@sjcrh/proteinpaint-client 2.211.0 → 2.212.0
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.
- package/dist/2dmaf-R23YQDZC.js +1367 -0
- package/dist/AggMatrixInput-4DIGZZN4.js +406 -0
- package/dist/AggregateMatrix-TF6XXFUN.js +41 -0
- package/dist/AppHeader-JB5HPAOQ.js +830 -0
- package/dist/BoxPlot-47TUXQDP.js +1208 -0
- package/dist/CorrelationVolcano-G7K5JEPM.js +617 -0
- package/dist/Cuminc-LBXPOENU.js +1220 -0
- package/dist/Cuminc-LBXPOENU.js.map +7 -0
- package/dist/DE-JSWA6HXV.js +89 -0
- package/dist/DEinput-LEYRVYK6.js +501 -0
- package/dist/DM-332QECUP.js +90 -0
- package/dist/DifferentialAnalysis-JGH2OMTH.js +239 -0
- package/dist/Disco-36PJXFM6.js +3389 -0
- package/dist/Disco.UI-PY2KOGKY.js +243 -0
- package/dist/DmrPlot-5WMOBZOJ.js +362 -0
- package/dist/GB-6WWLTBIW.js +1392 -0
- package/dist/GSEA-GYUVO2XA.js +875 -0
- package/dist/GeneExpInput-UABEICGS.js +42 -0
- package/dist/Geomap-QB6FNV5R.js +84 -0
- package/dist/HicApp-TQKQKJTN.js +2245 -0
- package/dist/IDCViewer-L27ICGR5.js +10812 -0
- package/dist/NumBinaryEditor-FHSSXZV4.js +279 -0
- package/dist/NumBinaryEditor.unit.spec-AMR32JHJ.js +312 -0
- package/dist/NumContEditor-R5JB5XPB.js +105 -0
- package/dist/NumContEditor.unit.spec-3PQRIC4G.js +164 -0
- package/dist/NumCustomBinEditor-B3PKD54F.js +33 -0
- package/dist/NumCustomBinEditor.unit.spec-YZKCYZQM.js +397 -0
- package/dist/NumDiscreteEditor-7AO35XU7.js +170 -0
- package/dist/NumDiscreteEditor.unit.spec-SNDHS6VK.js +233 -0
- package/dist/NumRegularBinEditor-OREKM2DX.js +33 -0
- package/dist/NumRegularBinEditor.unit.spec-SIGD7PLE.js +278 -0
- package/dist/NumSplineEditor-RDFDVNJG.js +210 -0
- package/dist/NumSplineEditor.unit.spec-TXRQVLUE.js +224 -0
- package/dist/NumericDensity-QPDF6UU5.js +33 -0
- package/dist/NumericDensity.unit.spec-JYUYDHDG.js +418 -0
- package/dist/NumericHandler-JW6DLSMJ.js +34 -0
- package/dist/NumericHandler.unit.spec-Q2ZNM5NH.js +214 -0
- package/dist/ProteomeInput-OS5JWC2O.js +388 -0
- package/dist/Regression-53XPZCCQ.js +1416 -0
- package/dist/RunChart2-WEO42KPP.js +749 -0
- package/dist/SC-VAWRWOUI.js +1348 -0
- package/dist/SC-VAWRWOUI.js.map +7 -0
- package/dist/Violin-7VOFUOLE.js +1064 -0
- package/dist/Volcano-DI2RLILX.js +2456 -0
- package/dist/Wsi-6DNY4RUG.js +629 -0
- package/dist/adSandbox-B7GQZDYQ.js +33 -0
- package/dist/animatedBubbleChart-QGO3OY5E.js +547 -0
- package/dist/app-XBLP7YZQ.js +32 -0
- package/dist/app-ZARZ2HWS.js +42 -0
- package/dist/app.js +12 -12
- package/dist/bam-FGNF7RYM.js +876 -0
- package/dist/barchart-6YLJJSRO.js +42 -0
- package/dist/barchart2-7TTZPYWA.js +309 -0
- package/dist/block-7WZWBQVA.js +6250 -0
- package/dist/block.init-YN4KHHJ2.js +33 -0
- package/dist/block.mds.expressionrank-6PKN3KIE.js +354 -0
- package/dist/block.mds.geneboxplot-M6TXRPKO.js +823 -0
- package/dist/block.mds.junction-WKRLLJBT.js +1539 -0
- package/dist/block.mds.svcnv-I3DNNGYV.js +6796 -0
- package/dist/block.svg-D72WTLKP.js +159 -0
- package/dist/block.tk.aicheck-QT5WYKTQ.js +278 -0
- package/dist/block.tk.ase-3WGJONXX.js +360 -0
- package/dist/block.tk.bam-Q5X7D5IR.js +1901 -0
- package/dist/block.tk.bedgraphdot-VWE2D2HR.js +379 -0
- package/dist/block.tk.bigwig.ui-Q22KXFQT.js +206 -0
- package/dist/block.tk.hicstraw-3BMDZCQH.js +818 -0
- package/dist/block.tk.junction-BMKRAVUI.js +2358 -0
- package/dist/block.tk.junction.textmatrixui-ERLXPLGI.js +194 -0
- package/dist/block.tk.ld-KT5KQUXC.js +94 -0
- package/dist/block.tk.menu-RO7IJGFY.js +1024 -0
- package/dist/block.tk.pgv-PZ4AVD3V.js +938 -0
- package/dist/brainImaging-ZU3JSXFP.js +555 -0
- package/dist/brainRegions-DJELNKKN.js +217 -0
- package/dist/bubbleHeatmap-CPJ5KI6E.js +378 -0
- package/dist/cellTypeBubbleHeatmap-6NGBETXV.js +278 -0
- package/dist/chunk-232OR2PG.js +263 -0
- package/dist/chunk-26Y2MYFN.js +129 -0
- package/dist/chunk-33FULV5M.js +302 -0
- package/dist/chunk-3AXQF6GL.js +103 -0
- package/dist/chunk-3JHCCJ4I.js +54 -0
- package/dist/chunk-4S7TWVOY.js +397 -0
- package/dist/chunk-4ZVOO3NI.js +217 -0
- package/dist/chunk-5U7AYOEZ.js +1988 -0
- package/dist/chunk-5WIA4KFA.js +178 -0
- package/dist/chunk-5WMFEMII.js +550 -0
- package/dist/chunk-6OCWNYW3.js +49 -0
- package/dist/chunk-6UAY2HAB.js +5217 -0
- package/dist/chunk-6UAY2HAB.js.map +7 -0
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- package/dist/chunk-7AOA5WZY.js +274 -0
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- package/dist/chunk-HH5JKOE6.js +339 -0
- package/dist/chunk-HL5B4NME.js +379 -0
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- package/dist/chunk-MXJKO73I.js +272 -0
- package/dist/chunk-N6NL4XG2.js +2676 -0
- package/dist/chunk-NC4RKYVE.js +158 -0
- package/dist/chunk-NK235VQ6.js +4375 -0
- package/dist/chunk-NK235VQ6.js.map +7 -0
- package/dist/chunk-O3QKYUDH.js +1812 -0
- package/dist/chunk-O3QKYUDH.js.map +7 -0
- package/dist/chunk-OSYSJHAA.js +170 -0
- package/dist/chunk-PBWB5ZG2.js +240 -0
- package/dist/chunk-PCJF5MGF.js +203 -0
- package/dist/chunk-PF5UMQEJ.js +692 -0
- package/dist/chunk-PGRTCNOV.js +217 -0
- package/dist/chunk-Q6I2OH4P.js +182 -0
- package/dist/chunk-QOF27J24.js +6360 -0
- package/dist/chunk-QWCKIRW2.js +237 -0
- package/dist/chunk-R3LWGFGS.js +54 -0
- package/dist/chunk-REWUPST7.js +1233 -0
- package/dist/chunk-RMUK3TLD.js +2149 -0
- package/dist/chunk-RU2UHH7M.js +424 -0
- package/dist/chunk-RU2UHH7M.js.map +7 -0
- package/dist/chunk-RXQRCRHC.js +134 -0
- package/dist/chunk-SAMS5XBH.js +2902 -0
- package/dist/chunk-SXYZ274A.js +2327 -0
- package/dist/chunk-TAZQU2LC.js +339 -0
- package/dist/chunk-TFS2JZTH.js +34 -0
- package/dist/chunk-UFQDWGZU.js +102 -0
- package/dist/chunk-UJRURRJ2.js +55 -0
- package/dist/chunk-UWRWFS3K.js +1278 -0
- package/dist/chunk-UYSYZM45.js +468 -0
- package/dist/chunk-VHDYIOWU.js +25009 -0
- package/dist/chunk-VHDYIOWU.js.map +7 -0
- package/dist/chunk-VPOAFNVL.js +70 -0
- package/dist/chunk-WB57TMJN.js +56 -0
- package/dist/chunk-WILJJPWV.js +255 -0
- package/dist/chunk-X2HEDRFQ.js +102 -0
- package/dist/chunk-X3UNVPC5.js +626 -0
- package/dist/chunk-XL4N3H32.js +276 -0
- package/dist/chunk-XNKLJMGF.js +123 -0
- package/dist/chunk-XZCRYWVL.js +243 -0
- package/dist/chunk-Y4MV62JA.js +56 -0
- package/dist/chunk-YKI4GLMT.js +98 -0
- package/dist/chunk-ZKINKYOJ.js +2784 -0
- package/dist/chunk-ZMSTQP6O.js +299 -0
- package/dist/cohort-CWGZR37O.js +70 -0
- package/dist/condition-B6XBQML4.js +327 -0
- package/dist/controls-QPW5HUAY.js +34 -0
- package/dist/controls.config-IUYTWRHA.js +34 -0
- package/dist/correlation-M2NKGTK2.js +95 -0
- package/dist/customdata.inputui-RKYIMOWO.js +284 -0
- package/dist/dataDownload-LPBLB7QD.js +329 -0
- package/dist/databrowser.ui-VTWHELDY.js +425 -0
- package/dist/dictionary-NINKMF3F.js +113 -0
- package/dist/dnaMethylation-LSVNG7FK.js +33 -0
- package/dist/dnaMethylation.integration.spec-6IT3Y3FS.js +198 -0
- package/dist/dofetch-HLMSTOMY.js +48 -0
- package/dist/e2pca-6PKLCC7L.js +344 -0
- package/dist/ep-3RFB6K3B.js +1249 -0
- package/dist/expclust.gdc.spec-MEWKHFMD.js +302 -0
- package/dist/facet-A4JH7FCW.js +519 -0
- package/dist/gb-PTF7CLDG.js +81 -0
- package/dist/geneExpClustering-VKUIAYCK.js +244 -0
- package/dist/geneExpression-3GQFWVJL.js +310 -0
- package/dist/geneExpression-VC7QPM3T.js +33 -0
- package/dist/geneExpression.unit.spec-PQS7BOMF.js +128 -0
- package/dist/geneORA-FCMFWZTN.js +273 -0
- package/dist/geneRanking-RTPPGBD4.js +548 -0
- package/dist/geneVariant-2TQ2JD4K.js +36 -0
- package/dist/geneVariant-4S6FLJTN.js +289 -0
- package/dist/geneVariant.integration.spec-YTFFHWQP.js +503 -0
- package/dist/genefusion.ui-P7YH32A6.js +303 -0
- package/dist/geneset-4J43JA3C.js +203 -0
- package/dist/genomeBrowser.spec-T2VFNUAV.js +276 -0
- package/dist/grin2-5TH4EBVQ.js +949 -0
- package/dist/grin2-KXMSYYYM.js +70 -0
- package/dist/hierCluster-2HFMEHAD.js +59 -0
- package/dist/hierCluster-5RQV7B5I.js +55 -0
- package/dist/hierCluster.config-PNBGJE6F.js +36 -0
- package/dist/hierCluster.integration.spec-TZLVKUC5.js +483 -0
- package/dist/hierCluster.interactivity-OQD3IQ4X.js +49 -0
- package/dist/hierCluster.renderers-DUDSHKDT.js +19 -0
- package/dist/imagePlot-6YH7S2PV.js +156 -0
- package/dist/importPlot-Z2UKA456.js +8 -0
- package/dist/isoformExpression-SRJMGXHD.js +35 -0
- package/dist/isoformExpression.unit.spec-PBVKSWCS.js +237 -0
- package/dist/junction-D4UP2AGY.js +36 -0
- package/dist/junction.unit.spec-M5CEGNUE.js +182 -0
- package/dist/launch.adhoc-SWJOT47S.js +37 -0
- package/dist/leftlabel.sample-4ZAM2JSS.js +258 -0
- package/dist/lollipop-GMGJPMJN.js +166 -0
- package/dist/maf-2TFOOAIF.js +455 -0
- package/dist/maftimeline-DRBM4ZYD.js +587 -0
- package/dist/matrix-22R4BC3F.js +54 -0
- package/dist/matrix-W4IRSBO5.js +59 -0
- package/dist/matrix.cells-QKWO5EP4.js +26 -0
- package/dist/matrix.config-ZZ7NFCIT.js +37 -0
- package/dist/matrix.data-3W6P6NBU.js +23 -0
- package/dist/matrix.groups-XW2G5BJH.js +26 -0
- package/dist/matrix.integration.spec-X4UPLQRI.js +3160 -0
- package/dist/matrix.interactivity-NGS3LJPV.js +37 -0
- package/dist/matrix.layout-SAGZVQPG.js +39 -0
- package/dist/matrix.legend-C3MQRAZJ.js +20 -0
- package/dist/matrix.renderers-IG7Q2F6Y.js +34 -0
- package/dist/matrix.serieses-SNMIQFKB.js +19 -0
- package/dist/matrix.sort-WHVUSUJZ.js +26 -0
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- package/dist/matrix.unit.spec-I6JGZHQZ.js +150 -0
- package/dist/mavb-MLVNZJSF.js +727 -0
- package/dist/mds.fimo-MOGZPFCK.js +513 -0
- package/dist/mds.samplescatterplot-YLGNYKTH.js +1545 -0
- package/dist/mds.survivalplot-R273N2GB.js +477 -0
- package/dist/multivalue-5GFBYENI.js +83 -0
- package/dist/numericDictTermCluster-MJK6SIWE.js +63 -0
- package/dist/oncomatrix-OAQT2CUN.js +290 -0
- package/dist/oncomatrix.spec-6C62LLJI.js +443 -0
- package/dist/plot.2dvaf-WDXWSC7L.js +372 -0
- package/dist/plot.app-YTHD3ZJQ.js +36 -0
- package/dist/plot.barplot-SRZM3GU3.js +97 -0
- package/dist/plot.boxplot-VWOMZPZE.js +146 -0
- package/dist/plot.brainImaging-6XL7YF5G.js +51 -0
- package/dist/plot.disco-VRKSTV5Z.js +99 -0
- package/dist/plot.ssgq-AXASDOZZ.js +134 -0
- package/dist/plot.vaf2cov-IF4DEEM5.js +253 -0
- package/dist/polar2-QQ3KHFME.js +232 -0
- package/dist/profileForms-2US7IYYM.js +941 -0
- package/dist/profilePlot-DZQCBKPA.js +49 -0
- package/dist/proteinView-TTLVQ43H.js +1357 -0
- package/dist/proteomeCohortCompare-BUZYOOIA.js +912 -0
- package/dist/pseudbulk.unit.spec-YNXQWDSU.js +86 -0
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- package/dist/qualitative-AKIZRNFO.js +38 -0
- package/dist/radar2-7GXYLICJ.js +327 -0
- package/dist/radarFacility2-WFKOWGH2.js +335 -0
- package/dist/render-F3CBMRD5.js +33 -0
- package/dist/report-6LHMHUDY.js +217 -0
- package/dist/sampleView-GWKPMVJH.js +43 -0
- package/dist/samplelst-TH6IBDVG.js +106 -0
- package/dist/samplematrix-RPCWT33H.js +2193 -0
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- package/dist/singleCellCellType-CLJFCBV6.js +33 -0
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- package/dist/singleCellGeneExpression-L6MG37XE.js +33 -0
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- package/dist/snplocus-GM6IEDPR.js +203 -0
- package/dist/spliceevent.a53ss.diagram-ZFQDHHPY.js +146 -0
- package/dist/spliceevent.exonskip.diagram-ZK6JOUMU.js +278 -0
- package/dist/spliceevent.noeventdiagram-YKTF2VZE.js +455 -0
- package/dist/ssGSEA-FDN4CH2Y.js +33 -0
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- package/dist/studyCatalog-X2IGVJ26.js +414 -0
- package/dist/summarizeCnvGeneexp-H7A5SI3R.js +158 -0
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- package/dist/summarizeMutationCnv-WQLMD2TR.js +159 -0
- package/dist/summarizeMutationDiagnosis-3S52IDWF.js +35 -0
- package/dist/summarizeMutationSurvival-NTQIUNW7.js +99 -0
- package/dist/summary-LMRFRKKI.js +44 -0
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- package/dist/sunburst-ICUSGIWV.js +278 -0
- package/dist/survival-K44Q2HAC.js +1249 -0
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- /package/dist/{summarizeCnvGeneexp-UJBTMXXH.js.map → summarizeCnvGeneexp-H7A5SI3R.js.map} +0 -0
- /package/dist/{summarizeGeneexpSurvival-XLQJGDRY.js.map → summarizeGeneexpSurvival-GJF6VD2S.js.map} +0 -0
- /package/dist/{summarizeMutationCnv-7RWSXB6F.js.map → summarizeMutationCnv-WQLMD2TR.js.map} +0 -0
- /package/dist/{summarizeMutationDiagnosis-42MG737O.js.map → summarizeMutationDiagnosis-3S52IDWF.js.map} +0 -0
- /package/dist/{summarizeMutationSurvival-FWVKVEHK.js.map → summarizeMutationSurvival-NTQIUNW7.js.map} +0 -0
- /package/dist/{summary-NR26ZPQB.js.map → summary-LMRFRKKI.js.map} +0 -0
- /package/dist/{summary.integration.spec-Z7JSUTGK.js.map → summary.integration.spec-KQMZKSEQ.js.map} +0 -0
- /package/dist/{summaryInput-DGKUOJVC.js.map → summaryInput-NNHZVHQA.js.map} +0 -0
- /package/dist/{sunburst-C5JNGFT7.js.map → sunburst-ICUSGIWV.js.map} +0 -0
- /package/dist/{survival-GCEX3EAZ.js.map → survival-K5YBNNVE.js.map} +0 -0
- /package/dist/{survival.integration.spec-ZX5RD6VQ.js.map → survival.integration.spec-4LRJW2V2.js.map} +0 -0
- /package/dist/{svgraph-XCFZ2WAG.js.map → svgraph-U7MS7YEM.js.map} +0 -0
- /package/dist/{svmr-4XTTURHA.js.map → svmr-2JGDBPAI.js.map} +0 -0
- /package/dist/{table-FQZ4UAH6.js.map → table-CBWOHYW6.js.map} +0 -0
- /package/dist/{termCollection-DN6A6HJU.js.map → termCollection-JFGGXVFI.js.map} +0 -0
- /package/dist/{termCollection-5QCR6LED.js.map → termCollection-VE3FFL6V.js.map} +0 -0
- /package/dist/{termCollection.unit.spec-RSSSXDHU.js.map → termCollection.unit.spec-XQQTDV4A.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection-OSN7FITY.js.map → termCollectionFractionSelection-TFGF27GR.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection.unit.spec-UW6D3DVK.js.map → termCollectionFractionSelection.unit.spec-MKGG4JBC.js.map} +0 -0
- /package/dist/{tk-4CZCVYBP.js.map → tk-74SGUUZY.js.map} +0 -0
- /package/dist/{tk-BIPJNXBZ.js.map → tk-K4JFYIZY.js.map} +0 -0
- /package/dist/{tp.ui-NI4U7567.js.map → tp.ui-727EXXMT.js.map} +0 -0
- /package/dist/{tvs.dt-YRDNDXUU.js.map → tvs.dt-YB2C3T33.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-REP4T33P.js.map → tvs.dtcnv.categorical-NOWMZOE5.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-K7OREEP5.js.map → tvs.dtcnv.continuous-3KWUNU76.js.map} +0 -0
- /package/dist/{tvs.dtfusion-AB5MPH3Q.js.map → tvs.dtfusion-NOJSTABU.js.map} +0 -0
- /package/dist/{tvs.dtitd-AFWU7ACY.js.map → tvs.dtitd-OD5B377P.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-G7XQEKEO.js.map → tvs.dtsnvindel-WIQMZTRH.js.map} +0 -0
- /package/dist/{tvs.dtsv-Y6BEY4J2.js.map → tvs.dtsv-HPERDN3R.js.map} +0 -0
- /package/dist/{tvs.samplelst-XRRWPC2E.js.map → tvs.samplelst-TC2Z7Z35.js.map} +0 -0
- /package/dist/{tvs.termCollection-PL4AN3GA.js.map → tvs.termCollection-F64BHWAL.js.map} +0 -0
- /package/dist/{vocabulary-DJZWOO6Q.js.map → vocabulary-ZOYF2VHS.js.map} +0 -0
- /package/dist/{wsi.direct-XUWANMKV.js.map → wsi.direct-Z5YUZEXG.js.map} +0 -0
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import {
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Map_default,
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Tile_default,
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View_default,
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Zoomify_default
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} from "./chunk-WTAPOH2W.js";
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import {
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PlotBase,
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Tabs,
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controlsInit,
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renderTable
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} from "./chunk-VHDYIOWU.js";
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import {
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dofetch3
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copyMerge,
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getCompInit
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import "./chunk-HS5PO5ZQ.js";
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// plots/w2/model/Model.ts
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var Model = class {
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constructor(genome, dslabel) {
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this.genome = genome;
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this.dslabel = dslabel;
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}
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// both requests address the dataset
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/** Every sample in the dataset that has at least one PLAIN slide on disk
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(a wsiFolder subfolder with a slide), with plain-slide counts. Spatial-only
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samples are not listed — spatial images are viewed through the sc app,
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which fetches them per sample via getImages(). */
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async getData() {
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return await dofetch3("termdb/wsiBySample", {
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body: { genome: this.genome, dslabel: this.dslabel }
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// no sample_id = list samples
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});
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}
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/** One sample's images (WsiImage | SpatialImage). imageType restricts the
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enumeration to that root ('wsi' = wsiFolder, 'spatial' = folder) so the
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other tree is never read; omitted = both kinds. */
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async getImages(sample_id, imageType) {
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return await dofetch3("termdb/wsiBySample", {
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body: { genome: this.genome, dslabel: this.dslabel, sample_id, imageType }
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// sample_id = list its images
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});
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}
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};
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// plots/w2/viewModel/ViewModel.ts
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var ViewModel = class {
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// built once in the constructor, read by View
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constructor(samples, settings) {
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this.viewData = {
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columns: [{ label: "Sample" }, { label: "Images" }],
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// two-column table
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rows: samples.map((s) => [{ value: s.sampleId }, { value: String(s.count) }]),
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// one row per sample
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selectedSample: samples[settings.selectedSampleIndex]
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// undefined when index is -1
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};
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}
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};
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// plots/w2/view/View.ts
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var View = class {
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constructor(dom, viewData, images, settings, interactions, vocab) {
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this.dom = dom;
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this.viewData = viewData;
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this.images = images;
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this.settings = settings;
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this.interactions = interactions;
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this.vocab = vocab;
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}
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async render() {
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this.renderSampleTable();
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await this.renderViewer();
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}
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renderSampleTable() {
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this.dom.table.selectAll("*").remove();
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renderTable({
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div: this.dom.table,
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// mount point
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columns: this.viewData.columns,
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// Sample | Images
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rows: this.viewData.rows,
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// one row per sample with images
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singleMode: true,
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// radio buttons: one sample viewed at a time
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selectedRows: this.settings.selectedSampleIndex != -1 ? [this.settings.selectedSampleIndex] : [],
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noButtonCallback: (index) => this.interactions.selectSample(index),
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// row click = select sample
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resize: true,
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// user-resizable table
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striped: true,
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// alternating row shading
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maxHeight: "30vh",
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// table scrolls; the viewer keeps the space below
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header: { style: { "text-transform": "capitalize" } }
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// 'sample' -> 'Sample'
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});
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}
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async renderViewer() {
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const holder = this.dom.viewer;
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holder.selectAll("*").remove();
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const sample = this.viewData.selectedSample;
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const selected = this.settings.selectedImageIndex;
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const image = this.images[selected] ?? this.images[0];
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if (!sample || !image) return;
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const imageName = (f) => f.split("/").slice(-2)[0] || f;
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new Tabs({
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holder: holder.append("div"),
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// tab strip sits above the map
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tabsPosition: "horizontal",
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tabs: this.images.map((img, i) => ({
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label: imageName(img.fileName),
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// e.g. 'image1'
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active: i == (this.images[selected] ? selected : 0),
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// highlight the shown image
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callback: () => this.interactions.selectImage(i)
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// dispatch -> re-render with image i
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}))
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}).main();
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const params = `wsimage=${encodeURIComponent(image.fileName)}&dslabel=${this.vocab.dslabel}&genome=${this.vocab.genome}&sample_id=${encodeURIComponent(sample.sampleId)}&imageType=${image.type}`;
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if (image.type == "spatial") {
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const s = this.settings;
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const genes = s.geneExpression ?? image.geneExpression;
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const direct = await import("./wsi.direct-Z5YUZEXG.js");
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await direct.init(
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{
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slideQuery: params,
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// addresses the slide through the dataset (no direct-path gate)
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label: image.fileName,
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// display name in the info line
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spatialData: image.spatialData,
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// the consolidated h5ad, source of every overlay
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hideCellStrokes: !s.showCellBoundaries,
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// polygons without their green outlines
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hideNucleusStrokes: !s.showNucleusBoundaries,
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// skip the nucleus overlay entirely
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showCellTypes: s.showCellTypes,
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// fill cells by their cell_type annotation
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cellTypeFilter: s.cellTypeFilter ?? void 0,
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// 'Types shown' dropdowns; []/null = all
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geneExpression: s.spatialMode == "gene_groups" ? void 0 : genes,
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// one overlay per gene
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geneGroups: s.spatialMode == "gene_groups" ? genes : void 0,
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// or one summed overlay
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hideExpressionFills: !s.showGeneExpression,
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172
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// checkbox off = hover counts only, no fills
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annotationLevel: s.annotationLevel ?? image.annotationLevel,
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// burger overrides dataset
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width: "100%",
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// fill the sandbox
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height: this.settings.viewerHeight
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// e.g. 70vh
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},
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180
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holder
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);
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return;
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}
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const meta = await dofetch3(`wsitiles/meta?${params}`);
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if (!meta || meta.error || meta.status === "error") {
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this.dom.error.text(`Error loading ${image.fileName}: ${meta?.error || "failed to load slide metadata"}`);
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return;
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}
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const [w, h] = meta.slide_dimensions;
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190
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const host = (sessionStorage.getItem("hostURL") || window.testHost || "").replace(/\/+$/, "");
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const source = new Zoomify_default({
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192
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+
// {z}/{x}/{y} hit wsitiles/tile; the unused {TileGroup} token only satisfies
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193
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+
// OpenLayers' requirement that a {TileGroup}/{tileIndex} placeholder be present.
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// v=<slide mtime>: tiles are served immutable, so a regenerated slide must
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195
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// change the URL to bust the browser cache
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+
url: `${host}/wsitiles/tile/{z}/{x}/{y}?${params}&v=${meta.version || 0}&_={TileGroup}`,
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197
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+
size: [w, h],
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198
|
+
// OL derives the tier count from this, same math as wsi_tile.py
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199
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+
crossOrigin: "anonymous",
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200
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// tiles come from the API origin, not the page's
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201
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zDirection: -1
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202
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// pick the sharper tier when between two zoom levels
|
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203
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});
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204
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+
const grid = source.getTileGrid();
|
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205
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+
const extent = grid.getExtent();
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206
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+
const mapDiv = holder.append("div").style("width", "100%").style("height", this.settings.viewerHeight);
|
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207
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+
const map = new Map_default({
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208
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+
target: mapDiv.node(),
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209
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+
// mount the map into the plot's viewer div
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210
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+
layers: [new Tile_default({ source })],
|
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211
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+
// OL fetches+mosaics tiles as the user pans/zooms
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212
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view: new View_default({ resolutions: grid.getResolutions(), extent })
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213
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// camera locked to the pyramid
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});
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215
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map.getView().fit(extent);
|
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216
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}
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217
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};
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218
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+
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219
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// plots/w2/interactions/WsiInteractions.ts
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220
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+
var WsiInteractions = class {
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221
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constructor(app, id) {
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222
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+
this.app = app;
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223
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+
this.id = id;
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224
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}
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225
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+
// rx app + this plot's id, for dispatching
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226
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+
/** a sample row was picked in the table; image selection resets to its first image */
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227
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+
selectSample(index) {
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228
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+
this.app.dispatch({
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type: "plot_edit",
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+
id: this.id,
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+
config: { settings: { wsi: { selectedSampleIndex: index, selectedImageIndex: 0 } } }
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+
});
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}
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234
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/** an image tab was picked for the selected sample */
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selectImage(index) {
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236
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this.app.dispatch({
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type: "plot_edit",
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+
id: this.id,
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+
config: { settings: { wsi: { selectedImageIndex: index } } }
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240
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+
});
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241
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+
}
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242
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+
};
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243
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+
|
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244
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// plots/w2/Wsi.ts
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245
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+
var Wsi = class _Wsi extends PlotBase {
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246
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constructor(opts, api) {
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247
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super(opts, api);
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248
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+
// created in init()
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249
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+
/** showCellTypes of the previous render, to tell which exclusive fill
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250
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+
checkbox was just toggled when both end up checked */
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251
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this.prevShowCellTypes = false;
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252
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+
/** gene names available in the current image's expression h5, cached per file */
|
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253
|
+
this.geneNames = [];
|
|
254
|
+
/** cell types available in the current image's annotations CSV, cached per file */
|
|
255
|
+
this.cellTypeNames = [];
|
|
256
|
+
this.type = _Wsi.type;
|
|
257
|
+
const holder = opts.holder.classed("sjpp-wsi-main", true);
|
|
258
|
+
const div = holder.append("div").style("padding", "5px");
|
|
259
|
+
this.dom = {
|
|
260
|
+
div,
|
|
261
|
+
// burger menu for spatial viewer settings; hidden until a spatial image is shown
|
|
262
|
+
controls: div.append("div").attr("id", "sjpp-wsi-controls").style("display", "none"),
|
|
263
|
+
error: div.append("div").attr("id", "sjpp-wsi-error").style("opacity", 0.75),
|
|
264
|
+
// inline errors
|
|
265
|
+
table: div.append("div").attr("id", "sjpp-wsi-table"),
|
|
266
|
+
// sample table mount
|
|
267
|
+
viewer: div.append("div").attr("id", "sjpp-wsi-viewer")
|
|
268
|
+
// tabs + map mount
|
|
269
|
+
};
|
|
270
|
+
if (opts.header)
|
|
271
|
+
this.dom.header = opts.header.text("WHOLE SLIDE IMAGES").style("font-size", "0.7em").style("opacity", 0.6);
|
|
272
|
+
}
|
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273
|
+
static {
|
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274
|
+
this.type = "wsi";
|
|
275
|
+
}
|
|
276
|
+
/** the app-state slice this plot reacts to */
|
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277
|
+
getState(appState) {
|
|
278
|
+
const config = appState.plots.find((p) => p.id === this.id);
|
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279
|
+
if (!config) {
|
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280
|
+
throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
|
|
281
|
+
}
|
|
282
|
+
return {
|
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283
|
+
vocab: appState.vocab,
|
|
284
|
+
// genome + dslabel for server requests
|
|
285
|
+
config
|
|
286
|
+
// the plot's own settings
|
|
287
|
+
};
|
|
288
|
+
}
|
|
289
|
+
/** rx lifecycle: one-time setup before the first main() */
|
|
290
|
+
async init() {
|
|
291
|
+
this.interactions = new WsiInteractions(this.app, this.id);
|
|
292
|
+
}
|
|
293
|
+
/** rx lifecycle: re-renders the whole plot on every relevant state change */
|
|
294
|
+
async main() {
|
|
295
|
+
const config = structuredClone(this.state.config);
|
|
296
|
+
if (config.childType != this.type && config.chartType != this.type) return;
|
|
297
|
+
if (!this.interactions) throw "Interactions not initialized [wsi main()]";
|
|
298
|
+
const settings = config.settings.wsi;
|
|
299
|
+
if (settings.showCellTypes && settings.showGeneExpression) {
|
|
300
|
+
const off = this.prevShowCellTypes ? "showCellTypes" : "showGeneExpression";
|
|
301
|
+
this.app.dispatch({ type: "plot_edit", id: this.id, config: { settings: { wsi: { [off]: false } } } });
|
|
302
|
+
return;
|
|
303
|
+
}
|
|
304
|
+
this.prevShowCellTypes = settings.showCellTypes;
|
|
305
|
+
this.dom.error.text("");
|
|
306
|
+
const fixedSample = config.sample?.sID;
|
|
307
|
+
const fixedKind = config.imageType == "wsi" ? "wsi" : "spatial";
|
|
308
|
+
const model = new Model(this.state.vocab.genome, this.state.vocab.dslabel);
|
|
309
|
+
let samples;
|
|
310
|
+
if (fixedSample) {
|
|
311
|
+
this.dom.table.style("display", "none");
|
|
312
|
+
settings.selectedSampleIndex = 0;
|
|
313
|
+
samples = [{ sampleId: fixedSample, count: 1 }];
|
|
314
|
+
} else {
|
|
315
|
+
const data = await model.getData();
|
|
316
|
+
if (!data || data.error || !data.samples?.length) {
|
|
317
|
+
this.dom.table.selectAll("*").remove();
|
|
318
|
+
this.dom.viewer.selectAll("*").remove();
|
|
319
|
+
this.dom.error.style("padding", "20px").text(data?.error || "No samples with whole-slide images.");
|
|
320
|
+
return;
|
|
321
|
+
}
|
|
322
|
+
samples = data.samples;
|
|
323
|
+
}
|
|
324
|
+
const viewModel = new ViewModel(samples, settings);
|
|
325
|
+
const selectedSample = viewModel.viewData.selectedSample;
|
|
326
|
+
const imageData = selectedSample ? await model.getImages(selectedSample.sampleId, fixedSample ? fixedKind : "wsi") : void 0;
|
|
327
|
+
if (imageData?.error) throw new Error(imageData.error);
|
|
328
|
+
const images = imageData?.images ?? [];
|
|
329
|
+
if (fixedSample && !images.length) {
|
|
330
|
+
this.dom.viewer.selectAll("*").remove();
|
|
331
|
+
this.dom.error.style("padding", "20px").text(`No ${fixedKind == "spatial" ? "spatial image" : "whole-slide image"} for sample ${fixedSample}.`);
|
|
332
|
+
return;
|
|
333
|
+
}
|
|
334
|
+
const image = images[settings.selectedImageIndex] ?? images[0];
|
|
335
|
+
const isSpatial = image?.type == "spatial";
|
|
336
|
+
this.dom.header?.text(isSpatial ? "SPATIAL VIEWER" : "WHOLE SLIDE IMAGES");
|
|
337
|
+
if (isSpatial) {
|
|
338
|
+
const spImage = image;
|
|
339
|
+
const genes = await this.fetchGeneNames(spImage, selectedSample.sampleId);
|
|
340
|
+
const cellTypes = await this.fetchCellTypes(spImage, selectedSample.sampleId);
|
|
341
|
+
if (settings.cellTypeFilter?.length && cellTypes.length) {
|
|
342
|
+
const cleaned = settings.cellTypeFilter.filter((t) => cellTypes.includes(t));
|
|
343
|
+
if (cleaned.length != settings.cellTypeFilter.length) {
|
|
344
|
+
this.app.dispatch({
|
|
345
|
+
type: "plot_edit",
|
|
346
|
+
id: this.id,
|
|
347
|
+
config: { settings: { wsi: { cellTypeFilter: cleaned } } }
|
|
348
|
+
});
|
|
349
|
+
return;
|
|
350
|
+
}
|
|
351
|
+
}
|
|
352
|
+
if (settings.geneExpression == null) {
|
|
353
|
+
const configured = (spImage.geneExpression || "").split(",").map((s) => s.trim()).filter((g) => genes.includes(g));
|
|
354
|
+
this.app.dispatch({
|
|
355
|
+
// one-time seeding edit; triggers a re-render with the seeded values
|
|
356
|
+
type: "plot_edit",
|
|
357
|
+
id: this.id,
|
|
358
|
+
config: {
|
|
359
|
+
settings: {
|
|
360
|
+
wsi: {
|
|
361
|
+
geneExpression: configured.join(",") || genes[0] || "",
|
|
362
|
+
annotationLevel: settings.annotationLevel ?? spImage.annotationLevel,
|
|
363
|
+
// dataset default (w2.cellTypes); the burger checkbox overrides
|
|
364
|
+
// after. Fills are mutually exclusive, so cell types on means
|
|
365
|
+
// expression fills off (hover counts stay either way)
|
|
366
|
+
showCellTypes: spImage.cellTypes ?? settings.showCellTypes,
|
|
367
|
+
showGeneExpression: spImage.cellTypes ? false : settings.showGeneExpression
|
|
368
|
+
}
|
|
369
|
+
}
|
|
370
|
+
}
|
|
371
|
+
});
|
|
372
|
+
return;
|
|
373
|
+
}
|
|
374
|
+
if (!this.components.controls) await this.setControls();
|
|
375
|
+
this.addGeneDatalist();
|
|
376
|
+
}
|
|
377
|
+
this.dom.controls.style("display", isSpatial ? "inline-block" : "none");
|
|
378
|
+
await new View(this.dom, viewModel.viewData, images, settings, this.interactions, this.state.vocab).render();
|
|
379
|
+
}
|
|
380
|
+
// the h5 the cache was built from
|
|
381
|
+
/** Discover the genes present in the image's cell_feature_matrix h5 via
|
|
382
|
+
wsitiles/genenames (same slide-scoped access checks as genecounts).
|
|
383
|
+
Returns [] when the image has no expression file or the request fails. */
|
|
384
|
+
async fetchGeneNames(image, sampleId) {
|
|
385
|
+
const src = image.spatialData;
|
|
386
|
+
if (!src) return [];
|
|
387
|
+
if (this.geneNamesFile == src) return this.geneNames;
|
|
388
|
+
const v = this.state.vocab;
|
|
389
|
+
const params = (
|
|
390
|
+
// standard wsitiles slide addressing + the expression file
|
|
391
|
+
`wsimage=${encodeURIComponent(image.fileName)}&dslabel=${v.dslabel}&genome=${v.genome}&sample_id=${encodeURIComponent(sampleId)}&imageType=spatial&file=${encodeURIComponent(src)}`
|
|
392
|
+
);
|
|
393
|
+
const r = await dofetch3(`wsitiles/genenames?${params}`).catch(() => null);
|
|
394
|
+
this.geneNames = Array.isArray(r?.genes) ? r.genes : [];
|
|
395
|
+
this.geneNamesFile = src;
|
|
396
|
+
return this.geneNames;
|
|
397
|
+
}
|
|
398
|
+
// the CSV the cache was built from
|
|
399
|
+
/** Discover the distinct cell_type values of the image's per-cell
|
|
400
|
+
annotations CSV via the meta request (?cellAnnotations= makes
|
|
401
|
+
wsitiles/meta scan it). Returns [] when the image has no annotations
|
|
402
|
+
file or the request fails. */
|
|
403
|
+
async fetchCellTypes(image, sampleId) {
|
|
404
|
+
const src = image.spatialData;
|
|
405
|
+
if (!src) {
|
|
406
|
+
this.cellTypeNames = [];
|
|
407
|
+
this.cellTypesFile = void 0;
|
|
408
|
+
return this.cellTypeNames;
|
|
409
|
+
}
|
|
410
|
+
if (this.cellTypesFile == src) return this.cellTypeNames;
|
|
411
|
+
const v = this.state.vocab;
|
|
412
|
+
const params = (
|
|
413
|
+
// standard wsitiles slide addressing + the annotations source to scan
|
|
414
|
+
`wsimage=${encodeURIComponent(image.fileName)}&dslabel=${v.dslabel}&genome=${v.genome}&sample_id=${encodeURIComponent(sampleId)}&imageType=spatial&cellAnnotations=${encodeURIComponent(src)}`
|
|
415
|
+
);
|
|
416
|
+
const r = await dofetch3(`wsitiles/meta?${params}`).catch(() => null);
|
|
417
|
+
this.cellTypeNames = Array.isArray(r?.cellTypes) ? r.cellTypes : [];
|
|
418
|
+
this.cellTypesFile = src;
|
|
419
|
+
return this.cellTypeNames;
|
|
420
|
+
}
|
|
421
|
+
/** Attach the discovered gene names to the Genes text input as a native
|
|
422
|
+
datalist, so typing autocompletes to genes that exist in the data.
|
|
423
|
+
(Autocomplete applies to the whole field, i.e. the first gene of a
|
|
424
|
+
comma-separated list — later genes are typed without suggestions.) */
|
|
425
|
+
addGeneDatalist() {
|
|
426
|
+
if (!this.geneNames.length) return;
|
|
427
|
+
const input = this.dom.controls.select("input[type=text]").node();
|
|
428
|
+
if (!input) return;
|
|
429
|
+
const id = `sjpp-wsi-genes-${this.id}`;
|
|
430
|
+
document.getElementById(id)?.remove();
|
|
431
|
+
const dl = document.createElement("datalist");
|
|
432
|
+
dl.id = id;
|
|
433
|
+
for (const g of this.geneNames) {
|
|
434
|
+
const opt = document.createElement("option");
|
|
435
|
+
opt.value = g;
|
|
436
|
+
dl.appendChild(opt);
|
|
437
|
+
}
|
|
438
|
+
input.after(dl);
|
|
439
|
+
input.setAttribute("list", id);
|
|
440
|
+
}
|
|
441
|
+
/** Burger menu with the spatial overlay settings; fields are pre-seeded
|
|
442
|
+
with defaults discovered from the data by main() before this runs. */
|
|
443
|
+
async setControls() {
|
|
444
|
+
this.components.controls = await controlsInit({
|
|
445
|
+
app: this.app,
|
|
446
|
+
// rx app the inputs dispatch through
|
|
447
|
+
id: this.id,
|
|
448
|
+
// this plot's id in app state
|
|
449
|
+
holder: this.dom.controls,
|
|
450
|
+
// the burger-menu div
|
|
451
|
+
inputs: [
|
|
452
|
+
{
|
|
453
|
+
// checkbox: toggle the blue nucleus outlines
|
|
454
|
+
label: "Nucleus boundaries",
|
|
455
|
+
title: "Show or hide the nucleus segmentation overlay",
|
|
456
|
+
type: "checkbox",
|
|
457
|
+
chartType: "wsi",
|
|
458
|
+
settingsKey: "showNucleusBoundaries",
|
|
459
|
+
boxLabel: "show"
|
|
460
|
+
},
|
|
461
|
+
{
|
|
462
|
+
// checkbox: toggle the green cell outlines
|
|
463
|
+
label: "Cell boundaries",
|
|
464
|
+
title: "Show or hide the cell segmentation overlay",
|
|
465
|
+
type: "checkbox",
|
|
466
|
+
chartType: "wsi",
|
|
467
|
+
settingsKey: "showCellBoundaries",
|
|
468
|
+
boxLabel: "show"
|
|
469
|
+
},
|
|
470
|
+
{
|
|
471
|
+
// checkbox: toggle the categorical cell-type fills (mutually
|
|
472
|
+
// exclusive with the gene expression fills, enforced in main())
|
|
473
|
+
label: "Cell types",
|
|
474
|
+
title: "Fill cells by their cell_type from the annotations CSV (when present)",
|
|
475
|
+
type: "checkbox",
|
|
476
|
+
chartType: "wsi",
|
|
477
|
+
settingsKey: "showCellTypes",
|
|
478
|
+
boxLabel: "show"
|
|
479
|
+
},
|
|
480
|
+
{
|
|
481
|
+
// chained dropdowns: one per selected type, plus an add-dropdown of
|
|
482
|
+
// the remaining types that appears once the previous is picked.
|
|
483
|
+
// No selection = all types. Hidden when the overlay is off or the
|
|
484
|
+
// image's CSV has no cell_type column.
|
|
485
|
+
label: "Types shown",
|
|
486
|
+
title: "Fill only the selected cell types; no selection = all types",
|
|
487
|
+
type: "custom",
|
|
488
|
+
settingsKey: "cellTypeFilter",
|
|
489
|
+
init: (self) => ({
|
|
490
|
+
main: (plot) => {
|
|
491
|
+
const td = self.dom.inputTd;
|
|
492
|
+
td.selectAll("*").remove();
|
|
493
|
+
const types = this.cellTypeNames;
|
|
494
|
+
const s = plot.settings.wsi;
|
|
495
|
+
if (!s.showCellTypes || !types.length) {
|
|
496
|
+
self.dom.row.style("display", "none");
|
|
497
|
+
return;
|
|
498
|
+
}
|
|
499
|
+
self.dom.row.style("display", "table-row");
|
|
500
|
+
const selected = (s.cellTypeFilter || []).filter((t) => types.includes(t));
|
|
501
|
+
const dispatch = (list) => (
|
|
502
|
+
// write the new selection back to state; re-render redraws the
|
|
503
|
+
// dropdowns. Stored as a LIST: type names are free text and may
|
|
504
|
+
// contain commas, so a joined string would corrupt them
|
|
505
|
+
this.app.dispatch({
|
|
506
|
+
type: "plot_edit",
|
|
507
|
+
id: this.id,
|
|
508
|
+
config: { settings: { wsi: { cellTypeFilter: list } } }
|
|
509
|
+
})
|
|
510
|
+
);
|
|
511
|
+
const addSelect = () => td.append("select").attr("aria-label", "Cell type filter").style("display", "block").style("margin", "2px 0").style("max-width", "180px");
|
|
512
|
+
for (const [i, t] of selected.entries()) {
|
|
513
|
+
const sel = addSelect().on("change", function() {
|
|
514
|
+
const next = selected.slice();
|
|
515
|
+
if (this.value) next[i] = this.value;
|
|
516
|
+
else next.splice(i, 1);
|
|
517
|
+
dispatch(next);
|
|
518
|
+
});
|
|
519
|
+
sel.append("option").attr("value", "").text("\xD7 remove");
|
|
520
|
+
for (const ty of types)
|
|
521
|
+
if (ty == t || !selected.includes(ty))
|
|
522
|
+
sel.append("option").attr("value", ty).property("selected", ty == t).text(ty);
|
|
523
|
+
}
|
|
524
|
+
const remaining = types.filter((ty) => !selected.includes(ty));
|
|
525
|
+
if (remaining.length) {
|
|
526
|
+
const add = addSelect().on("change", function() {
|
|
527
|
+
if (this.value) dispatch([...selected, this.value]);
|
|
528
|
+
});
|
|
529
|
+
add.append("option").attr("value", "").text(selected.length ? "Add type\u2026" : "All types");
|
|
530
|
+
for (const ty of remaining) add.append("option").attr("value", ty).text(ty);
|
|
531
|
+
}
|
|
532
|
+
}
|
|
533
|
+
})
|
|
534
|
+
},
|
|
535
|
+
{
|
|
536
|
+
// checkbox: toggle the expression FILLS only — hover counts stay
|
|
537
|
+
// either way (View.ts always loads the genes)
|
|
538
|
+
label: "Gene expression",
|
|
539
|
+
title: "Show or hide the gene expression overlay",
|
|
540
|
+
type: "checkbox",
|
|
541
|
+
chartType: "wsi",
|
|
542
|
+
settingsKey: "showGeneExpression",
|
|
543
|
+
boxLabel: "show"
|
|
544
|
+
},
|
|
545
|
+
{
|
|
546
|
+
// text field: which genes to load, with datalist autocomplete
|
|
547
|
+
label: "Genes",
|
|
548
|
+
title: "Comma-separated gene names to overlay",
|
|
549
|
+
type: "text",
|
|
550
|
+
chartType: "wsi",
|
|
551
|
+
settingsKey: "geneExpression",
|
|
552
|
+
placeholder: "gene1,gene2,\u2026"
|
|
553
|
+
},
|
|
554
|
+
{
|
|
555
|
+
// radio: per-gene overlays vs one summed gene-group overlay
|
|
556
|
+
label: "Overlay mode",
|
|
557
|
+
title: "Color each gene separately (gene_expression), or sum all genes into one overlay (gene_groups)",
|
|
558
|
+
type: "radio",
|
|
559
|
+
chartType: "wsi",
|
|
560
|
+
settingsKey: "spatialMode",
|
|
561
|
+
options: [
|
|
562
|
+
{ label: "Per gene", value: "gene_expression" },
|
|
563
|
+
{ label: "Gene group", value: "gene_groups" }
|
|
564
|
+
]
|
|
565
|
+
},
|
|
566
|
+
{
|
|
567
|
+
// number: how many zoomed-in levels show the boundary strokes
|
|
568
|
+
label: "Annotation level",
|
|
569
|
+
title: "Show boundaries only within the n most zoomed-in levels; 0 = always show",
|
|
570
|
+
type: "number",
|
|
571
|
+
chartType: "wsi",
|
|
572
|
+
settingsKey: "annotationLevel",
|
|
573
|
+
min: 0,
|
|
574
|
+
step: 1
|
|
575
|
+
}
|
|
576
|
+
]
|
|
577
|
+
});
|
|
578
|
+
}
|
|
579
|
+
};
|
|
580
|
+
var wsiInit = getCompInit(Wsi);
|
|
581
|
+
var componentInit = wsiInit;
|
|
582
|
+
function getDefaultWsiSettings(overrides = {}) {
|
|
583
|
+
const defaults = {
|
|
584
|
+
selectedSampleIndex: 0,
|
|
585
|
+
// first sample selected on launch
|
|
586
|
+
selectedImageIndex: 0,
|
|
587
|
+
// the sample's first image displayed by default
|
|
588
|
+
viewerHeight: "70vh",
|
|
589
|
+
// map height in the sandbox
|
|
590
|
+
// spatial overlay settings; null = fall back to the dataset's values
|
|
591
|
+
showCellBoundaries: true,
|
|
592
|
+
// green cell outlines on
|
|
593
|
+
showNucleusBoundaries: true,
|
|
594
|
+
// blue nucleus outlines on
|
|
595
|
+
showGeneExpression: true,
|
|
596
|
+
// expression fills on (seeding may flip this off)
|
|
597
|
+
showCellTypes: false,
|
|
598
|
+
// opt-in: fills all annotated cells, visually heavy
|
|
599
|
+
cellTypeFilter: null,
|
|
600
|
+
// null/[] = fill every annotated type
|
|
601
|
+
geneExpression: null,
|
|
602
|
+
// null = seed from the data on first spatial render
|
|
603
|
+
annotationLevel: null,
|
|
604
|
+
// null = dataset default
|
|
605
|
+
spatialMode: "gene_expression"
|
|
606
|
+
// per-gene overlays by default
|
|
607
|
+
};
|
|
608
|
+
return Object.assign(defaults, overrides);
|
|
609
|
+
}
|
|
610
|
+
async function getPlotConfig(opts, _app) {
|
|
611
|
+
const config = {
|
|
612
|
+
chartType: "wsi",
|
|
613
|
+
// routes state updates to this component
|
|
614
|
+
settings: {
|
|
615
|
+
wsi: getDefaultWsiSettings(opts.overrides)
|
|
616
|
+
// defaults + dataset overrides
|
|
617
|
+
},
|
|
618
|
+
hidePlotFilter: true
|
|
619
|
+
// the mass filter UI doesn't apply to slides
|
|
620
|
+
};
|
|
621
|
+
return copyMerge(config, opts);
|
|
622
|
+
}
|
|
623
|
+
export {
|
|
624
|
+
componentInit,
|
|
625
|
+
getDefaultWsiSettings,
|
|
626
|
+
getPlotConfig,
|
|
627
|
+
wsiInit
|
|
628
|
+
};
|
|
629
|
+
//# sourceMappingURL=Wsi-6DNY4RUG.js.map
|
|
@@ -0,0 +1,33 @@
|
|
|
1
|
+
import {
|
|
2
|
+
openSandbox
|
|
3
|
+
} from "./chunk-ZKINKYOJ.js";
|
|
4
|
+
import "./chunk-VHDYIOWU.js";
|
|
5
|
+
import "./chunk-HJ6L54YS.js";
|
|
6
|
+
import "./chunk-KV4W2ACA.js";
|
|
7
|
+
import "./chunk-5WIA4KFA.js";
|
|
8
|
+
import "./chunk-7XZA2XR2.js";
|
|
9
|
+
import "./chunk-DD3DWHUY.js";
|
|
10
|
+
import "./chunk-EEB5VE2A.js";
|
|
11
|
+
import "./chunk-6RRZRISL.js";
|
|
12
|
+
import "./chunk-2KM4PRQM.js";
|
|
13
|
+
import "./chunk-RMUK3TLD.js";
|
|
14
|
+
import "./chunk-HH5JKOE6.js";
|
|
15
|
+
import "./chunk-RU2UHH7M.js";
|
|
16
|
+
import "./chunk-57Z4VYLM.js";
|
|
17
|
+
import "./chunk-WINIL2KN.js";
|
|
18
|
+
import "./chunk-PF4DSFDR.js";
|
|
19
|
+
import "./chunk-7X6NF7NI.js";
|
|
20
|
+
import "./chunk-W5J3LTYS.js";
|
|
21
|
+
import "./chunk-Z2ZITHT4.js";
|
|
22
|
+
import "./chunk-4OLM3KSB.js";
|
|
23
|
+
import "./chunk-6XKAOSQE.js";
|
|
24
|
+
import "./chunk-TLT4YIG3.js";
|
|
25
|
+
import "./chunk-5R63Q5KH.js";
|
|
26
|
+
import "./chunk-I6Y4O3RR.js";
|
|
27
|
+
import "./chunk-Q5RDQNIT.js";
|
|
28
|
+
import "./chunk-DQC5FFGV.js";
|
|
29
|
+
import "./chunk-HS5PO5ZQ.js";
|
|
30
|
+
export {
|
|
31
|
+
openSandbox
|
|
32
|
+
};
|
|
33
|
+
//# sourceMappingURL=adSandbox-B7GQZDYQ.js.map
|