@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

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 (977) hide show
  1. package/dist/2dmaf-BZWQ4YZF.js +1362 -0
  2. package/dist/AggMatrixInput-OXUENYYF.js +402 -0
  3. package/dist/AggregateMatrix-7PYLWY3X.js +37 -0
  4. package/dist/AppHeader-QOLLABH4.js +826 -0
  5. package/dist/BoxPlot-PDRYKWXF.js +1233 -0
  6. package/dist/CorrelationVolcano-Z3ABRHL6.js +613 -0
  7. package/dist/Cuminc-ATQT3KDO.js +1217 -0
  8. package/dist/DE-5LMMF5QB.js +85 -0
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  11. package/dist/DifferentialAnalysis-23WQKT6I.js +235 -0
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  18. package/dist/GeneExpInput-PW6HP5LO.js +38 -0
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  168. package/dist/condition-QROUALBG.js +323 -0
  169. package/dist/controls-GH37YWOP.js +30 -0
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  176. package/dist/dnaMethylation-2YU2HDD4.js +29 -0
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  849. /package/dist/{hierCluster-BJ5VBPXR.js.map → hierCluster-SU4BDK6I.js.map} +0 -0
  850. /package/dist/{hierCluster.config-4EERP4KK.js.map → hierCluster.config-4OZ65GKH.js.map} +0 -0
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  855. /package/dist/{importPlot-3CG6ASNH.js.map → importPlot-W3HPE4LZ.js.map} +0 -0
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  866. /package/dist/{maftimeline-NABCAMHG.js.map → maftimeline-CRQEUTRY.js.map} +0 -0
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  868. /package/dist/{matrix-UCHESWVK.js.map → matrix-SOBGWBTY.js.map} +0 -0
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  899. /package/dist/{polar2-GECELCTG.js.map → polar2-4YHPENAV.js.map} +0 -0
  900. /package/dist/{profileForms-2USYOA34.js.map → profileForms-KMECFO3K.js.map} +0 -0
  901. /package/dist/{profilePlot-YGD2CF6P.js.map → profilePlot-3AXSIXCK.js.map} +0 -0
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  903. /package/dist/{proteomeCohortCompare-TYYUF5A5.js.map → proteomeCohortCompare-DL2QLFL3.js.map} +0 -0
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  906. /package/dist/{qualitative-27BZGASV.js.map → qualitative-LK2QEYHU.js.map} +0 -0
  907. /package/dist/{qualitative-N4F6NITI.js.map → qualitative-YY4NQGO5.js.map} +0 -0
  908. /package/dist/{radar2-X465RPJX.js.map → radar2-TJUPENQF.js.map} +0 -0
  909. /package/dist/{radarFacility2-AE7BA62N.js.map → radarFacility2-Q7LBWLCV.js.map} +0 -0
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  911. /package/dist/{render-TD2QWOHT.js.map → render-AHR6SCQX.js.map} +0 -0
  912. /package/dist/{report-3Y2OWDF7.js.map → report-BPHJTRTO.js.map} +0 -0
  913. /package/dist/{sampleView-BUMMYRHJ.js.map → sampleView-CS2FB3K3.js.map} +0 -0
  914. /package/dist/{samplelst-BWK53BLI.js.map → samplelst-A3DHKP6U.js.map} +0 -0
  915. /package/dist/{samplematrix-RQU43UYR.js.map → samplematrix-5X7MFT3G.js.map} +0 -0
  916. /package/dist/{sc-LCBFWCZZ.js.map → sc-RCYXZMN6.js.map} +0 -0
  917. /package/dist/{scatter-6S5I7OW3.js.map → scatter-2ITGMX5N.js.map} +0 -0
  918. /package/dist/{scatter-MJELX75N.js.map → scatter-OAL4YOCA.js.map} +0 -0
  919. /package/dist/{selectGenomeWithTklst-WAVXHXR5.js.map → selectGenomeWithTklst-PB5KDW2N.js.map} +0 -0
  920. /package/dist/{singleCellCellType-WMCAJ7JF.js.map → singleCellCellType-FEFNOHOP.js.map} +0 -0
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  922. /package/dist/{singleCellGeneExpression-7Q5ZJT4R.js.map → singleCellGeneExpression-RUQQMKDE.js.map} +0 -0
  923. /package/dist/{singleCellGeneExpression.unit.spec-6C7PDGRH.js.map → singleCellGeneExpression.unit.spec-VCMJRMT7.js.map} +0 -0
  924. /package/dist/{singleCellNumericValue-QGYITZRC.js.map → singleCellNumericValue-JLXZQWNT.js.map} +0 -0
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  926. /package/dist/{singleCellPlot-JJMFJ2KQ.js.map → singleCellPlot-4EBYWOJ2.js.map} +0 -0
  927. /package/dist/{singlecell-J23S3JR2.js.map → singlecell-UKZJAYVH.js.map} +0 -0
  928. /package/dist/{singlecell-Y4OGUWEC.js.map → singlecell-VNRWPXGV.js.map} +0 -0
  929. /package/dist/{snp-IO6TKWGD.js.map → snp-2RJDJQZC.js.map} +0 -0
  930. /package/dist/{snp.unit.spec-X7ILEEPO.js.map → snp.unit.spec-Z4DNBFAH.js.map} +0 -0
  931. /package/dist/{snplocus-Z2NGIKMO.js.map → snplocus-OZLIZ7R7.js.map} +0 -0
  932. /package/dist/{snplst-XCS2FCQV.js.map → snplst-EVRJ4OCL.js.map} +0 -0
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  935. /package/dist/{spliceevent.noeventdiagram-UK3X667E.js.map → spliceevent.noeventdiagram-EI72A6L3.js.map} +0 -0
  936. /package/dist/{ssGSEA-ZRPNQKJ5.js.map → ssGSEA-NONMMNF7.js.map} +0 -0
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  938. /package/dist/{stattable-XYSC3CYU.js.map → stattable-NNUHKPF4.js.map} +0 -0
  939. /package/dist/{studyCatalog-Y75LMI62.js.map → studyCatalog-KMLE7Q55.js.map} +0 -0
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  944. /package/dist/{summarizeMutationSurvival-55JW5LA6.js.map → summarizeMutationSurvival-F4CJILS3.js.map} +0 -0
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  948. /package/dist/{sunburst-JFY6V5E2.js.map → sunburst-Y4LNCKMR.js.map} +0 -0
  949. /package/dist/{survival-PBBU6PA5.js.map → survival-4FYQHQHX.js.map} +0 -0
  950. /package/dist/{survival-6FLR4YCJ.js.map → survival-6GC267GY.js.map} +0 -0
  951. /package/dist/{survival.integration.spec-WAKTGYGP.js.map → survival.integration.spec-5ERXR6MG.js.map} +0 -0
  952. /package/dist/{svg2pdf.es.min-NIFE2BIE.js.map → svg2pdf.es.min-KKHWPFWG.js.map} +0 -0
  953. /package/dist/{svgraph-WD3DUZV7.js.map → svgraph-XIQIA7OJ.js.map} +0 -0
  954. /package/dist/{swimmer-VPKSBV6V.js.map → swimmer-643B5Q6F.js.map} +0 -0
  955. /package/dist/{table-GX3VJLPZ.js.map → table-JQIBRXTJ.js.map} +0 -0
  956. /package/dist/{termCollection-YQ332WKB.js.map → termCollection-LU5NW6KT.js.map} +0 -0
  957. /package/dist/{termCollection-QE7U5QBD.js.map → termCollection-XZCPBXRV.js.map} +0 -0
  958. /package/dist/{termCollection.unit.spec-ELLN7VRA.js.map → termCollection.unit.spec-H5LBV3N4.js.map} +0 -0
  959. /package/dist/{termCollectionFractionSelection-V3RP5KAT.js.map → termCollectionFractionSelection-3YHOFXEL.js.map} +0 -0
  960. /package/dist/{termCollectionFractionSelection.unit.spec-JR7Q7TJI.js.map → termCollectionFractionSelection.unit.spec-G5X3Y5YI.js.map} +0 -0
  961. /package/dist/{tk-J5VPFEX6.js.map → tk-NPWNBXLB.js.map} +0 -0
  962. /package/dist/{tk-GD2KJM5W.js.map → tk-YSW5NPW2.js.map} +0 -0
  963. /package/dist/{tvs.categorical-RPACB4VU.js.map → tvs.categorical-TUX6KRZI.js.map} +0 -0
  964. /package/dist/{tvs.condition-O6JBUM6D.js.map → tvs.condition-2CH25PLO.js.map} +0 -0
  965. /package/dist/{tvs.dt-5EVBSRX3.js.map → tvs.dt-YKP3F75O.js.map} +0 -0
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  968. /package/dist/{tvs.dtfusion-CCMUFDMQ.js.map → tvs.dtfusion-SJ64HNKE.js.map} +0 -0
  969. /package/dist/{tvs.dtitd-P3ED3MWA.js.map → tvs.dtitd-WQLHZK2P.js.map} +0 -0
  970. /package/dist/{tvs.dtsnvindel-X2MXPLC6.js.map → tvs.dtsnvindel-WMFJ7W7U.js.map} +0 -0
  971. /package/dist/{tvs.dtsv-4FOWFNVV.js.map → tvs.dtsv-GKEC5OGA.js.map} +0 -0
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  974. /package/dist/{tvs.samplelst-CBU6ATI5.js.map → tvs.samplelst-DEMMYRKK.js.map} +0 -0
  975. /package/dist/{tvs.survival-3K5ASAXV.js.map → tvs.survival-M4QUVP5L.js.map} +0 -0
  976. /package/dist/{tvs.termCollection-MXEWO6KJ.js.map → tvs.termCollection-J367GZY3.js.map} +0 -0
  977. /package/dist/{vocabulary-GQBHDP3K.js.map → vocabulary-RAVWS5IS.js.map} +0 -0
@@ -1,625 +0,0 @@
1
- import {
2
- Map_default,
3
- Tile_default,
4
- View_default,
5
- Zoomify_default
6
- } from "./chunk-WTAPOH2W.js";
7
- import {
8
- PlotBase,
9
- Tabs,
10
- controlsInit,
11
- renderTable
12
- } from "./chunk-NNDKYTUV.js";
13
- import "./chunk-HJ6L54YS.js";
14
- import "./chunk-HWNQOADC.js";
15
- import "./chunk-CNFTQSNE.js";
16
- import "./chunk-PLFPXOGX.js";
17
- import "./chunk-EEB5VE2A.js";
18
- import "./chunk-3CIL7KH7.js";
19
- import "./chunk-T4XPCSLP.js";
20
- import {
21
- dofetch3
22
- } from "./chunk-BIJOXCLN.js";
23
- import "./chunk-W5J3LTYS.js";
24
- import "./chunk-L2WOLNZK.js";
25
- import "./chunk-AMW5LCUB.js";
26
- import "./chunk-ZPWBYHNE.js";
27
- import {
28
- copyMerge,
29
- getCompInit
30
- } from "./chunk-HBNB5TRH.js";
31
- import "./chunk-PF4DSFDR.js";
32
- import "./chunk-4OLM3KSB.js";
33
- import "./chunk-6XKAOSQE.js";
34
- import "./chunk-TLT4YIG3.js";
35
- import "./chunk-5R63Q5KH.js";
36
- import "./chunk-I6Y4O3RR.js";
37
- import "./chunk-Q5RDQNIT.js";
38
- import "./chunk-HS5PO5ZQ.js";
39
-
40
- // plots/w2/model/Model.ts
41
- var Model = class {
42
- constructor(genome, dslabel) {
43
- this.genome = genome;
44
- this.dslabel = dslabel;
45
- }
46
- // both requests address the dataset
47
- /** Every sample in the dataset that has at least one PLAIN slide on disk
48
- (a wsiFolder subfolder with a slide), with plain-slide counts. Spatial-only
49
- samples are not listed — spatial images are viewed through the sc app,
50
- which fetches them per sample via getImages(). */
51
- async getData() {
52
- return await dofetch3("termdb/wsiBySample", {
53
- body: { genome: this.genome, dslabel: this.dslabel }
54
- // no sample_id = list samples
55
- });
56
- }
57
- /** One sample's images (WsiImage | SpatialImage). imageType restricts the
58
- enumeration to that root ('wsi' = wsiFolder, 'spatial' = folder) so the
59
- other tree is never read; omitted = both kinds. */
60
- async getImages(sample_id, imageType) {
61
- return await dofetch3("termdb/wsiBySample", {
62
- body: { genome: this.genome, dslabel: this.dslabel, sample_id, imageType }
63
- // sample_id = list its images
64
- });
65
- }
66
- };
67
-
68
- // plots/w2/viewModel/ViewModel.ts
69
- var ViewModel = class {
70
- // built once in the constructor, read by View
71
- constructor(samples, settings) {
72
- this.viewData = {
73
- columns: [{ label: "Sample" }, { label: "Images" }],
74
- // two-column table
75
- rows: samples.map((s) => [{ value: s.sampleId }, { value: String(s.count) }]),
76
- // one row per sample
77
- selectedSample: samples[settings.selectedSampleIndex]
78
- // undefined when index is -1
79
- };
80
- }
81
- };
82
-
83
- // plots/w2/view/View.ts
84
- var View = class {
85
- constructor(dom, viewData, images, settings, interactions, vocab) {
86
- this.dom = dom;
87
- this.viewData = viewData;
88
- this.images = images;
89
- this.settings = settings;
90
- this.interactions = interactions;
91
- this.vocab = vocab;
92
- }
93
- async render() {
94
- this.renderSampleTable();
95
- await this.renderViewer();
96
- }
97
- renderSampleTable() {
98
- this.dom.table.selectAll("*").remove();
99
- renderTable({
100
- div: this.dom.table,
101
- // mount point
102
- columns: this.viewData.columns,
103
- // Sample | Images
104
- rows: this.viewData.rows,
105
- // one row per sample with images
106
- singleMode: true,
107
- // radio buttons: one sample viewed at a time
108
- selectedRows: this.settings.selectedSampleIndex != -1 ? [this.settings.selectedSampleIndex] : [],
109
- noButtonCallback: (index) => this.interactions.selectSample(index),
110
- // row click = select sample
111
- resize: true,
112
- // user-resizable table
113
- striped: true,
114
- // alternating row shading
115
- maxHeight: "30vh",
116
- // table scrolls; the viewer keeps the space below
117
- header: { style: { "text-transform": "capitalize" } }
118
- // 'sample' -> 'Sample'
119
- });
120
- }
121
- async renderViewer() {
122
- const holder = this.dom.viewer;
123
- holder.selectAll("*").remove();
124
- const sample = this.viewData.selectedSample;
125
- const selected = this.settings.selectedImageIndex;
126
- const image = this.images[selected] ?? this.images[0];
127
- if (!sample || !image) return;
128
- const imageName = (f) => f.split("/").slice(-2)[0] || f;
129
- new Tabs({
130
- holder: holder.append("div"),
131
- // tab strip sits above the map
132
- tabsPosition: "horizontal",
133
- tabs: this.images.map((img, i) => ({
134
- label: imageName(img.fileName),
135
- // e.g. 'image1'
136
- active: i == (this.images[selected] ? selected : 0),
137
- // highlight the shown image
138
- callback: () => this.interactions.selectImage(i)
139
- // dispatch -> re-render with image i
140
- }))
141
- }).main();
142
- const params = `wsimage=${encodeURIComponent(image.fileName)}&dslabel=${this.vocab.dslabel}&genome=${this.vocab.genome}&sample_id=${encodeURIComponent(sample.sampleId)}&imageType=${image.type}`;
143
- if (image.type == "spatial") {
144
- const s = this.settings;
145
- const genes = s.geneExpression ?? image.geneExpression;
146
- const direct = await import("./wsi.direct-25JUHWEF.js");
147
- await direct.init(
148
- {
149
- slideQuery: params,
150
- // addresses the slide through the dataset (no direct-path gate)
151
- label: image.fileName,
152
- // display name in the info line
153
- spatialData: image.spatialData,
154
- // the consolidated h5ad, source of every overlay
155
- hideCellStrokes: !s.showCellBoundaries,
156
- // polygons without their green outlines
157
- hideNucleusStrokes: !s.showNucleusBoundaries,
158
- // skip the nucleus overlay entirely
159
- showCellTypes: s.showCellTypes,
160
- // fill cells by their cell_type annotation
161
- cellTypeFilter: s.cellTypeFilter ?? void 0,
162
- // 'Types shown' dropdowns; []/null = all
163
- geneExpression: s.spatialMode == "gene_groups" ? void 0 : genes,
164
- // one overlay per gene
165
- geneGroups: s.spatialMode == "gene_groups" ? genes : void 0,
166
- // or one summed overlay
167
- hideExpressionFills: !s.showGeneExpression,
168
- // checkbox off = hover counts only, no fills
169
- annotationLevel: s.annotationLevel ?? image.annotationLevel,
170
- // burger overrides dataset
171
- width: "100%",
172
- // fill the sandbox
173
- height: this.settings.viewerHeight
174
- // e.g. 70vh
175
- },
176
- holder
177
- );
178
- return;
179
- }
180
- const meta = await dofetch3(`wsitiles/meta?${params}`);
181
- if (!meta || meta.error || meta.status === "error") {
182
- this.dom.error.text(`Error loading ${image.fileName}: ${meta?.error || "failed to load slide metadata"}`);
183
- return;
184
- }
185
- const [w, h] = meta.slide_dimensions;
186
- const host = (sessionStorage.getItem("hostURL") || window.testHost || "").replace(/\/+$/, "");
187
- const source = new Zoomify_default({
188
- // {z}/{x}/{y} hit wsitiles/tile; the unused {TileGroup} token only satisfies
189
- // OpenLayers' requirement that a {TileGroup}/{tileIndex} placeholder be present.
190
- // v=<slide mtime>: tiles are served immutable, so a regenerated slide must
191
- // change the URL to bust the browser cache
192
- url: `${host}/wsitiles/tile/{z}/{x}/{y}?${params}&v=${meta.version || 0}&_={TileGroup}`,
193
- size: [w, h],
194
- // OL derives the tier count from this, same math as wsi_tile.py
195
- crossOrigin: "anonymous",
196
- // tiles come from the API origin, not the page's
197
- zDirection: -1
198
- // pick the sharper tier when between two zoom levels
199
- });
200
- const grid = source.getTileGrid();
201
- const extent = grid.getExtent();
202
- const mapDiv = holder.append("div").style("width", "100%").style("height", this.settings.viewerHeight);
203
- const map = new Map_default({
204
- target: mapDiv.node(),
205
- // mount the map into the plot's viewer div
206
- layers: [new Tile_default({ source })],
207
- // OL fetches+mosaics tiles as the user pans/zooms
208
- view: new View_default({ resolutions: grid.getResolutions(), extent })
209
- // camera locked to the pyramid
210
- });
211
- map.getView().fit(extent);
212
- }
213
- };
214
-
215
- // plots/w2/interactions/WsiInteractions.ts
216
- var WsiInteractions = class {
217
- constructor(app, id) {
218
- this.app = app;
219
- this.id = id;
220
- }
221
- // rx app + this plot's id, for dispatching
222
- /** a sample row was picked in the table; image selection resets to its first image */
223
- selectSample(index) {
224
- this.app.dispatch({
225
- type: "plot_edit",
226
- id: this.id,
227
- config: { settings: { wsi: { selectedSampleIndex: index, selectedImageIndex: 0 } } }
228
- });
229
- }
230
- /** an image tab was picked for the selected sample */
231
- selectImage(index) {
232
- this.app.dispatch({
233
- type: "plot_edit",
234
- id: this.id,
235
- config: { settings: { wsi: { selectedImageIndex: index } } }
236
- });
237
- }
238
- };
239
-
240
- // plots/w2/Wsi.ts
241
- var Wsi = class _Wsi extends PlotBase {
242
- constructor(opts, api) {
243
- super(opts, api);
244
- // created in init()
245
- /** showCellTypes of the previous render, to tell which exclusive fill
246
- checkbox was just toggled when both end up checked */
247
- this.prevShowCellTypes = false;
248
- /** gene names available in the current image's expression h5, cached per file */
249
- this.geneNames = [];
250
- /** cell types available in the current image's annotations CSV, cached per file */
251
- this.cellTypeNames = [];
252
- this.type = _Wsi.type;
253
- const holder = opts.holder.classed("sjpp-wsi-main", true);
254
- const div = holder.append("div").style("padding", "5px");
255
- this.dom = {
256
- div,
257
- // burger menu for spatial viewer settings; hidden until a spatial image is shown
258
- controls: div.append("div").attr("id", "sjpp-wsi-controls").style("display", "none"),
259
- error: div.append("div").attr("id", "sjpp-wsi-error").style("opacity", 0.75),
260
- // inline errors
261
- table: div.append("div").attr("id", "sjpp-wsi-table"),
262
- // sample table mount
263
- viewer: div.append("div").attr("id", "sjpp-wsi-viewer")
264
- // tabs + map mount
265
- };
266
- if (opts.header)
267
- this.dom.header = opts.header.text("WHOLE SLIDE IMAGES").style("font-size", "0.7em").style("opacity", 0.6);
268
- }
269
- static {
270
- this.type = "wsi";
271
- }
272
- /** the app-state slice this plot reacts to */
273
- getState(appState) {
274
- const config = appState.plots.find((p) => p.id === this.id);
275
- if (!config) {
276
- throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
277
- }
278
- return {
279
- vocab: appState.vocab,
280
- // genome + dslabel for server requests
281
- config
282
- // the plot's own settings
283
- };
284
- }
285
- /** rx lifecycle: one-time setup before the first main() */
286
- async init() {
287
- this.interactions = new WsiInteractions(this.app, this.id);
288
- }
289
- /** rx lifecycle: re-renders the whole plot on every relevant state change */
290
- async main() {
291
- const config = structuredClone(this.state.config);
292
- if (config.childType != this.type && config.chartType != this.type) return;
293
- if (!this.interactions) throw "Interactions not initialized [wsi main()]";
294
- const settings = config.settings.wsi;
295
- if (settings.showCellTypes && settings.showGeneExpression) {
296
- const off = this.prevShowCellTypes ? "showCellTypes" : "showGeneExpression";
297
- this.app.dispatch({ type: "plot_edit", id: this.id, config: { settings: { wsi: { [off]: false } } } });
298
- return;
299
- }
300
- this.prevShowCellTypes = settings.showCellTypes;
301
- this.dom.error.text("");
302
- const fixedSample = config.sample?.sID;
303
- const fixedKind = config.imageType == "wsi" ? "wsi" : "spatial";
304
- const model = new Model(this.state.vocab.genome, this.state.vocab.dslabel);
305
- let samples;
306
- if (fixedSample) {
307
- this.dom.table.style("display", "none");
308
- settings.selectedSampleIndex = 0;
309
- samples = [{ sampleId: fixedSample, count: 1 }];
310
- } else {
311
- const data = await model.getData();
312
- if (!data || data.error || !data.samples?.length) {
313
- this.dom.table.selectAll("*").remove();
314
- this.dom.viewer.selectAll("*").remove();
315
- this.dom.error.style("padding", "20px").text(data?.error || "No samples with whole-slide images.");
316
- return;
317
- }
318
- samples = data.samples;
319
- }
320
- const viewModel = new ViewModel(samples, settings);
321
- const selectedSample = viewModel.viewData.selectedSample;
322
- const imageData = selectedSample ? await model.getImages(selectedSample.sampleId, fixedSample ? fixedKind : "wsi") : void 0;
323
- if (imageData?.error) throw new Error(imageData.error);
324
- const images = imageData?.images ?? [];
325
- if (fixedSample && !images.length) {
326
- this.dom.viewer.selectAll("*").remove();
327
- this.dom.error.style("padding", "20px").text(`No ${fixedKind == "spatial" ? "spatial image" : "whole-slide image"} for sample ${fixedSample}.`);
328
- return;
329
- }
330
- const image = images[settings.selectedImageIndex] ?? images[0];
331
- const isSpatial = image?.type == "spatial";
332
- this.dom.header?.text(isSpatial ? "SPATIAL VIEWER" : "WHOLE SLIDE IMAGES");
333
- if (isSpatial) {
334
- const spImage = image;
335
- const genes = await this.fetchGeneNames(spImage, selectedSample.sampleId);
336
- const cellTypes = await this.fetchCellTypes(spImage, selectedSample.sampleId);
337
- if (settings.cellTypeFilter?.length && cellTypes.length) {
338
- const cleaned = settings.cellTypeFilter.filter((t) => cellTypes.includes(t));
339
- if (cleaned.length != settings.cellTypeFilter.length) {
340
- this.app.dispatch({
341
- type: "plot_edit",
342
- id: this.id,
343
- config: { settings: { wsi: { cellTypeFilter: cleaned } } }
344
- });
345
- return;
346
- }
347
- }
348
- if (settings.geneExpression == null) {
349
- const configured = (spImage.geneExpression || "").split(",").map((s) => s.trim()).filter((g) => genes.includes(g));
350
- this.app.dispatch({
351
- // one-time seeding edit; triggers a re-render with the seeded values
352
- type: "plot_edit",
353
- id: this.id,
354
- config: {
355
- settings: {
356
- wsi: {
357
- geneExpression: configured.join(",") || genes[0] || "",
358
- annotationLevel: settings.annotationLevel ?? spImage.annotationLevel,
359
- // dataset default (w2.cellTypes); the burger checkbox overrides
360
- // after. Fills are mutually exclusive, so cell types on means
361
- // expression fills off (hover counts stay either way)
362
- showCellTypes: spImage.cellTypes ?? settings.showCellTypes,
363
- showGeneExpression: spImage.cellTypes ? false : settings.showGeneExpression
364
- }
365
- }
366
- }
367
- });
368
- return;
369
- }
370
- if (!this.components.controls) await this.setControls();
371
- this.addGeneDatalist();
372
- }
373
- this.dom.controls.style("display", isSpatial ? "inline-block" : "none");
374
- await new View(this.dom, viewModel.viewData, images, settings, this.interactions, this.state.vocab).render();
375
- }
376
- // the h5 the cache was built from
377
- /** Discover the genes present in the image's cell_feature_matrix h5 via
378
- wsitiles/genenames (same slide-scoped access checks as genecounts).
379
- Returns [] when the image has no expression file or the request fails. */
380
- async fetchGeneNames(image, sampleId) {
381
- const src = image.spatialData;
382
- if (!src) return [];
383
- if (this.geneNamesFile == src) return this.geneNames;
384
- const v = this.state.vocab;
385
- const params = (
386
- // standard wsitiles slide addressing + the expression file
387
- `wsimage=${encodeURIComponent(image.fileName)}&dslabel=${v.dslabel}&genome=${v.genome}&sample_id=${encodeURIComponent(sampleId)}&imageType=spatial&file=${encodeURIComponent(src)}`
388
- );
389
- const r = await dofetch3(`wsitiles/genenames?${params}`).catch(() => null);
390
- this.geneNames = Array.isArray(r?.genes) ? r.genes : [];
391
- this.geneNamesFile = src;
392
- return this.geneNames;
393
- }
394
- // the CSV the cache was built from
395
- /** Discover the distinct cell_type values of the image's per-cell
396
- annotations CSV via the meta request (?cellAnnotations= makes
397
- wsitiles/meta scan it). Returns [] when the image has no annotations
398
- file or the request fails. */
399
- async fetchCellTypes(image, sampleId) {
400
- const src = image.spatialData;
401
- if (!src) {
402
- this.cellTypeNames = [];
403
- this.cellTypesFile = void 0;
404
- return this.cellTypeNames;
405
- }
406
- if (this.cellTypesFile == src) return this.cellTypeNames;
407
- const v = this.state.vocab;
408
- const params = (
409
- // standard wsitiles slide addressing + the annotations source to scan
410
- `wsimage=${encodeURIComponent(image.fileName)}&dslabel=${v.dslabel}&genome=${v.genome}&sample_id=${encodeURIComponent(sampleId)}&imageType=spatial&cellAnnotations=${encodeURIComponent(src)}`
411
- );
412
- const r = await dofetch3(`wsitiles/meta?${params}`).catch(() => null);
413
- this.cellTypeNames = Array.isArray(r?.cellTypes) ? r.cellTypes : [];
414
- this.cellTypesFile = src;
415
- return this.cellTypeNames;
416
- }
417
- /** Attach the discovered gene names to the Genes text input as a native
418
- datalist, so typing autocompletes to genes that exist in the data.
419
- (Autocomplete applies to the whole field, i.e. the first gene of a
420
- comma-separated list — later genes are typed without suggestions.) */
421
- addGeneDatalist() {
422
- if (!this.geneNames.length) return;
423
- const input = this.dom.controls.select("input[type=text]").node();
424
- if (!input) return;
425
- const id = `sjpp-wsi-genes-${this.id}`;
426
- document.getElementById(id)?.remove();
427
- const dl = document.createElement("datalist");
428
- dl.id = id;
429
- for (const g of this.geneNames) {
430
- const opt = document.createElement("option");
431
- opt.value = g;
432
- dl.appendChild(opt);
433
- }
434
- input.after(dl);
435
- input.setAttribute("list", id);
436
- }
437
- /** Burger menu with the spatial overlay settings; fields are pre-seeded
438
- with defaults discovered from the data by main() before this runs. */
439
- async setControls() {
440
- this.components.controls = await controlsInit({
441
- app: this.app,
442
- // rx app the inputs dispatch through
443
- id: this.id,
444
- // this plot's id in app state
445
- holder: this.dom.controls,
446
- // the burger-menu div
447
- inputs: [
448
- {
449
- // checkbox: toggle the blue nucleus outlines
450
- label: "Nucleus boundaries",
451
- title: "Show or hide the nucleus segmentation overlay",
452
- type: "checkbox",
453
- chartType: "wsi",
454
- settingsKey: "showNucleusBoundaries",
455
- boxLabel: "show"
456
- },
457
- {
458
- // checkbox: toggle the green cell outlines
459
- label: "Cell boundaries",
460
- title: "Show or hide the cell segmentation overlay",
461
- type: "checkbox",
462
- chartType: "wsi",
463
- settingsKey: "showCellBoundaries",
464
- boxLabel: "show"
465
- },
466
- {
467
- // checkbox: toggle the categorical cell-type fills (mutually
468
- // exclusive with the gene expression fills, enforced in main())
469
- label: "Cell types",
470
- title: "Fill cells by their cell_type from the annotations CSV (when present)",
471
- type: "checkbox",
472
- chartType: "wsi",
473
- settingsKey: "showCellTypes",
474
- boxLabel: "show"
475
- },
476
- {
477
- // chained dropdowns: one per selected type, plus an add-dropdown of
478
- // the remaining types that appears once the previous is picked.
479
- // No selection = all types. Hidden when the overlay is off or the
480
- // image's CSV has no cell_type column.
481
- label: "Types shown",
482
- title: "Fill only the selected cell types; no selection = all types",
483
- type: "custom",
484
- settingsKey: "cellTypeFilter",
485
- init: (self) => ({
486
- main: (plot) => {
487
- const td = self.dom.inputTd;
488
- td.selectAll("*").remove();
489
- const types = this.cellTypeNames;
490
- const s = plot.settings.wsi;
491
- if (!s.showCellTypes || !types.length) {
492
- self.dom.row.style("display", "none");
493
- return;
494
- }
495
- self.dom.row.style("display", "table-row");
496
- const selected = (s.cellTypeFilter || []).filter((t) => types.includes(t));
497
- const dispatch = (list) => (
498
- // write the new selection back to state; re-render redraws the
499
- // dropdowns. Stored as a LIST: type names are free text and may
500
- // contain commas, so a joined string would corrupt them
501
- this.app.dispatch({
502
- type: "plot_edit",
503
- id: this.id,
504
- config: { settings: { wsi: { cellTypeFilter: list } } }
505
- })
506
- );
507
- const addSelect = () => td.append("select").attr("aria-label", "Cell type filter").style("display", "block").style("margin", "2px 0").style("max-width", "180px");
508
- for (const [i, t] of selected.entries()) {
509
- const sel = addSelect().on("change", function() {
510
- const next = selected.slice();
511
- if (this.value) next[i] = this.value;
512
- else next.splice(i, 1);
513
- dispatch(next);
514
- });
515
- sel.append("option").attr("value", "").text("\xD7 remove");
516
- for (const ty of types)
517
- if (ty == t || !selected.includes(ty))
518
- sel.append("option").attr("value", ty).property("selected", ty == t).text(ty);
519
- }
520
- const remaining = types.filter((ty) => !selected.includes(ty));
521
- if (remaining.length) {
522
- const add = addSelect().on("change", function() {
523
- if (this.value) dispatch([...selected, this.value]);
524
- });
525
- add.append("option").attr("value", "").text(selected.length ? "Add type\u2026" : "All types");
526
- for (const ty of remaining) add.append("option").attr("value", ty).text(ty);
527
- }
528
- }
529
- })
530
- },
531
- {
532
- // checkbox: toggle the expression FILLS only — hover counts stay
533
- // either way (View.ts always loads the genes)
534
- label: "Gene expression",
535
- title: "Show or hide the gene expression overlay",
536
- type: "checkbox",
537
- chartType: "wsi",
538
- settingsKey: "showGeneExpression",
539
- boxLabel: "show"
540
- },
541
- {
542
- // text field: which genes to load, with datalist autocomplete
543
- label: "Genes",
544
- title: "Comma-separated gene names to overlay",
545
- type: "text",
546
- chartType: "wsi",
547
- settingsKey: "geneExpression",
548
- placeholder: "gene1,gene2,\u2026"
549
- },
550
- {
551
- // radio: per-gene overlays vs one summed gene-group overlay
552
- label: "Overlay mode",
553
- title: "Color each gene separately (gene_expression), or sum all genes into one overlay (gene_groups)",
554
- type: "radio",
555
- chartType: "wsi",
556
- settingsKey: "spatialMode",
557
- options: [
558
- { label: "Per gene", value: "gene_expression" },
559
- { label: "Gene group", value: "gene_groups" }
560
- ]
561
- },
562
- {
563
- // number: how many zoomed-in levels show the boundary strokes
564
- label: "Annotation level",
565
- title: "Show boundaries only within the n most zoomed-in levels; 0 = always show",
566
- type: "number",
567
- chartType: "wsi",
568
- settingsKey: "annotationLevel",
569
- min: 0,
570
- step: 1
571
- }
572
- ]
573
- });
574
- }
575
- };
576
- var wsiInit = getCompInit(Wsi);
577
- var componentInit = wsiInit;
578
- function getDefaultWsiSettings(overrides = {}) {
579
- const defaults = {
580
- selectedSampleIndex: 0,
581
- // first sample selected on launch
582
- selectedImageIndex: 0,
583
- // the sample's first image displayed by default
584
- viewerHeight: "70vh",
585
- // map height in the sandbox
586
- // spatial overlay settings; null = fall back to the dataset's values
587
- showCellBoundaries: true,
588
- // green cell outlines on
589
- showNucleusBoundaries: true,
590
- // blue nucleus outlines on
591
- showGeneExpression: true,
592
- // expression fills on (seeding may flip this off)
593
- showCellTypes: false,
594
- // opt-in: fills all annotated cells, visually heavy
595
- cellTypeFilter: null,
596
- // null/[] = fill every annotated type
597
- geneExpression: null,
598
- // null = seed from the data on first spatial render
599
- annotationLevel: null,
600
- // null = dataset default
601
- spatialMode: "gene_expression"
602
- // per-gene overlays by default
603
- };
604
- return Object.assign(defaults, overrides);
605
- }
606
- async function getPlotConfig(opts, _app) {
607
- const config = {
608
- chartType: "wsi",
609
- // routes state updates to this component
610
- settings: {
611
- wsi: getDefaultWsiSettings(opts.overrides)
612
- // defaults + dataset overrides
613
- },
614
- hidePlotFilter: true
615
- // the mass filter UI doesn't apply to slides
616
- };
617
- return copyMerge(config, opts);
618
- }
619
- export {
620
- componentInit,
621
- getDefaultWsiSettings,
622
- getPlotConfig,
623
- wsiInit
624
- };
625
- //# sourceMappingURL=Wsi-G7OCAJ3R.js.map