+ CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
565
+ CoordinationType.OBS_COLOR_ENCODING,
566
+ CoordinationType.ADDITIONAL_OBS_SETS,
567
+ CoordinationType.TOOLTIPS_VISIBLE,
568
+ CoordinationType.SAMPLE_TYPE,
569
+ CoordinationType.SAMPLE_SET_SELECTION,
570
+ CoordinationType.SAMPLE_SET_FILTER,
571
+ CoordinationType.SAMPLE_SET_COLOR,
572
+ CoordinationType.EMBEDDING_POINTS_VISIBLE,
573
+ CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
574
+ CoordinationType.EMBEDDING_CONTOURS_FILLED,
575
+ CoordinationType.EMBEDDING_CONTOUR_PERCENTILES,
576
+ CoordinationType.CONTOUR_COLOR_ENCODING,
577
+ CoordinationType.CONTOUR_COLOR
578
+ ],
579
+ [ViewType.DUAL_SCATTERPLOT]: [
580
+ CoordinationType.DATASET,
581
+ CoordinationType.OBS_TYPE,
582
+ CoordinationType.FEATURE_TYPE,
583
+ CoordinationType.FEATURE_VALUE_TYPE,
584
+ CoordinationType.OBS_LABELS_TYPE,
585
+ CoordinationType.EMBEDDING_TYPE,
586
+ CoordinationType.EMBEDDING_ZOOM,
587
+ CoordinationType.EMBEDDING_ROTATION,
588
+ CoordinationType.EMBEDDING_TARGET_X,
589
+ CoordinationType.EMBEDDING_TARGET_Y,
590
+ CoordinationType.EMBEDDING_TARGET_Z,
591
+ CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE,
592
+ CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE,
593
+ CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE,
594
+ CoordinationType.EMBEDDING_OBS_RADIUS,
595
+ CoordinationType.EMBEDDING_OBS_RADIUS_MODE,
596
+ CoordinationType.EMBEDDING_OBS_OPACITY,
597
+ CoordinationType.EMBEDDING_OBS_OPACITY_MODE,
598
+ CoordinationType.OBS_FILTER,
599
+ CoordinationType.OBS_HIGHLIGHT,
600
+ CoordinationType.OBS_SET_SELECTION,
601
+ CoordinationType.OBS_SET_FILTER,
531
602
  CoordinationType.OBS_SET_HIGHLIGHT,
532
603
  CoordinationType.OBS_SET_COLOR,
533
604
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -539,6 +610,7 @@ const COMPONENT_COORDINATION_TYPES = {
539
610
  CoordinationType.TOOLTIPS_VISIBLE,
540
611
  CoordinationType.SAMPLE_TYPE,
541
612
  CoordinationType.SAMPLE_SET_SELECTION,
613
+ CoordinationType.SAMPLE_SET_FILTER,
542
614
  CoordinationType.SAMPLE_SET_COLOR,
543
615
  CoordinationType.EMBEDDING_POINTS_VISIBLE,
544
616
  CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
@@ -605,6 +677,7 @@ const COMPONENT_COORDINATION_TYPES = {
605
677
  CoordinationType.OBS_FILTER,
606
678
  CoordinationType.OBS_HIGHLIGHT,
607
679
  CoordinationType.OBS_SET_SELECTION,
680
+ CoordinationType.OBS_SET_FILTER,
608
681
  CoordinationType.OBS_SET_HIGHLIGHT,
609
682
  CoordinationType.OBS_SET_COLOR,
610
683
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -641,6 +714,7 @@ const COMPONENT_COORDINATION_TYPES = {
641
714
  CoordinationType.OBS_FILTER,
642
715
  CoordinationType.OBS_HIGHLIGHT,
643
716
  CoordinationType.OBS_SET_SELECTION,
717
+ CoordinationType.OBS_SET_FILTER,
644
718
  CoordinationType.OBS_SET_HIGHLIGHT,
645
719
  CoordinationType.OBS_SET_COLOR,
646
720
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -700,6 +774,7 @@ const COMPONENT_COORDINATION_TYPES = {
700
774
  CoordinationType.OBS_FILTER,
701
775
  CoordinationType.OBS_HIGHLIGHT,
702
776
  CoordinationType.OBS_SET_SELECTION,
777
+ CoordinationType.OBS_SET_FILTER,
703
778
  CoordinationType.OBS_SET_HIGHLIGHT,
704
779
  CoordinationType.OBS_SET_COLOR,
705
780
  CoordinationType.FEATURE_FILTER,
@@ -715,6 +790,7 @@ const COMPONENT_COORDINATION_TYPES = {
715
790
  CoordinationType.DATASET,
716
791
  CoordinationType.OBS_TYPE,
717
792
  CoordinationType.OBS_SET_SELECTION,
793
+ CoordinationType.OBS_SET_FILTER,
718
794
  CoordinationType.OBS_SET_EXPANSION,
719
795
  CoordinationType.OBS_SET_HIGHLIGHT,
720
796
  CoordinationType.OBS_SET_COLOR,
@@ -726,6 +802,7 @@ const COMPONENT_COORDINATION_TYPES = {
726
802
  CoordinationType.DATASET,
727
803
  CoordinationType.OBS_TYPE,
728
804
  CoordinationType.OBS_SET_SELECTION,
805
+ CoordinationType.OBS_SET_FILTER,
729
806
  CoordinationType.OBS_SET_EXPANSION,
730
807
  CoordinationType.OBS_SET_HIGHLIGHT,
731
808
  CoordinationType.OBS_SET_COLOR,
@@ -758,6 +835,7 @@ const COMPONENT_COORDINATION_TYPES = {
758
835
  CoordinationType.FEATURE_VALUE_TRANSFORM,
759
836
  CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
760
837
  CoordinationType.OBS_SET_SELECTION,
838
+ CoordinationType.OBS_SET_FILTER,
761
839
  CoordinationType.OBS_SET_HIGHLIGHT,
762
840
  CoordinationType.OBS_SET_COLOR,
763
841
  CoordinationType.ADDITIONAL_OBS_SETS,
@@ -774,7 +852,8 @@ const COMPONENT_COORDINATION_TYPES = {
774
852
  CoordinationType.ADDITIONAL_OBS_SETS,
775
853
  CoordinationType.OBS_SET_COLOR,
776
854
  CoordinationType.OBS_COLOR_ENCODING,
777
- CoordinationType.OBS_SET_SELECTION
855
+ CoordinationType.OBS_SET_SELECTION,
856
+ CoordinationType.OBS_SET_FILTER
778
857
  ],
779
858
  [ViewType.LAYER_CONTROLLER]: [
780
859
  CoordinationType.DATASET,
@@ -889,11 +968,13 @@ const COMPONENT_COORDINATION_TYPES = {
889
968
  CoordinationType.FEATURE_VALUE_POSITIVITY_THRESHOLD,
890
969
  CoordinationType.FEATURE_VALUE_COLORMAP,
891
970
  CoordinationType.OBS_SET_SELECTION,
971
+ CoordinationType.OBS_SET_FILTER,
892
972
  CoordinationType.OBS_SET_HIGHLIGHT,
893
973
  CoordinationType.OBS_SET_COLOR,
894
974
  CoordinationType.ADDITIONAL_OBS_SETS,
895
975
  CoordinationType.SAMPLE_TYPE,
896
976
  CoordinationType.SAMPLE_SET_SELECTION,
977
+ CoordinationType.SAMPLE_SET_FILTER,
897
978
  CoordinationType.SAMPLE_SET_COLOR
898
979
  ],
899
980
  higlass: [
@@ -924,15 +1005,44 @@ const COMPONENT_COORDINATION_TYPES = {
924
1005
  [ViewType.LINK_CONTROLLER]: [],
925
1006
  [ViewType.BIOMARKER_SELECT]: [
926
1007
  CoordinationType.FEATURE_SELECTION,
927
- CoordinationType.SAMPLE_SET_SELECTION
1008
+ CoordinationType.SAMPLE_SET_SELECTION,
1009
+ CoordinationType.SAMPLE_SET_FILTER,
1010
+ CoordinationType.OBS_SET_SELECTION,
1011
+ CoordinationType.OBS_SET_FILTER
928
1012
  // TODO: create coordination types for internal state of the biomarker selection view?
1013
+ ],
1014
+ [ViewType.TREEMAP]: [
1015
+ CoordinationType.DATASET,
1016
+ CoordinationType.OBS_TYPE,
1017
+ CoordinationType.FEATURE_TYPE,
1018
+ CoordinationType.FEATURE_VALUE_TYPE,
1019
+ CoordinationType.OBS_FILTER,
1020
+ CoordinationType.OBS_HIGHLIGHT,
1021
+ CoordinationType.OBS_SET_SELECTION,
1022
+ CoordinationType.OBS_SET_FILTER,
1023
+ CoordinationType.OBS_SELECTION,
1024
+ CoordinationType.OBS_SELECTION_MODE,
1025
+ CoordinationType.OBS_SET_HIGHLIGHT,
1026
+ CoordinationType.OBS_SET_COLOR,
1027
+ CoordinationType.OBS_COLOR_ENCODING,
1028
+ CoordinationType.ADDITIONAL_OBS_SETS,
1029
+ CoordinationType.SAMPLE_TYPE,
1030
+ CoordinationType.SAMPLE_SET_SELECTION,
1031
+ CoordinationType.SAMPLE_SET_FILTER,
1032
+ CoordinationType.SAMPLE_SET_COLOR,
1033
+ CoordinationType.SAMPLE_SELECTION,
1034
+ CoordinationType.SAMPLE_SELECTION_MODE,
1035
+ CoordinationType.SAMPLE_FILTER,
1036
+ CoordinationType.SAMPLE_FILTER_MODE,
1037
+ CoordinationType.SAMPLE_HIGHLIGHT,
1038
+ CoordinationType.HIERARCHY_LEVELS
929
1039
  ]
930
1040
  };
931
1041
  const note = "This file is autogenerated by .changeset/post-changelog.mjs.";
932
- const version = "3.5.5";
933
- const date = "2025-01-17";
1042
+ const version = "3.5.7";
1043
+ const date = "2025-02-19";
934
1044
  const branch = "changeset-release/main";
935
- const hash = "fe1f84e9";
1045
+ const hash = "a4bc3a6a";
936
1046
  const version$1 = {
937
1047
  note,
938
1048
  version,
package/dist-tsc/constant-relationships.d.ts.map CHANGED
@@ -1 +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;;;;;;;;CAqDhC,CAAC"}
1
+ {"version":3,"file":"constant-relationships.d.ts","sourceRoot":"","sources":["../src/constant-relationships.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,eAAO,MAAM,2BAA2B;;CAgEvC,CAAC;AAEF;;;;GAIG;AACH,eAAO,MAAM,kCAAkC;;CA6C9C,CAAC;AAKF,eAAO,MAAM,oBAAoB;;;;;;;;CAyDhC,CAAC"}
package/dist-tsc/constant-relationships.js CHANGED
@@ -30,6 +30,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
30
30
  [FileType.OBS_LABELS_ANNDATA_ZARR]: DataType.OBS_LABELS,
31
31
  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
32
32
  [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
33
+ [FileType.SAMPLE_SETS_ANNDATA_ZARR]: DataType.SAMPLE_SETS,
33
34
  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
34
35
  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
35
36
  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -166,6 +167,10 @@ export const ALT_ZARR_STORE_TYPES = {
166
167
  zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
167
168
  h5ad: FileType.SAMPLE_EDGES_ANNDATA_H5AD,
168
169
  },
170
+ [FileType.SAMPLE_SETS_ANNDATA_ZARR]: {
171
+ zip: FileType.SAMPLE_SETS_ANNDATA_ZARR_ZIP,
172
+ h5ad: FileType.SAMPLE_SETS_ANNDATA_H5AD,
173
+ },
169
174
  // For OME-Zarr:
170
175
  [FileType.IMAGE_OME_ZARR]: {
171
176
  zip: FileType.IMAGE_OME_ZARR_ZIP,
package/dist-tsc/constants.d.ts CHANGED
@@ -23,6 +23,8 @@ export declare const ViewType: {
23
23
  FEATURE_BAR_PLOT: string;
24
24
  BIOMARKER_SELECT: string;
25
25
  LINK_CONTROLLER: string;
26
+ DUAL_SCATTERPLOT: string;
27
+ TREEMAP: string;
26
28
  };
27
29
  export declare const DataType: {
28
30
  OBS_LABELS: string;
@@ -82,6 +84,7 @@ export declare const FileType: {
82
84
  OBS_LABELS_ANNDATA_ZARR: string;
83
85
  FEATURE_LABELS_ANNDATA_ZARR: string;
84
86
  SAMPLE_EDGES_ANNDATA_ZARR: string;
87
+ SAMPLE_SETS_ANNDATA_ZARR: string;
85
88
  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: string;
86
89
  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: string;
87
90
  OBS_SETS_ANNDATA_ZARR_ZIP: string;
@@ -93,6 +96,7 @@ export declare const FileType: {
93
96
  OBS_LABELS_ANNDATA_ZARR_ZIP: string;
94
97
  FEATURE_LABELS_ANNDATA_ZARR_ZIP: string;
95
98
  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: string;
99
+ SAMPLE_SETS_ANNDATA_ZARR_ZIP: string;
96
100
  OBS_FEATURE_MATRIX_ANNDATA_H5AD: string;
97
101
  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: string;
98
102
  OBS_SETS_ANNDATA_H5AD: string;
@@ -104,6 +108,7 @@ export declare const FileType: {
104
108
  OBS_LABELS_ANNDATA_H5AD: string;
105
109
  FEATURE_LABELS_ANNDATA_H5AD: string;
106
110
  SAMPLE_EDGES_ANNDATA_H5AD: string;
111
+ SAMPLE_SETS_ANNDATA_H5AD: string;
107
112
  IMAGE_SPATIALDATA_ZARR: string;
108
113
  LABELS_SPATIALDATA_ZARR: string;
109
114
  SHAPES_SPATIALDATA_ZARR: string;
@@ -191,15 +196,23 @@ export declare const CoordinationType: {
191
196
  HEATMAP_ZOOM_Y: string;
192
197
  HEATMAP_TARGET_X: string;
193
198
  HEATMAP_TARGET_Y: string;
194
- OBS_FILTER: string;
195
199
  OBS_HIGHLIGHT: string;
200
+ OBS_SELECTION: string;
196
201
  OBS_SET_SELECTION: string;
202
+ OBS_SELECTION_MODE: string;
203
+ OBS_FILTER: string;
204
+ OBS_SET_FILTER: string;
205
+ OBS_FILTER_MODE: string;
197
206
  OBS_SET_HIGHLIGHT: string;
198
207
  OBS_SET_EXPANSION: string;
199
208
  OBS_SET_COLOR: string;
200
- FEATURE_FILTER: string;
201
209
  FEATURE_HIGHLIGHT: string;
202
210
  FEATURE_SELECTION: string;
211
+ FEATURE_SET_SELECTION: string;
212
+ FEATURE_SELECTION_MODE: string;
213
+ FEATURE_FILTER: string;
214
+ FEATURE_SET_FILTER: string;
215
+ FEATURE_FILTER_MODE: string;
203
216
  FEATURE_VALUE_COLORMAP: string;
204
217
  FEATURE_VALUE_TRANSFORM: string;
205
218
  FEATURE_VALUE_COLORMAP_RANGE: string;
@@ -256,14 +269,21 @@ export declare const CoordinationType: {
256
269
  SPATIAL_CHANNEL_LABELS_ORIENTATION: string;
257
270
  SPATIAL_CHANNEL_LABEL_SIZE: string;
258
271
  SAMPLE_TYPE: string;
272
+ SAMPLE_SELECTION: string;
259
273
  SAMPLE_SET_SELECTION: string;
274
+ SAMPLE_SELECTION_MODE: string;
275
+ SAMPLE_FILTER: string;
276
+ SAMPLE_SET_FILTER: string;
277
+ SAMPLE_FILTER_MODE: string;
260
278
  SAMPLE_SET_COLOR: string;
279
+ SAMPLE_HIGHLIGHT: string;
261
280
  EMBEDDING_POINTS_VISIBLE: string;
262
281
  EMBEDDING_CONTOURS_VISIBLE: string;
263
282
  EMBEDDING_CONTOURS_FILLED: string;
264
283
  EMBEDDING_CONTOUR_PERCENTILES: string;
265
284
  CONTOUR_COLOR_ENCODING: string;
266
285
  CONTOUR_COLOR: string;
286
+ HIERARCHY_LEVELS: string;
267
287
  };
268
288
  export declare const STATUS: {
269
289
  LOADING: string;
@@ -294,5 +314,6 @@ export declare const ViewHelpMapping: {
294
314
  FEATURE_VALUE_HISTOGRAM: string;
295
315
  DOT_PLOT: string;
296
316
  FEATURE_BAR_PLOT: string;
317
+ TREEMAP: string;
297
318
  };
298
319
  //# sourceMappingURL=constants.d.ts.map
package/dist-tsc/constants.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;CAoBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;;;;;CAc7B,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAwHpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsH5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC;AAEF,eAAO,MAAM,eAAe;;;CAG3B,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;CAgB3B,CAAC"}
1
+ {"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;CAsBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;;;;;CAc7B,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA2HpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsI5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC;AAEF,eAAO,MAAM,eAAe;;;CAG3B,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;CAiB3B,CAAC"}
package/dist-tsc/constants.js CHANGED
@@ -23,6 +23,8 @@ export const ViewType = {
23
23
  FEATURE_BAR_PLOT: 'featureBarPlot',
24
24
  BIOMARKER_SELECT: 'biomarkerSelect',
25
25
  LINK_CONTROLLER: 'linkController',
26
+ DUAL_SCATTERPLOT: 'dualScatterplot',
27
+ TREEMAP: 'treemap',
26
28
  };
27
29
  export const DataType = {
28
30
  OBS_LABELS: 'obsLabels',
@@ -89,6 +91,7 @@ export const FileType = {
89
91
  OBS_LABELS_ANNDATA_ZARR: 'obsLabels.anndata.zarr',
90
92
  FEATURE_LABELS_ANNDATA_ZARR: 'featureLabels.anndata.zarr',
91
93
  SAMPLE_EDGES_ANNDATA_ZARR: 'sampleEdges.anndata.zarr',
94
+ SAMPLE_SETS_ANNDATA_ZARR: 'sampleSets.anndata.zarr',
92
95
  // AnnData - zipped
93
96
  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: 'obsFeatureMatrix.anndata.zarr.zip',
94
97
  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: 'obsFeatureColumns.anndata.zarr.zip',
@@ -101,6 +104,7 @@ export const FileType = {
101
104
  OBS_LABELS_ANNDATA_ZARR_ZIP: 'obsLabels.anndata.zarr.zip',
102
105
  FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
103
106
  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
107
+ SAMPLE_SETS_ANNDATA_ZARR_ZIP: 'sampleSets.anndata.zarr.zip',
104
108
  // AnnData - h5ad via reference spec
105
109
  OBS_FEATURE_MATRIX_ANNDATA_H5AD: 'obsFeatureMatrix.anndata.h5ad',
106
110
  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: 'obsFeatureColumns.anndata.h5ad',
@@ -113,6 +117,7 @@ export const FileType = {
113
117
  OBS_LABELS_ANNDATA_H5AD: 'obsLabels.anndata.h5ad',
114
118
  FEATURE_LABELS_ANNDATA_H5AD: 'featureLabels.anndata.h5ad',
115
119
  SAMPLE_EDGES_ANNDATA_H5AD: 'sampleEdges.anndata.h5ad',
120
+ SAMPLE_SETS_ANNDATA_H5AD: 'sampleSets.anndata.h5ad',
116
121
  // SpatialData
117
122
  IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
118
123
  LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -218,15 +223,23 @@ export const CoordinationType = {
218
223
  HEATMAP_ZOOM_Y: 'heatmapZoomY',
219
224
  HEATMAP_TARGET_X: 'heatmapTargetX',
220
225
  HEATMAP_TARGET_Y: 'heatmapTargetY',
221
- OBS_FILTER: 'obsFilter',
222
226
  OBS_HIGHLIGHT: 'obsHighlight',
227
+ OBS_SELECTION: 'obsSelection',
223
228
  OBS_SET_SELECTION: 'obsSetSelection',
229
+ OBS_SELECTION_MODE: 'obsSelectionMode',
230
+ OBS_FILTER: 'obsFilter',
231
+ OBS_SET_FILTER: 'obsSetFilter',
232
+ OBS_FILTER_MODE: 'obsFilterMode',
224
233
  OBS_SET_HIGHLIGHT: 'obsSetHighlight',
225
234
  OBS_SET_EXPANSION: 'obsSetExpansion',
226
235
  OBS_SET_COLOR: 'obsSetColor',
227
- FEATURE_FILTER: 'featureFilter',
228
236
  FEATURE_HIGHLIGHT: 'featureHighlight',
229
237
  FEATURE_SELECTION: 'featureSelection',
238
+ FEATURE_SET_SELECTION: 'featureSetSelection',
239
+ FEATURE_SELECTION_MODE: 'featureSelectionMode',
240
+ FEATURE_FILTER: 'featureFilter',
241
+ FEATURE_SET_FILTER: 'featureSetFilter',
242
+ FEATURE_FILTER_MODE: 'featureFilterMode',
230
243
  FEATURE_VALUE_COLORMAP: 'featureValueColormap',
231
244
  FEATURE_VALUE_TRANSFORM: 'featureValueTransform',
232
245
  FEATURE_VALUE_COLORMAP_RANGE: 'featureValueColormapRange',
@@ -288,14 +301,22 @@ export const CoordinationType = {
288
301
  SPATIAL_CHANNEL_LABEL_SIZE: 'spatialChannelLabelSize',
289
302
  // Multi-sample / comparative
290
303
  SAMPLE_TYPE: 'sampleType',
304
+ SAMPLE_SELECTION: 'sampleSelection',
291
305
  SAMPLE_SET_SELECTION: 'sampleSetSelection',
306
+ SAMPLE_SELECTION_MODE: 'sampleSelectionMode',
307
+ SAMPLE_FILTER: 'sampleFilter',
308
+ SAMPLE_SET_FILTER: 'sampleSetFilter',
309
+ SAMPLE_FILTER_MODE: 'sampleFilterMode',
292
310
  SAMPLE_SET_COLOR: 'sampleSetColor',
311
+ SAMPLE_HIGHLIGHT: 'sampleHighlight',
293
312
  EMBEDDING_POINTS_VISIBLE: 'embeddingPointsVisible',
294
313
  EMBEDDING_CONTOURS_VISIBLE: 'embeddingContoursVisible',
295
314
  EMBEDDING_CONTOURS_FILLED: 'embeddingContoursFilled',
296
315
  EMBEDDING_CONTOUR_PERCENTILES: 'embeddingContourPercentiles',
297
316
  CONTOUR_COLOR_ENCODING: 'contourColorEncoding',
298
317
  CONTOUR_COLOR: 'contourColor',
318
+ // Treemap
319
+ HIERARCHY_LEVELS: 'hierarchyLevels',
299
320
  };
300
321
  export const STATUS = {
301
322
  LOADING: 'loading',
@@ -326,4 +347,5 @@ export const ViewHelpMapping = {
326
347
  FEATURE_VALUE_HISTOGRAM: 'The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).',
327
348
  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).',
328
349
  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.',
350
+ TREEMAP: 'The treemap provides an overview of the current state of sample-level or cell-level selection and filtering.',
329
351
  };
package/dist-tsc/coordination.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CAsaxC,CAAC"}
1
+ {"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CAyfxC,CAAC"}
package/dist-tsc/coordination.js CHANGED
@@ -52,6 +52,7 @@ export const COMPONENT_COORDINATION_TYPES = {
52
52
  CoordinationType.OBS_FILTER,
53
53
  CoordinationType.OBS_HIGHLIGHT,
54
54
  CoordinationType.OBS_SET_SELECTION,
55
+ CoordinationType.OBS_SET_FILTER,
55
56
  CoordinationType.OBS_SET_HIGHLIGHT,
56
57
  CoordinationType.OBS_SET_COLOR,
57
58
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -63,6 +64,50 @@ export const COMPONENT_COORDINATION_TYPES = {
63
64
  CoordinationType.TOOLTIPS_VISIBLE,
64
65
  CoordinationType.SAMPLE_TYPE,
65
66
  CoordinationType.SAMPLE_SET_SELECTION,
67
+ CoordinationType.SAMPLE_SET_FILTER,
68
+ CoordinationType.SAMPLE_SET_COLOR,
69
+ CoordinationType.EMBEDDING_POINTS_VISIBLE,
70
+ CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
71
+ CoordinationType.EMBEDDING_CONTOURS_FILLED,
72
+ CoordinationType.EMBEDDING_CONTOUR_PERCENTILES,
73
+ CoordinationType.CONTOUR_COLOR_ENCODING,
74
+ CoordinationType.CONTOUR_COLOR,
75
+ ],
76
+ [ViewType.DUAL_SCATTERPLOT]: [
77
+ CoordinationType.DATASET,
78
+ CoordinationType.OBS_TYPE,
79
+ CoordinationType.FEATURE_TYPE,
80
+ CoordinationType.FEATURE_VALUE_TYPE,
81
+ CoordinationType.OBS_LABELS_TYPE,
82
+ CoordinationType.EMBEDDING_TYPE,
83
+ CoordinationType.EMBEDDING_ZOOM,
84
+ CoordinationType.EMBEDDING_ROTATION,
85
+ CoordinationType.EMBEDDING_TARGET_X,
86
+ CoordinationType.EMBEDDING_TARGET_Y,
87
+ CoordinationType.EMBEDDING_TARGET_Z,
88
+ CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE,
89
+ CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE,
90
+ CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE,
91
+ CoordinationType.EMBEDDING_OBS_RADIUS,
92
+ CoordinationType.EMBEDDING_OBS_RADIUS_MODE,
93
+ CoordinationType.EMBEDDING_OBS_OPACITY,
94
+ CoordinationType.EMBEDDING_OBS_OPACITY_MODE,
95
+ CoordinationType.OBS_FILTER,
96
+ CoordinationType.OBS_HIGHLIGHT,
97
+ CoordinationType.OBS_SET_SELECTION,
98
+ CoordinationType.OBS_SET_FILTER,
99
+ CoordinationType.OBS_SET_HIGHLIGHT,
100
+ CoordinationType.OBS_SET_COLOR,
101
+ CoordinationType.FEATURE_HIGHLIGHT,
102
+ CoordinationType.FEATURE_SELECTION,
103
+ CoordinationType.FEATURE_VALUE_COLORMAP,
104
+ CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
105
+ CoordinationType.OBS_COLOR_ENCODING,
106
+ CoordinationType.ADDITIONAL_OBS_SETS,
107
+ CoordinationType.TOOLTIPS_VISIBLE,
108
+ CoordinationType.SAMPLE_TYPE,
109
+ CoordinationType.SAMPLE_SET_SELECTION,
110
+ CoordinationType.SAMPLE_SET_FILTER,
66
111
  CoordinationType.SAMPLE_SET_COLOR,
67
112
  CoordinationType.EMBEDDING_POINTS_VISIBLE,
68
113
  CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
@@ -129,6 +174,7 @@ export const COMPONENT_COORDINATION_TYPES = {
129
174
  CoordinationType.OBS_FILTER,
130
175
  CoordinationType.OBS_HIGHLIGHT,
131
176
  CoordinationType.OBS_SET_SELECTION,
177
+ CoordinationType.OBS_SET_FILTER,
132
178
  CoordinationType.OBS_SET_HIGHLIGHT,
133
179
  CoordinationType.OBS_SET_COLOR,
134
180
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -165,6 +211,7 @@ export const COMPONENT_COORDINATION_TYPES = {
165
211
  CoordinationType.OBS_FILTER,
166
212
  CoordinationType.OBS_HIGHLIGHT,
167
213
  CoordinationType.OBS_SET_SELECTION,
214
+ CoordinationType.OBS_SET_FILTER,
168
215
  CoordinationType.OBS_SET_HIGHLIGHT,
169
216
  CoordinationType.OBS_SET_COLOR,
170
217
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -224,6 +271,7 @@ export const COMPONENT_COORDINATION_TYPES = {
224
271
  CoordinationType.OBS_FILTER,
225
272
  CoordinationType.OBS_HIGHLIGHT,
226
273
  CoordinationType.OBS_SET_SELECTION,
274
+ CoordinationType.OBS_SET_FILTER,
227
275
  CoordinationType.OBS_SET_HIGHLIGHT,
228
276
  CoordinationType.OBS_SET_COLOR,
229
277
  CoordinationType.FEATURE_FILTER,
@@ -239,6 +287,7 @@ export const COMPONENT_COORDINATION_TYPES = {
239
287
  CoordinationType.DATASET,
240
288
  CoordinationType.OBS_TYPE,
241
289
  CoordinationType.OBS_SET_SELECTION,
290
+ CoordinationType.OBS_SET_FILTER,
242
291
  CoordinationType.OBS_SET_EXPANSION,
243
292
  CoordinationType.OBS_SET_HIGHLIGHT,
244
293
  CoordinationType.OBS_SET_COLOR,
@@ -250,6 +299,7 @@ export const COMPONENT_COORDINATION_TYPES = {
250
299
  CoordinationType.DATASET,
251
300
  CoordinationType.OBS_TYPE,
252
301
  CoordinationType.OBS_SET_SELECTION,
302
+ CoordinationType.OBS_SET_FILTER,
253
303
  CoordinationType.OBS_SET_EXPANSION,
254
304
  CoordinationType.OBS_SET_HIGHLIGHT,
255
305
  CoordinationType.OBS_SET_COLOR,
@@ -282,6 +332,7 @@ export const COMPONENT_COORDINATION_TYPES = {
282
332
  CoordinationType.FEATURE_VALUE_TRANSFORM,
283
333
  CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
284
334
  CoordinationType.OBS_SET_SELECTION,
335
+ CoordinationType.OBS_SET_FILTER,
285
336
  CoordinationType.OBS_SET_HIGHLIGHT,
286
337
  CoordinationType.OBS_SET_COLOR,
287
338
  CoordinationType.ADDITIONAL_OBS_SETS,
@@ -299,6 +350,7 @@ export const COMPONENT_COORDINATION_TYPES = {
299
350
  CoordinationType.OBS_SET_COLOR,
300
351
  CoordinationType.OBS_COLOR_ENCODING,
301
352
  CoordinationType.OBS_SET_SELECTION,
353
+ CoordinationType.OBS_SET_FILTER,
302
354
  ],
303
355
  [ViewType.LAYER_CONTROLLER]: [
304
356
  CoordinationType.DATASET,
@@ -413,11 +465,13 @@ export const COMPONENT_COORDINATION_TYPES = {
413
465
  CoordinationType.FEATURE_VALUE_POSITIVITY_THRESHOLD,
414
466
  CoordinationType.FEATURE_VALUE_COLORMAP,
415
467
  CoordinationType.OBS_SET_SELECTION,
468
+ CoordinationType.OBS_SET_FILTER,
416
469
  CoordinationType.OBS_SET_HIGHLIGHT,
417
470
  CoordinationType.OBS_SET_COLOR,
418
471
  CoordinationType.ADDITIONAL_OBS_SETS,
419
472
  CoordinationType.SAMPLE_TYPE,
420
473
  CoordinationType.SAMPLE_SET_SELECTION,
474
+ CoordinationType.SAMPLE_SET_FILTER,
421
475
  CoordinationType.SAMPLE_SET_COLOR,
422
476
  ],
423
477
  higlass: [
@@ -449,6 +503,35 @@ export const COMPONENT_COORDINATION_TYPES = {
449
503
  [ViewType.BIOMARKER_SELECT]: [
450
504
  CoordinationType.FEATURE_SELECTION,
451
505
  CoordinationType.SAMPLE_SET_SELECTION,
506
+ CoordinationType.SAMPLE_SET_FILTER,
507
+ CoordinationType.OBS_SET_SELECTION,
508
+ CoordinationType.OBS_SET_FILTER,
452
509
  // TODO: create coordination types for internal state of the biomarker selection view?
453
510
  ],
511
+ [ViewType.TREEMAP]: [
512
+ CoordinationType.DATASET,
513
+ CoordinationType.OBS_TYPE,
514
+ CoordinationType.FEATURE_TYPE,
515
+ CoordinationType.FEATURE_VALUE_TYPE,
516
+ CoordinationType.OBS_FILTER,
517
+ CoordinationType.OBS_HIGHLIGHT,
518
+ CoordinationType.OBS_SET_SELECTION,
519
+ CoordinationType.OBS_SET_FILTER,
520
+ CoordinationType.OBS_SELECTION,
521
+ CoordinationType.OBS_SELECTION_MODE,
522
+ CoordinationType.OBS_SET_HIGHLIGHT,
523
+ CoordinationType.OBS_SET_COLOR,
524
+ CoordinationType.OBS_COLOR_ENCODING,
525
+ CoordinationType.ADDITIONAL_OBS_SETS,
526
+ CoordinationType.SAMPLE_TYPE,
527
+ CoordinationType.SAMPLE_SET_SELECTION,
528
+ CoordinationType.SAMPLE_SET_FILTER,
529
+ CoordinationType.SAMPLE_SET_COLOR,
530
+ CoordinationType.SAMPLE_SELECTION,
531
+ CoordinationType.SAMPLE_SELECTION_MODE,
532
+ CoordinationType.SAMPLE_FILTER,
533
+ CoordinationType.SAMPLE_FILTER_MODE,
534
+ CoordinationType.SAMPLE_HIGHLIGHT,
535
+ CoordinationType.HIERARCHY_LEVELS,
536
+ ],
454
537
  };
package/dist-tsc/version.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
3
- "version": "3.5.5",
4
- "date": "2025-01-17",
3
+ "version": "3.5.7",
4
+ "date": "2025-02-19",
5
5
  "branch": "changeset-release/main",
6
- "hash": "fe1f84e9"
6
+ "hash": "a4bc3a6a"
7
7
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@vitessce/constants-internal",
3
- "version": "3.5.5",
3
+ "version": "3.5.7",
4
4
  "author": "HIDIVE Lab at HMS",
5
5
  "homepage": "http://vitessce.io",
6
6
  "repository": {
package/src/constant-relationships.ts CHANGED
@@ -31,6 +31,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
31
31
  [FileType.OBS_LABELS_ANNDATA_ZARR]: DataType.OBS_LABELS,
32
32
  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
33
33
  [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
34
+ [FileType.SAMPLE_SETS_ANNDATA_ZARR]: DataType.SAMPLE_SETS,
34
35
  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
35
36
  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
36
37
  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -171,6 +172,10 @@ export const ALT_ZARR_STORE_TYPES = {
171
172
  zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
172
173
  h5ad: FileType.SAMPLE_EDGES_ANNDATA_H5AD,
173
174
  },
175
+ [FileType.SAMPLE_SETS_ANNDATA_ZARR]: {
176
+ zip: FileType.SAMPLE_SETS_ANNDATA_ZARR_ZIP,
177
+ h5ad: FileType.SAMPLE_SETS_ANNDATA_H5AD,
178
+ },
174
179
  // For OME-Zarr:
175
180
  [FileType.IMAGE_OME_ZARR]: {
176
181
  zip: FileType.IMAGE_OME_ZARR_ZIP,
package/src/constants.ts CHANGED
@@ -23,6 +23,8 @@ export const ViewType = {
23
23
  FEATURE_BAR_PLOT: 'featureBarPlot',
24
24
  BIOMARKER_SELECT: 'biomarkerSelect',
25
25
  LINK_CONTROLLER: 'linkController',
26
+ DUAL_SCATTERPLOT: 'dualScatterplot',
27
+ TREEMAP: 'treemap',
26
28
  };
27
29
 
28
30
  export const DataType = {
@@ -94,6 +96,7 @@ export const FileType = {
94
96
  OBS_LABELS_ANNDATA_ZARR: 'obsLabels.anndata.zarr',
95
97
  FEATURE_LABELS_ANNDATA_ZARR: 'featureLabels.anndata.zarr',
96
98
  SAMPLE_EDGES_ANNDATA_ZARR: 'sampleEdges.anndata.zarr',
99
+ SAMPLE_SETS_ANNDATA_ZARR: 'sampleSets.anndata.zarr',
97
100
  // AnnData - zipped
98
101
  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: 'obsFeatureMatrix.anndata.zarr.zip',
99
102
  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: 'obsFeatureColumns.anndata.zarr.zip',
@@ -106,6 +109,7 @@ export const FileType = {
106
109
  OBS_LABELS_ANNDATA_ZARR_ZIP: 'obsLabels.anndata.zarr.zip',
107
110
  FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
108
111
  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
112
+ SAMPLE_SETS_ANNDATA_ZARR_ZIP: 'sampleSets.anndata.zarr.zip',
109
113
  // AnnData - h5ad via reference spec
110
114
  OBS_FEATURE_MATRIX_ANNDATA_H5AD: 'obsFeatureMatrix.anndata.h5ad',
111
115
  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: 'obsFeatureColumns.anndata.h5ad',
@@ -118,6 +122,7 @@ export const FileType = {
118
122
  OBS_LABELS_ANNDATA_H5AD: 'obsLabels.anndata.h5ad',
119
123
  FEATURE_LABELS_ANNDATA_H5AD: 'featureLabels.anndata.h5ad',
120
124
  SAMPLE_EDGES_ANNDATA_H5AD: 'sampleEdges.anndata.h5ad',
125
+ SAMPLE_SETS_ANNDATA_H5AD: 'sampleSets.anndata.h5ad',
121
126
  // SpatialData
122
127
  IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
123
128
  LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -224,15 +229,23 @@ export const CoordinationType = {
224
229
  HEATMAP_ZOOM_Y: 'heatmapZoomY',
225
230
  HEATMAP_TARGET_X: 'heatmapTargetX',
226
231
  HEATMAP_TARGET_Y: 'heatmapTargetY',
227
- OBS_FILTER: 'obsFilter',
228
232
  OBS_HIGHLIGHT: 'obsHighlight',
233
+ OBS_SELECTION: 'obsSelection',
229
234
  OBS_SET_SELECTION: 'obsSetSelection',
235
+ OBS_SELECTION_MODE: 'obsSelectionMode',
236
+ OBS_FILTER: 'obsFilter',
237
+ OBS_SET_FILTER: 'obsSetFilter',
238
+ OBS_FILTER_MODE: 'obsFilterMode',
230
239
  OBS_SET_HIGHLIGHT: 'obsSetHighlight',
231
240
  OBS_SET_EXPANSION: 'obsSetExpansion',
232
241
  OBS_SET_COLOR: 'obsSetColor',
233
- FEATURE_FILTER: 'featureFilter',
234
242
  FEATURE_HIGHLIGHT: 'featureHighlight',
235
243
  FEATURE_SELECTION: 'featureSelection',
244
+ FEATURE_SET_SELECTION: 'featureSetSelection',
245
+ FEATURE_SELECTION_MODE: 'featureSelectionMode',
246
+ FEATURE_FILTER: 'featureFilter',
247
+ FEATURE_SET_FILTER: 'featureSetFilter',
248
+ FEATURE_FILTER_MODE: 'featureFilterMode',
236
249
  FEATURE_VALUE_COLORMAP: 'featureValueColormap',
237
250
  FEATURE_VALUE_TRANSFORM: 'featureValueTransform',
238
251
  FEATURE_VALUE_COLORMAP_RANGE: 'featureValueColormapRange',
@@ -294,14 +307,22 @@ export const CoordinationType = {
294
307
  SPATIAL_CHANNEL_LABEL_SIZE: 'spatialChannelLabelSize',
295
308
  // Multi-sample / comparative
296
309
  SAMPLE_TYPE: 'sampleType',
310
+ SAMPLE_SELECTION: 'sampleSelection',
297
311
  SAMPLE_SET_SELECTION: 'sampleSetSelection',
312
+ SAMPLE_SELECTION_MODE: 'sampleSelectionMode',
313
+ SAMPLE_FILTER: 'sampleFilter',
314
+ SAMPLE_SET_FILTER: 'sampleSetFilter',
315
+ SAMPLE_FILTER_MODE: 'sampleFilterMode',
298
316
  SAMPLE_SET_COLOR: 'sampleSetColor',
317
+ SAMPLE_HIGHLIGHT: 'sampleHighlight',
299
318
  EMBEDDING_POINTS_VISIBLE: 'embeddingPointsVisible',
300
319
  EMBEDDING_CONTOURS_VISIBLE: 'embeddingContoursVisible',
301
320
  EMBEDDING_CONTOURS_FILLED: 'embeddingContoursFilled',
302
321
  EMBEDDING_CONTOUR_PERCENTILES: 'embeddingContourPercentiles',
303
322
  CONTOUR_COLOR_ENCODING: 'contourColorEncoding',
304
323
  CONTOUR_COLOR: 'contourColor',
324
+ // Treemap
325
+ HIERARCHY_LEVELS: 'hierarchyLevels',
305
326
  };
306
327
 
307
328
  export const STATUS = {
@@ -335,4 +356,5 @@ export const ViewHelpMapping = {
335
356
  FEATURE_VALUE_HISTOGRAM: 'The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).',
336
357
  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).',
337
358
  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.',
359
+ TREEMAP: 'The treemap provides an overview of the current state of sample-level or cell-level selection and filtering.',
338
360
  };
package/src/coordination.ts CHANGED
@@ -54,6 +54,7 @@ export const COMPONENT_COORDINATION_TYPES = {
54
54
  CoordinationType.OBS_FILTER,
55
55
  CoordinationType.OBS_HIGHLIGHT,
56
56
  CoordinationType.OBS_SET_SELECTION,
57
+ CoordinationType.OBS_SET_FILTER,
57
58
  CoordinationType.OBS_SET_HIGHLIGHT,
58
59
  CoordinationType.OBS_SET_COLOR,
59
60
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -65,6 +66,50 @@ export const COMPONENT_COORDINATION_TYPES = {
65
66
  CoordinationType.TOOLTIPS_VISIBLE,
66
67
  CoordinationType.SAMPLE_TYPE,
67
68
  CoordinationType.SAMPLE_SET_SELECTION,
69
+ CoordinationType.SAMPLE_SET_FILTER,
70
+ CoordinationType.SAMPLE_SET_COLOR,
71
+ CoordinationType.EMBEDDING_POINTS_VISIBLE,
72
+ CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
73
+ CoordinationType.EMBEDDING_CONTOURS_FILLED,
74
+ CoordinationType.EMBEDDING_CONTOUR_PERCENTILES,
75
+ CoordinationType.CONTOUR_COLOR_ENCODING,
76
+ CoordinationType.CONTOUR_COLOR,
77
+ ],
78
+ [ViewType.DUAL_SCATTERPLOT]: [
79
+ CoordinationType.DATASET,
80
+ CoordinationType.OBS_TYPE,
81
+ CoordinationType.FEATURE_TYPE,
82
+ CoordinationType.FEATURE_VALUE_TYPE,
83
+ CoordinationType.OBS_LABELS_TYPE,
84
+ CoordinationType.EMBEDDING_TYPE,
85
+ CoordinationType.EMBEDDING_ZOOM,
86
+ CoordinationType.EMBEDDING_ROTATION,
87
+ CoordinationType.EMBEDDING_TARGET_X,
88
+ CoordinationType.EMBEDDING_TARGET_Y,
89
+ CoordinationType.EMBEDDING_TARGET_Z,
90
+ CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE,
91
+ CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE,
92
+ CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE,
93
+ CoordinationType.EMBEDDING_OBS_RADIUS,
94
+ CoordinationType.EMBEDDING_OBS_RADIUS_MODE,
95
+ CoordinationType.EMBEDDING_OBS_OPACITY,
96
+ CoordinationType.EMBEDDING_OBS_OPACITY_MODE,
97
+ CoordinationType.OBS_FILTER,
98
+ CoordinationType.OBS_HIGHLIGHT,
99
+ CoordinationType.OBS_SET_SELECTION,
100
+ CoordinationType.OBS_SET_FILTER,
101
+ CoordinationType.OBS_SET_HIGHLIGHT,
102
+ CoordinationType.OBS_SET_COLOR,
103
+ CoordinationType.FEATURE_HIGHLIGHT,
104
+ CoordinationType.FEATURE_SELECTION,
105
+ CoordinationType.FEATURE_VALUE_COLORMAP,
106
+ CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
107
+ CoordinationType.OBS_COLOR_ENCODING,
108
+ CoordinationType.ADDITIONAL_OBS_SETS,
109
+ CoordinationType.TOOLTIPS_VISIBLE,
110
+ CoordinationType.SAMPLE_TYPE,
111
+ CoordinationType.SAMPLE_SET_SELECTION,
112
+ CoordinationType.SAMPLE_SET_FILTER,
68
113
  CoordinationType.SAMPLE_SET_COLOR,
69
114
  CoordinationType.EMBEDDING_POINTS_VISIBLE,
70
115
  CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
@@ -131,6 +176,7 @@ export const COMPONENT_COORDINATION_TYPES = {
131
176
  CoordinationType.OBS_FILTER,
132
177
  CoordinationType.OBS_HIGHLIGHT,
133
178
  CoordinationType.OBS_SET_SELECTION,
179
+ CoordinationType.OBS_SET_FILTER,
134
180
  CoordinationType.OBS_SET_HIGHLIGHT,
135
181
  CoordinationType.OBS_SET_COLOR,
136
182
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -167,6 +213,7 @@ export const COMPONENT_COORDINATION_TYPES = {
167
213
  CoordinationType.OBS_FILTER,
168
214
  CoordinationType.OBS_HIGHLIGHT,
169
215
  CoordinationType.OBS_SET_SELECTION,
216
+ CoordinationType.OBS_SET_FILTER,
170
217
  CoordinationType.OBS_SET_HIGHLIGHT,
171
218
  CoordinationType.OBS_SET_COLOR,
172
219
  CoordinationType.FEATURE_HIGHLIGHT,
@@ -226,6 +273,7 @@ export const COMPONENT_COORDINATION_TYPES = {
226
273
  CoordinationType.OBS_FILTER,
227
274
  CoordinationType.OBS_HIGHLIGHT,
228
275
  CoordinationType.OBS_SET_SELECTION,
276
+ CoordinationType.OBS_SET_FILTER,
229
277
  CoordinationType.OBS_SET_HIGHLIGHT,
230
278
  CoordinationType.OBS_SET_COLOR,
231
279
  CoordinationType.FEATURE_FILTER,
@@ -241,6 +289,7 @@ export const COMPONENT_COORDINATION_TYPES = {
241
289
  CoordinationType.DATASET,
242
290
  CoordinationType.OBS_TYPE,
243
291
  CoordinationType.OBS_SET_SELECTION,
292
+ CoordinationType.OBS_SET_FILTER,
244
293
  CoordinationType.OBS_SET_EXPANSION,
245
294
  CoordinationType.OBS_SET_HIGHLIGHT,
246
295
  CoordinationType.OBS_SET_COLOR,
@@ -252,6 +301,7 @@ export const COMPONENT_COORDINATION_TYPES = {
252
301
  CoordinationType.DATASET,
253
302
  CoordinationType.OBS_TYPE,
254
303
  CoordinationType.OBS_SET_SELECTION,
304
+ CoordinationType.OBS_SET_FILTER,
255
305
  CoordinationType.OBS_SET_EXPANSION,
256
306
  CoordinationType.OBS_SET_HIGHLIGHT,
257
307
  CoordinationType.OBS_SET_COLOR,
@@ -284,6 +334,7 @@ export const COMPONENT_COORDINATION_TYPES = {
284
334
  CoordinationType.FEATURE_VALUE_TRANSFORM,
285
335
  CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
286
336
  CoordinationType.OBS_SET_SELECTION,
337
+ CoordinationType.OBS_SET_FILTER,
287
338
  CoordinationType.OBS_SET_HIGHLIGHT,
288
339
  CoordinationType.OBS_SET_COLOR,
289
340
  CoordinationType.ADDITIONAL_OBS_SETS,
@@ -301,6 +352,7 @@ export const COMPONENT_COORDINATION_TYPES = {
301
352
  CoordinationType.OBS_SET_COLOR,
302
353
  CoordinationType.OBS_COLOR_ENCODING,
303
354
  CoordinationType.OBS_SET_SELECTION,
355
+ CoordinationType.OBS_SET_FILTER,
304
356
  ],
305
357
  [ViewType.LAYER_CONTROLLER]: [
306
358
  CoordinationType.DATASET,
@@ -415,11 +467,13 @@ export const COMPONENT_COORDINATION_TYPES = {
415
467
  CoordinationType.FEATURE_VALUE_POSITIVITY_THRESHOLD,
416
468
  CoordinationType.FEATURE_VALUE_COLORMAP,
417
469
  CoordinationType.OBS_SET_SELECTION,
470
+ CoordinationType.OBS_SET_FILTER,
418
471
  CoordinationType.OBS_SET_HIGHLIGHT,
419
472
  CoordinationType.OBS_SET_COLOR,
420
473
  CoordinationType.ADDITIONAL_OBS_SETS,
421
474
  CoordinationType.SAMPLE_TYPE,
422
475
  CoordinationType.SAMPLE_SET_SELECTION,
476
+ CoordinationType.SAMPLE_SET_FILTER,
423
477
  CoordinationType.SAMPLE_SET_COLOR,
424
478
  ],
425
479
  higlass: [
@@ -451,6 +505,35 @@ export const COMPONENT_COORDINATION_TYPES = {
451
505
  [ViewType.BIOMARKER_SELECT]: [
452
506
  CoordinationType.FEATURE_SELECTION,
453
507
  CoordinationType.SAMPLE_SET_SELECTION,
508
+ CoordinationType.SAMPLE_SET_FILTER,
509
+ CoordinationType.OBS_SET_SELECTION,
510
+ CoordinationType.OBS_SET_FILTER,
454
511
  // TODO: create coordination types for internal state of the biomarker selection view?
455
512
  ],
513
+ [ViewType.TREEMAP]: [
514
+ CoordinationType.DATASET,
515
+ CoordinationType.OBS_TYPE,
516
+ CoordinationType.FEATURE_TYPE,
517
+ CoordinationType.FEATURE_VALUE_TYPE,
518
+ CoordinationType.OBS_FILTER,
519
+ CoordinationType.OBS_HIGHLIGHT,
520
+ CoordinationType.OBS_SET_SELECTION,
521
+ CoordinationType.OBS_SET_FILTER,
522
+ CoordinationType.OBS_SELECTION,
523
+ CoordinationType.OBS_SELECTION_MODE,
524
+ CoordinationType.OBS_SET_HIGHLIGHT,
525
+ CoordinationType.OBS_SET_COLOR,
526
+ CoordinationType.OBS_COLOR_ENCODING,
527
+ CoordinationType.ADDITIONAL_OBS_SETS,
528
+ CoordinationType.SAMPLE_TYPE,
529
+ CoordinationType.SAMPLE_SET_SELECTION,
530
+ CoordinationType.SAMPLE_SET_FILTER,
531
+ CoordinationType.SAMPLE_SET_COLOR,
532
+ CoordinationType.SAMPLE_SELECTION,
533
+ CoordinationType.SAMPLE_SELECTION_MODE,
534
+ CoordinationType.SAMPLE_FILTER,
535
+ CoordinationType.SAMPLE_FILTER_MODE,
536
+ CoordinationType.SAMPLE_HIGHLIGHT,
537
+ CoordinationType.HIERARCHY_LEVELS,
538
+ ],
456
539
  };
package/src/version.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
3
- "version": "3.5.5",
4
- "date": "2025-01-17",
3
+ "version": "3.5.7",
4
+ "date": "2025-02-19",
5
5
  "branch": "changeset-release/main",
6
- "hash": "fe1f84e9"
6
+ "hash": "a4bc3a6a"
7
7
  }