@sjcrh/proteinpaint-client 2.224.0 → 2.224.1
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-7HOQRW25.js +1362 -0
- package/dist/AggMatrixInput-LMVRNQBN.js +402 -0
- package/dist/AggregateMatrix-AMQTLJV2.js +37 -0
- package/dist/AppHeader-AK7O2HUI.js +826 -0
- package/dist/BoxPlot-CE5JWPJH.js +1229 -0
- package/dist/CorrelationVolcano-DO7I63FR.js +613 -0
- package/dist/Cuminc-NHABXYET.js +1217 -0
- package/dist/DE-A327BZNW.js +85 -0
- package/dist/DEinput-VKRBFYUE.js +479 -0
- package/dist/DM-NU23H5PL.js +86 -0
- package/dist/DifferentialAnalysis-SH47YDQQ.js +236 -0
- package/dist/Disco-DOLET5UY.js +3384 -0
- package/dist/Disco.UI-6J6INV56.js +239 -0
- package/dist/DmrPlot-KYZOQB2Y.js +361 -0
- package/dist/GB-LQCK6YNB.js +1388 -0
- package/dist/GSEA-KLTV4JDP.js +870 -0
- package/dist/GeneExpInput-ZMTWWDO7.js +38 -0
- package/dist/Geomap-4NP2JPMA.js +80 -0
- package/dist/HicApp-DXF6B4YR.js +2240 -0
- package/dist/IDCViewer-HEQYB6AY.js +10808 -0
- package/dist/NumBinaryEditor-JZZS67NB.js +274 -0
- package/dist/NumBinaryEditor.unit.spec-S2MKCJYX.js +308 -0
- package/dist/NumContEditor-IRZPIDJU.js +100 -0
- package/dist/NumContEditor.unit.spec-JDSSEJLJ.js +160 -0
- package/dist/NumCustomBinEditor-E2FJNISZ.js +29 -0
- package/dist/NumCustomBinEditor.unit.spec-26GWME2W.js +393 -0
- package/dist/NumDiscreteEditor-JECWQKST.js +165 -0
- package/dist/NumDiscreteEditor.unit.spec-DG52CSV5.js +229 -0
- package/dist/NumRegularBinEditor-W726TJIB.js +29 -0
- package/dist/NumRegularBinEditor.unit.spec-GG7XXYLQ.js +274 -0
- package/dist/NumSplineEditor-7UYPJI57.js +205 -0
- package/dist/NumSplineEditor.unit.spec-MESJVLZV.js +220 -0
- package/dist/NumericDensity-VFXO6VZ7.js +29 -0
- package/dist/NumericDensity.unit.spec-OQDBGUQJ.js +414 -0
- package/dist/NumericHandler-EJHWVASI.js +30 -0
- package/dist/NumericHandler.unit.spec-VUIGKU4C.js +225 -0
- package/dist/ProteomeInput-ATBCNQLN.js +610 -0
- package/dist/Regression-ZL6XKZA6.js +1412 -0
- package/dist/RunChart2-NUSOF6LW.js +744 -0
- package/dist/SC-A55NDRZ2.js +1290 -0
- package/dist/Violin-DRTD42BR.js +1092 -0
- package/dist/Volcano-UNZ6OAWB.js +2657 -0
- package/dist/Wsi-CC7GX3HL.js +636 -0
- package/dist/aboutSunburst-VTBLSKCY.js +93 -0
- package/dist/adSandbox-7RA6NVM4.js +29 -0
- package/dist/animatedBubbleChart-BRGFUEYW.js +542 -0
- package/dist/app-2GMWQIJZ.js +28 -0
- package/dist/app-4KI25R4S.js +38 -0
- package/dist/app.js +8 -8
- package/dist/bam-B3JWSAZ5.js +872 -0
- package/dist/barchart-E2IWHDLL.js +38 -0
- package/dist/barchart2-QDATDPDT.js +305 -0
- package/dist/block-IS3WJCNW.js +6203 -0
- package/dist/block.init-ZCEUPHX2.js +29 -0
- package/dist/block.mds.expressionrank-WCJNZ63X.js +350 -0
- package/dist/block.mds.geneboxplot-BCXVN3GL.js +819 -0
- package/dist/block.mds.junction-J7H7WNMN.js +1534 -0
- package/dist/block.mds.svcnv-GJ6BSNGY.js +6325 -0
- package/dist/block.svg-SR5EQSKQ.js +155 -0
- package/dist/block.tk.aicheck-RPKZMKLM.js +274 -0
- package/dist/block.tk.bam-BDF3UFRA.js +1906 -0
- package/dist/block.tk.bigwig.ui-2MG6M4CP.js +202 -0
- package/dist/block.tk.hicstraw-JFMLXXLH.js +814 -0
- package/dist/block.tk.junction-ZDFTQJGA.js +2353 -0
- package/dist/block.tk.junction.textmatrixui-OHAZEQNT.js +190 -0
- package/dist/block.tk.ld-BRYYNH55.js +90 -0
- package/dist/block.tk.menu-XQKB62BG.js +1050 -0
- package/dist/block.tk.pgv-76I52IUX.js +934 -0
- package/dist/brainImaging-65UMKH6J.js +550 -0
- package/dist/brainRegions-AURQKH5R.js +213 -0
- package/dist/bubbleHeatmap-T3LEYZBU.js +374 -0
- package/dist/cellTypeBubbleHeatmap-UPY53IPQ.js +274 -0
- package/dist/chunk-2CQ4YA7M.js +257 -0
- package/dist/chunk-2FTQ5RMP.js +340 -0
- package/dist/chunk-2VBU42YX.js +299 -0
- package/dist/chunk-36CCFKWS.js +134 -0
- package/dist/chunk-3A2CWTBI.js +159 -0
- package/dist/chunk-3I26BABG.js +182 -0
- package/dist/chunk-3TO7TWHS.js +2008 -0
- package/dist/chunk-3WU2KUY2.js +13624 -0
- package/dist/chunk-3YQYWX4M.js +26716 -0
- package/dist/chunk-4MGXKCPS.js +2685 -0
- package/dist/chunk-53VTLOOW.js +1339 -0
- package/dist/chunk-76SL5VYA.js +255 -0
- package/dist/chunk-7BD532EJ.js +70 -0
- package/dist/chunk-7CE2X6HL.js +56 -0
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- package/dist/chunk-MNN6NFZK.js +203 -0
- package/dist/chunk-N4ULQIGJ.js +379 -0
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- package/dist/chunk-S72DZX6B.js +848 -0
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- package/dist/chunk-TLWU7JWO.js +692 -0
- package/dist/chunk-TUZ3MJVF.js +6375 -0
- package/dist/chunk-TZVSDB7S.js +2102 -0
- package/dist/chunk-UHPFEULI.js +480 -0
- package/dist/chunk-XYAT642G.js +305 -0
- package/dist/chunk-Y3CSXSOZ.js +652 -0
- package/dist/chunk-YJFK6C2M.js +35 -0
- package/dist/chunk-Z44FLO2F.js +626 -0
- package/dist/chunk-Z6CMJQKG.js +1253 -0
- package/dist/chunk-Z6LQ3URB.js +14 -0
- package/dist/chunk-ZESHWW2R.js +54 -0
- package/dist/chunk-ZK4JKSUK.js +56 -0
- package/dist/chunk-ZV7LZY67.js +550 -0
- package/dist/cohort-T3SEGYG3.js +66 -0
- package/dist/cohortSunburst-HIWGWD7A.js +402 -0
- package/dist/condition-KEFHKNUU.js +323 -0
- package/dist/controls-MDUZLMY7.js +30 -0
- package/dist/controls.config-4XZZXUZV.js +30 -0
- package/dist/correlation-55LF7GPF.js +91 -0
- package/dist/customdata.inputui-6KIPVY2Q.js +280 -0
- package/dist/dataDownload-XCFCSKDO.js +326 -0
- package/dist/databrowser.ui-HLWUAHSZ.js +421 -0
- package/dist/dictionary-P5JGXQSW.js +109 -0
- package/dist/dnaMethylation-ZNR5U6HS.js +29 -0
- package/dist/dnaMethylation.integration.spec-7AMBXA4M.js +194 -0
- package/dist/e2pca-AJQ22AHJ.js +340 -0
- package/dist/ep-3ZEN3C4U.js +1247 -0
- package/dist/expclust.gdc.spec-IQXJYSCH.js +298 -0
- package/dist/facet-RPFQA3DH.js +556 -0
- package/dist/gb-R4D647D2.js +77 -0
- package/dist/geneExpClustering-JLJL6S3Q.js +240 -0
- package/dist/geneExpression-NWNOCRVM.js +309 -0
- package/dist/geneExpression-NWNOCRVM.js.map +7 -0
- package/dist/geneExpression-TK75VNQG.js +29 -0
- package/dist/geneExpression.unit.spec-4HTUTQ5K.js +151 -0
- package/dist/geneORA-7FP6KZSE.js +269 -0
- package/dist/geneRanking-SBFOUZTQ.js +544 -0
- package/dist/geneVariant-3DHX4LQL.js +289 -0
- package/dist/geneVariant-SUQWO6ON.js +32 -0
- package/dist/geneVariant.integration.spec-KOUVJAFB.js +672 -0
- package/dist/genefusion.ui-DAIBYS5I.js +299 -0
- package/dist/geneset-MKSYRPV4.js +199 -0
- package/dist/genomeBrowser.spec-JSHMD3CR.js +272 -0
- package/dist/grin2-RFRYBHBV.js +945 -0
- package/dist/grin2-Z4ETF6OM.js +66 -0
- package/dist/hierCluster-C67VO3VF.js +55 -0
- package/dist/hierCluster-CEJTROX7.js +51 -0
- package/dist/hierCluster.config-G3X5I72U.js +32 -0
- package/dist/hierCluster.integration.spec-HTS2GNUR.js +479 -0
- package/dist/hierCluster.interactivity-4JVDLIPZ.js +45 -0
- package/dist/imagePlot-HNKJX6YK.js +152 -0
- package/dist/importPlot-XUL6XFBL.js +8 -0
- package/dist/isoformExpression-ZJJUXJDF.js +31 -0
- package/dist/isoformExpression.unit.spec-INU6WFAM.js +233 -0
- package/dist/jspdf.es.min-THXUXEDC.js +40 -0
- package/dist/junction-FKYIKDC4.js +32 -0
- package/dist/junction.unit.spec-VRFIOT4T.js +178 -0
- package/dist/launch.adhoc-SDMXDSHS.js +33 -0
- package/dist/leftlabel.sample-S33KB225.js +253 -0
- package/dist/lollipop-WXQOGEY7.js +162 -0
- package/dist/maf-K6ZUNABR.js +451 -0
- package/dist/maftimeline-Y2LETT7W.js +583 -0
- package/dist/matrix-LADX4K5W.js +50 -0
- package/dist/matrix-M63KP6IL.js +55 -0
- package/dist/matrix.config-ZMT7A2D5.js +33 -0
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- package/dist/matrix.interactivity-2ISWFOK2.js +33 -0
- package/dist/matrix.layout-EAYTUK2H.js +35 -0
- package/dist/matrix.renderers-XUMZZUDW.js +30 -0
- package/dist/matrix.sort.unit.spec-UPG3D6GE.js +464 -0
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- package/dist/matrix.unit.spec-Z2HXOXM4.js +146 -0
- package/dist/mavb-WT4XM6U3.js +726 -0
- package/dist/mds.samplescatterplot-UTEBJF66.js +1545 -0
- package/dist/mds.survivalplot-DXWJA4IJ.js +472 -0
- package/dist/multivalue-LR7Z3OLZ.js +79 -0
- package/dist/oncomatrix-WV2LSH3X.js +286 -0
- package/dist/oncomatrix.spec-S7KHSJJG.js +439 -0
- package/dist/plot.2dvaf-FH7PMZ3U.js +368 -0
- package/dist/plot.app-DDB6YZJ3.js +32 -0
- package/dist/plot.barplot-XVSZDYKB.js +93 -0
- package/dist/plot.boxplot-M6URTYED.js +142 -0
- package/dist/plot.brainImaging-GNIBY3XC.js +51 -0
- package/dist/plot.disco-EH4E7B3O.js +98 -0
- package/dist/plot.ssgq-7HIGQHOT.js +130 -0
- package/dist/plot.ssgq-7HIGQHOT.js.map +7 -0
- package/dist/plot.vaf2cov-MGJHP2PV.js +249 -0
- package/dist/polar2-VYUW5GZO.js +228 -0
- package/dist/profileForms-LHJCFAP6.js +937 -0
- package/dist/profilePlot-UF2KERDD.js +45 -0
- package/dist/proteinView-5AF4I3PB.js +1346 -0
- package/dist/proteomeCohortCompare-4DYWZTLQ.js +866 -0
- package/dist/pseudbulk.unit.spec-ZTAP2YYA.js +82 -0
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- package/dist/sampleView-BQ6HCCKT.js +39 -0
- package/dist/samplelst-RQWH7WOX.js +114 -0
- package/dist/samplematrix-7FDWXSZA.js +2188 -0
- package/dist/sc-J2ZPQFGP.js +77 -0
- package/dist/scatter-7FQLITP7.js +919 -0
- package/dist/scatter-BDIZX73F.js +84 -0
- package/dist/selectGenomeWithTklst-52BHWMVR.js +125 -0
- package/dist/singleCellCellType-OC6QG6MU.js +29 -0
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- /package/dist/{termCollection.unit.spec-QHKLFPWO.js.map → termCollection.unit.spec-22E76H2W.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection-ZNMCUSN4.js.map → termCollectionFractionSelection-VZ5JJ7KV.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection.unit.spec-PO4BHCMC.js.map → termCollectionFractionSelection.unit.spec-KCAQU2BV.js.map} +0 -0
- /package/dist/{tk-R6IBTAYE.js.map → tk-GBNB42AI.js.map} +0 -0
- /package/dist/{tk-7OE7QMYG.js.map → tk-YOBCGYFC.js.map} +0 -0
- /package/dist/{tp.ui-BGSBCIR7.js.map → tp.ui-OEL4S73T.js.map} +0 -0
- /package/dist/{tvs.categorical-RTSI5L6T.js.map → tvs.categorical-3X6CO5EA.js.map} +0 -0
- /package/dist/{tvs.condition-VBDUN33K.js.map → tvs.condition-YZQSSONN.js.map} +0 -0
- /package/dist/{tvs.dt-NP6556P7.js.map → tvs.dt-GCMLLAJC.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-RERJRI5J.js.map → tvs.dtcnv.categorical-ZSYUQQXP.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-UEVWYT3H.js.map → tvs.dtcnv.continuous-T67YFFAE.js.map} +0 -0
- /package/dist/{tvs.dtfusion-CRJ77JUK.js.map → tvs.dtfusion-VR2NAX3F.js.map} +0 -0
- /package/dist/{tvs.dtitd-ZOCNVICE.js.map → tvs.dtitd-O3MIZPZO.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-LFWG54AQ.js.map → tvs.dtsnvindel-6G7UNHSQ.js.map} +0 -0
- /package/dist/{tvs.dtsv-SNIZC3C6.js.map → tvs.dtsv-VZ2I4AMH.js.map} +0 -0
- /package/dist/{tvs.multivalue-UJS4743S.js.map → tvs.multivalue-6KFI5ELB.js.map} +0 -0
- /package/dist/{tvs.numeric-KKMUTKSJ.js.map → tvs.numeric-SFSOLXVF.js.map} +0 -0
- /package/dist/{tvs.samplelst-AW3IY3CB.js.map → tvs.samplelst-WD5UMMTP.js.map} +0 -0
- /package/dist/{tvs.survival-LH2Z3WTM.js.map → tvs.survival-A2RUXAXJ.js.map} +0 -0
- /package/dist/{tvs.termCollection-OQNMYVX5.js.map → tvs.termCollection-NVW4LO44.js.map} +0 -0
- /package/dist/{vocabulary-6XMG22NZ.js.map → vocabulary-FASF5IUM.js.map} +0 -0
- /package/dist/{wsi.direct-EJ2ENH64.js.map → wsi.direct-O6HFKPCP.js.map} +0 -0
package/dist/chunk-VFLGHCUO.js
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import {
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violinRenderer
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import {
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getValueConversionFactor
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import {
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linear
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drag_default
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import {
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pointer_default,
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select_default
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} from "./chunk-I6Y4O3RR.js";
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// termsetting/handlers/NumericDensity.ts
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var NumericDensity = class {
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constructor(opts) {
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this.dom = {};
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// WeakMap allows deletion of value when the object/DOM key is deleted,
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// so better for avoiding memory leak
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this.vrByDiv = /* @__PURE__ */ new WeakMap();
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this.ranges = [];
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this.no_density_data = false;
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this.brushes = [];
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this.plot_size = {
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width: 500,
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height: 100,
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xpad: 10,
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ypad: 20,
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radius: 8
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};
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this.opts = opts;
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this.termsetting = opts.termsetting;
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this.tw = opts.termsetting.tw;
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}
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/* the boundary values exchanged with the bin/knot editors, and the domain of this.xscale, are in
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the term's user-facing unit; density_data is in the unit the values are stored in. only the two
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getters below cross that line, to put the plot's endpoints in the same unit as those values.
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they multiply instead of calling toUserUnit(), which rounds: rounding is right for a number shown
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in an input, but a rounded domain endpoint distorts every scaled x by up to half of the last shown
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digit, and collapses the domain outright when the converted range is smaller than that (a stored
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range of under 2 days at scaleFactor=1/365.25). it would also disagree with violinRenderer, whose
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axis this plot's lines overlay and which scales its own domain unrounded */
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get scaleFactor() {
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return getValueConversionFactor(this.tw.term);
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}
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get displayMin() {
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return this.density_data.min * this.scaleFactor;
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}
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get displayMax() {
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return this.density_data.max * this.scaleFactor;
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}
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async setData() {
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const self = this.termsetting;
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const d = await self.vocabApi.getViolinBox(
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{
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plotType: "violin",
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tw: { type: self.tw.type, term: self.term, q: self.q },
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svgw: this.plot_size.width,
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radius: this.plot_size.radius,
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filter: self.filter
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},
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self.opts.getBodyParams?.()
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);
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if (d.error) throw d;
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this.density_data = d;
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return this.density_data;
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}
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async showViolin(div, boundaryOpts) {
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await this.setData();
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if (!this.vrByDiv.has(div)) {
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div.style("padding", "5px").selectAll("*").remove();
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const loadingDiv = div.append("div").style("padding", "10px").style("text-align", "center").html("Getting distribution data ...<br/>");
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const densityDiv = div.append("div");
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loadingDiv.remove();
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const vr = new violinRenderer({
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holder: densityDiv,
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rd: this.density_data,
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width: this.plot_size.width,
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height: this.plot_size.height,
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radius: this.plot_size.radius,
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// axis ticks are labeled in the term's user-facing unit, e.g. years and not days
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scaleFactor: this.scaleFactor
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});
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this.vrByDiv.set(div, vr);
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}
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this.vr = this.vrByDiv.get(div);
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this.dom.svg = this.vr.svg;
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this.vr.render();
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if (boundaryOpts) await this.setBinLines(boundaryOpts);
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return this.density_data;
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}
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async setBinLines(boundaryOpts) {
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if (this.density_data.max == this.density_data.min) {
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this.handleNoDensity();
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} else {
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if (this.dom.binsize_g) this.dom.binsize_g.selectAll("*").remove();
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this.dom.binsize_g = this.dom.svg.append("g").attr("transform", `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`).attr("class", "binsize_g");
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const maxvalue = this.displayMax;
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const minvalue = this.displayMin;
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this.xscale = linear().domain([minvalue, maxvalue]).range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad]);
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this.ranges = [];
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this.brushes = [];
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this.renderBinLines(boundaryOpts);
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}
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}
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handleNoDensity() {
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this.no_density_data = true;
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this.ranges = [];
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this.brushes = [];
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}
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renderBinLines(boundaryOpts) {
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const { plot_size, tw, xscale, scaleFactor } = this;
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if (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`;
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const scaledMinX = Math.round(this.xscale(this.displayMin));
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const scaledMaxX = Math.round(this.xscale(this.displayMax));
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const lines = [];
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for (const [index, v] of boundaryOpts.values.entries()) {
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lines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) });
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}
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const lastVisibleLine = lines.find((l) => l.isLastVisibleLine);
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const lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX;
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const dragger = drag_default().on("drag", onDrag).on("end", onDrag);
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this.dom.binsize_g.selectAll("line").remove();
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this.dom.binsize_g.selectAll("line").data(lines).enter().append("line").style("stroke", (d) => d.isDraggable ? "#cc0000" : "#555").style("stroke-width", 1).attr("x1", (d) => d.scaledX).attr("y1", 0).attr("x2", (d) => d.scaledX).attr("y2", plot_size.height).style("cursor", (d) => d.isDraggable ? "ew-resize" : "").attr("display", (d) => !d.isDraggable && d.scaledX > lastVisibleScaledX ? "none" : "").on("mouseover", function(_, d) {
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if (d.isDraggable) select_default(this).style("stroke-width", 3);
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}).on("mouseout", function() {
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select_default(this).style("stroke-width", 1);
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}).each(function(d) {
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if (d.isDraggable) select_default(this).call(dragger);
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});
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const lineElems = this.dom.binsize_g.node().querySelectorAll("line");
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function toBoundaryValue(x) {
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const inverted = xscale.invert(x);
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return Number(
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scaleFactor != 1 ? inverted.toFixed(2) : tw.term.type == "integer" ? Math.round(inverted) : inverted.toFixed(3)
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);
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}
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function toLineValue(line) {
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return line.draggedX === void 0 ? line.x : toBoundaryValue(line.draggedX);
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}
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function getNeighbors(d) {
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const x = d.draggedX ?? d.scaledX;
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let lower, upper;
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for (const line of lines) {
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if (line.index === d.index || !line.isDraggable) continue;
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const lineX = line.draggedX ?? line.scaledX;
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if (lineX <= x) {
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if (!lower || lineX > (lower.draggedX ?? lower.scaledX)) lower = line;
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} else if (!upper || lineX < (upper.draggedX ?? upper.scaledX)) upper = line;
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}
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return [lower, upper];
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}
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function onDrag(event, _d) {
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const d = _d;
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const [lower, upper] = getNeighbors(d);
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const lowerX = Math.max(scaledMinX, lower ? lower.draggedX ?? lower.scaledX : scaledMinX);
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const upperX = Math.min(scaledMaxX, upper ? upper.draggedX ?? upper.scaledX : scaledMaxX);
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if (upperX - lowerX < 2) return;
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const draggedX = Math.min(Math.max(pointer_default(event, this)[0], lowerX + 1), upperX - 1);
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const value = toBoundaryValue(draggedX);
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if (lower && value === toLineValue(lower)) return;
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if (upper && value === toLineValue(upper)) return;
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d.draggedX = draggedX;
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select_default(this).attr("x1", d.draggedX).attr("y1", 0).attr("x2", d.draggedX).attr("y2", plot_size.height);
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const lastVisibleScaledX2 = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX;
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const xOffset = d.draggedX - d.scaledX;
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if (xOffset) {
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for (const elem of lineElems) {
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const c = elem.__data__;
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if (c.movesWithLineIndex !== d.index) continue;
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c.draggedX = c.scaledX + xOffset;
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select_default(elem).attr("x1", c.draggedX).attr("x2", c.draggedX).style("display", c.draggedX >= lastVisibleScaledX2 ? "none" : "");
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}
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boundaryOpts.callback(d, value);
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}
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}
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}
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destroy() {
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for (const [k, v] of Object.entries(this.dom)) {
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delete this.dom[k];
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if (typeof v.remove == "function") v.remove();
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}
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}
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};
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export {
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NumericDensity
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};
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//# sourceMappingURL=chunk-VFLGHCUO.js.map
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package/dist/chunk-VJALVBYH.js
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import {
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2
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getPlotConfig
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3
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} from "./chunk-2Q3ETPV2.js";
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4
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import {
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fillTermWrapper
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} from "./chunk-U45YALDI.js";
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import {
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dictionaryNumericTypes,
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numericTypes
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} from "./chunk-JHLF2ZC2.js";
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import {
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copyMerge
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} from "./chunk-HBNB5TRH.js";
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// plots/matrix/hierCluster.config.js
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async function getPlotConfig2(opts = {}, app) {
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opts.chartType = "hierCluster";
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if (dictionaryNumericTypes.has(opts.dataType) || opts.dataType == "numericDictTerm") {
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const grp = opts.termgroups?.find((g) => g.type == "hierCluster");
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for (const tw of grp?.lst || []) tw.q = { ...tw.q, mode: "continuous" };
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}
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const config = await getPlotConfig(opts, app);
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delete config.genes;
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if (config.dataType == "numericDictTerm") {
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const lst = config.termgroups?.find((g) => g.type == "hierCluster")?.lst;
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config.dataType = lst?.[0]?.term?.type || "float";
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}
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config.settings.hierCluster = {
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/* type of data used for clustering
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exciting todo: (to introduce new dt values)
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- gene dependency
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- numeric dic term
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- non-gene genomic stuff that resolves into numeric quantities (cpg meth)
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- metabolite
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*/
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dataType: config.dataType,
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// adjust the default group name based on automatically detected term types
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// Done in matrix.cells.js: setHierClusterCellProps
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// termGroupName: 'Expression',
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40
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-
clusterSamples: true,
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clusterRows: true,
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42
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-
clusterMethod: "average",
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// complete
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44
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distanceMethod: "euclidean",
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45
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-
zScoreCap: 5,
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46
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-
zScoreTransformation: true,
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47
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-
xDendrogramHeight: 100,
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48
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-
yDendrogramHeight: 200,
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49
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-
colorScale: "blueWhiteRed"
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50
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-
};
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51
|
-
const overrides = app.vocabApi.termdbConfig.hierCluster || {};
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52
|
-
const numericDictTermClusterOverrides = dictionaryNumericTypes.has(config.dataType) && app.vocabApi.termdbConfig.numericDictTermCluster ? app.vocabApi.termdbConfig.numericDictTermCluster : {};
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53
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copyMerge(
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config.settings.hierCluster,
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55
|
-
overrides.settings,
|
|
56
|
-
opts.settings?.hierCluster || {},
|
|
57
|
-
numericDictTermClusterOverrides.settings
|
|
58
|
-
);
|
|
59
|
-
{
|
|
60
|
-
const c = config.settings.hierCluster.colorScale;
|
|
61
|
-
if (!c) throw "colorScale missing";
|
|
62
|
-
}
|
|
63
|
-
config.settings.matrix.collabelpos = "top";
|
|
64
|
-
const termGroupName = config.settings.hierCluster.termGroupName;
|
|
65
|
-
const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
|
|
66
|
-
name: termGroupName
|
|
67
|
-
};
|
|
68
|
-
hcTermGroup.type = "hierCluster";
|
|
69
|
-
if (!hcTermGroup.lst?.length) {
|
|
70
|
-
if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
|
|
71
|
-
const promises = [];
|
|
72
|
-
for (const i of opts.terms) {
|
|
73
|
-
const tw = i.term ? i : { term: i };
|
|
74
|
-
if (!tw.term.type) {
|
|
75
|
-
if (config.dataType && numericTypes.has(config.dataType)) {
|
|
76
|
-
tw.term.type = config.dataType;
|
|
77
|
-
} else {
|
|
78
|
-
throw `term type missing and cannot be assigned by dataType '${config.dataType}'`;
|
|
79
|
-
}
|
|
80
|
-
} else if (!numericTypes.has(tw.term.type)) {
|
|
81
|
-
throw "term type is not numeric";
|
|
82
|
-
} else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
|
|
83
|
-
throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
|
|
84
|
-
}
|
|
85
|
-
if (dictionaryNumericTypes.has(tw.term.type)) tw.q = { ...tw.q, mode: "continuous" };
|
|
86
|
-
promises.push(fillTermWrapper(tw, app.vocabApi));
|
|
87
|
-
}
|
|
88
|
-
hcTermGroup.lst = await Promise.all(promises);
|
|
89
|
-
if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
|
|
90
|
-
}
|
|
91
|
-
config.settings.matrix.maxSample = 1e5;
|
|
92
|
-
return config;
|
|
93
|
-
}
|
|
94
|
-
function canTermBeInHierGrp(grpType, twType) {
|
|
95
|
-
if (dictionaryNumericTypes.has(grpType) && dictionaryNumericTypes.has(twType)) return true;
|
|
96
|
-
return twType == grpType;
|
|
97
|
-
}
|
|
98
|
-
|
|
99
|
-
export {
|
|
100
|
-
getPlotConfig2 as getPlotConfig
|
|
101
|
-
};
|
|
102
|
-
//# sourceMappingURL=chunk-VJALVBYH.js.map
|
package/dist/chunk-W3DJIU4H.js
DELETED
|
@@ -1,102 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
addGeneSearchbox,
|
|
3
|
-
first_genetrack_tolist,
|
|
4
|
-
getDNAMethUnit,
|
|
5
|
-
sayerror
|
|
6
|
-
} from "./chunk-U45YALDI.js";
|
|
7
|
-
import {
|
|
8
|
-
Menu
|
|
9
|
-
} from "./chunk-CNFTQSNE.js";
|
|
10
|
-
import {
|
|
11
|
-
DNA_METHYLATION
|
|
12
|
-
} from "./chunk-WJLRU5OF.js";
|
|
13
|
-
|
|
14
|
-
// termdb/handlers/dnaMethylation.ts
|
|
15
|
-
var SearchHandler = class {
|
|
16
|
-
init(opts) {
|
|
17
|
-
this.opts = opts;
|
|
18
|
-
this.callback = opts.callback;
|
|
19
|
-
this.app = opts.app;
|
|
20
|
-
const holder = opts.holder.append("div").style("margin", "10px 0px");
|
|
21
|
-
this.dom = {};
|
|
22
|
-
this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
|
|
23
|
-
this.dom.geneSearchDiv = holder.append("div");
|
|
24
|
-
this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
|
|
25
|
-
const geneSearch = addGeneSearchbox({
|
|
26
|
-
tip: new Menu({ padding: "0px" }),
|
|
27
|
-
genome: opts.genomeObj,
|
|
28
|
-
row: this.dom.geneSearchDiv,
|
|
29
|
-
callback: async () => {
|
|
30
|
-
try {
|
|
31
|
-
this.dom.errDiv.style("display", "none");
|
|
32
|
-
await this.handleGeneSearch(geneSearch);
|
|
33
|
-
} catch (e) {
|
|
34
|
-
this.dom.errDiv.style("display", "block");
|
|
35
|
-
sayerror(this.dom.errDiv, "Error: " + (e.message || e));
|
|
36
|
-
if (e.stack) console.log(e.stack);
|
|
37
|
-
}
|
|
38
|
-
}
|
|
39
|
-
});
|
|
40
|
-
}
|
|
41
|
-
async handleGeneSearch(geneSearch) {
|
|
42
|
-
if (geneSearch.geneSymbol) {
|
|
43
|
-
const { chr, start, stop } = geneSearch;
|
|
44
|
-
if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
|
|
45
|
-
throw new Error("unable to retrieve gene coordinate");
|
|
46
|
-
this.dom.blockDiv.selectAll("*").remove();
|
|
47
|
-
this.dom.blockDiv.style("display", "block");
|
|
48
|
-
this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
|
|
49
|
-
const arg = {
|
|
50
|
-
holder: this.dom.blockDiv,
|
|
51
|
-
genome: this.opts.genomeObj,
|
|
52
|
-
// genome obj
|
|
53
|
-
chr,
|
|
54
|
-
start,
|
|
55
|
-
stop,
|
|
56
|
-
tklst: [],
|
|
57
|
-
nobox: true,
|
|
58
|
-
width: 500,
|
|
59
|
-
hidegenelegend: true,
|
|
60
|
-
debugmode: this.opts.debug
|
|
61
|
-
};
|
|
62
|
-
first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
|
|
63
|
-
const _ = await import("./block-LYSTIZKO.js");
|
|
64
|
-
this.blockInstance = new _.Block(arg);
|
|
65
|
-
this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
|
|
66
|
-
const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
|
|
67
|
-
const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
|
|
68
|
-
await this.callback(term);
|
|
69
|
-
});
|
|
70
|
-
} else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
|
|
71
|
-
const { chr } = geneSearch;
|
|
72
|
-
let { start, stop } = geneSearch;
|
|
73
|
-
if (geneSearch.actualposition?.len <= 1) {
|
|
74
|
-
start = geneSearch.actualposition.position;
|
|
75
|
-
stop = start + 1;
|
|
76
|
-
}
|
|
77
|
-
const term = this.makeTerm({ chr, start, stop });
|
|
78
|
-
await this.callback(term);
|
|
79
|
-
} else {
|
|
80
|
-
throw new Error("invalid gene search input");
|
|
81
|
-
}
|
|
82
|
-
}
|
|
83
|
-
makeTerm(opts) {
|
|
84
|
-
const { chr, start, stop } = opts;
|
|
85
|
-
if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
|
|
86
|
-
const unit = getDNAMethUnit("region", this.app.vocabApi);
|
|
87
|
-
const term = {
|
|
88
|
-
chr,
|
|
89
|
-
start,
|
|
90
|
-
stop,
|
|
91
|
-
type: DNA_METHYLATION,
|
|
92
|
-
unit,
|
|
93
|
-
genomicFeatureType: "region"
|
|
94
|
-
};
|
|
95
|
-
return term;
|
|
96
|
-
}
|
|
97
|
-
};
|
|
98
|
-
|
|
99
|
-
export {
|
|
100
|
-
SearchHandler
|
|
101
|
-
};
|
|
102
|
-
//# sourceMappingURL=chunk-W3DJIU4H.js.map
|
package/dist/chunk-W46Q37IZ.js
DELETED
|
@@ -1,141 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
skipPrevActionAbort,
|
|
3
|
-
storeInit
|
|
4
|
-
} from "./chunk-T3VFO5NA.js";
|
|
5
|
-
import {
|
|
6
|
-
recoverInit
|
|
7
|
-
} from "./chunk-4E2F26CC.js";
|
|
8
|
-
import {
|
|
9
|
-
AppBase,
|
|
10
|
-
sayerror,
|
|
11
|
-
vocabInit
|
|
12
|
-
} from "./chunk-U45YALDI.js";
|
|
13
|
-
import {
|
|
14
|
-
importPlot
|
|
15
|
-
} from "./chunk-KZXFNO75.js";
|
|
16
|
-
import {
|
|
17
|
-
Menu
|
|
18
|
-
} from "./chunk-CNFTQSNE.js";
|
|
19
|
-
import {
|
|
20
|
-
AppApi
|
|
21
|
-
} from "./chunk-HBNB5TRH.js";
|
|
22
|
-
|
|
23
|
-
// plots/plot.app.ts
|
|
24
|
-
var PlotApp = class _PlotApp extends AppBase {
|
|
25
|
-
constructor(opts, api) {
|
|
26
|
-
super(opts);
|
|
27
|
-
this.components = {};
|
|
28
|
-
this.wasDestroyed = false;
|
|
29
|
-
this.api = api;
|
|
30
|
-
this.type = _PlotApp.type;
|
|
31
|
-
this.dom = this.getDom(opts);
|
|
32
|
-
}
|
|
33
|
-
static {
|
|
34
|
-
this.type = "app";
|
|
35
|
-
}
|
|
36
|
-
getDom(opts) {
|
|
37
|
-
const dom = {
|
|
38
|
-
holder: opts.holder,
|
|
39
|
-
errdiv: opts.holder.append("div"),
|
|
40
|
-
plotDiv: opts.holder.append("div")
|
|
41
|
-
};
|
|
42
|
-
const controls = opts.violin?.mode == "minimal" ? null : opts.holder.append("div").style("white-space", "nowrap");
|
|
43
|
-
if (controls) {
|
|
44
|
-
dom.plotControls = controls.append("div").style("display", "inline-block");
|
|
45
|
-
dom.recoverControls = controls.append("div").style("display", "inline-block");
|
|
46
|
-
}
|
|
47
|
-
return dom;
|
|
48
|
-
}
|
|
49
|
-
async preApiFreeze(api) {
|
|
50
|
-
try {
|
|
51
|
-
api.tip = new Menu({ padding: "5px" });
|
|
52
|
-
api.printError = (e) => this.printError(e);
|
|
53
|
-
const vocab = this.opts.state.vocab;
|
|
54
|
-
api.vocabApi = this.opts.vocabApi ? this.opts.vocabApi : await vocabInit({
|
|
55
|
-
app: api,
|
|
56
|
-
state: {
|
|
57
|
-
vocab: {
|
|
58
|
-
// either (genome + dslabel) XOR (terms) can be undefined
|
|
59
|
-
genome: vocab?.genome || this.opts.state.genome,
|
|
60
|
-
dslabel: vocab?.dslabel || this.opts.state.dslabel,
|
|
61
|
-
terms: vocab?.terms
|
|
62
|
-
}
|
|
63
|
-
},
|
|
64
|
-
fetchOpts: this.opts.fetchOpts
|
|
65
|
-
});
|
|
66
|
-
this.opts.state.vocab = api.vocabApi.vocab;
|
|
67
|
-
} catch (e) {
|
|
68
|
-
console.log(`preApiFreeze error`, e);
|
|
69
|
-
throw e;
|
|
70
|
-
}
|
|
71
|
-
}
|
|
72
|
-
async init() {
|
|
73
|
-
try {
|
|
74
|
-
this.opts.state.nav = { header_mode: "hidden" };
|
|
75
|
-
this.store = await storeInit({ app: this.api, state: this.opts.state });
|
|
76
|
-
this.state = await this.store.copyState();
|
|
77
|
-
this.components = {
|
|
78
|
-
plots: {}
|
|
79
|
-
};
|
|
80
|
-
if (this.opts.app?.features?.includes("recover"))
|
|
81
|
-
this.components.recover = await recoverInit({
|
|
82
|
-
app: this.api,
|
|
83
|
-
holder: this.dom.recoverControls,
|
|
84
|
-
// TODO: ???? may limit the tracked state to only the filter, activeCohort ???
|
|
85
|
-
getState: (appState) => appState,
|
|
86
|
-
//reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',
|
|
87
|
-
maxHistoryLen: 10
|
|
88
|
-
});
|
|
89
|
-
if (this.opts.app?.doNotAwaitInitRender) {
|
|
90
|
-
this.api.dispatch();
|
|
91
|
-
} else {
|
|
92
|
-
await this.api.dispatch();
|
|
93
|
-
}
|
|
94
|
-
} catch (e) {
|
|
95
|
-
this.printError(e);
|
|
96
|
-
throw e;
|
|
97
|
-
}
|
|
98
|
-
}
|
|
99
|
-
async main() {
|
|
100
|
-
this.api.vocabApi.main();
|
|
101
|
-
for (const id in this.components.plots) {
|
|
102
|
-
const plot = this.components.plots[id];
|
|
103
|
-
if (!this.state.plots.find((p) => p.id === plot.id)) {
|
|
104
|
-
plot.destroy();
|
|
105
|
-
delete this.components.plots[id];
|
|
106
|
-
}
|
|
107
|
-
}
|
|
108
|
-
for (const plot of this.state.plots.values()) {
|
|
109
|
-
if (plot.parentId) continue;
|
|
110
|
-
if (!this.components.plots[plot.id]) {
|
|
111
|
-
const holder = this.opts?.app?.getPlotHolder ? this.opts.app.getPlotHolder(plot, this.dom.holder) : this.dom.holder.append("div");
|
|
112
|
-
if (!this.dom.plotDiv) this.dom.plotDiv = holder;
|
|
113
|
-
const { componentInit } = await importPlot(plot.chartType);
|
|
114
|
-
const plotApi = await componentInit({
|
|
115
|
-
id: plot.id,
|
|
116
|
-
app: this.api,
|
|
117
|
-
holder,
|
|
118
|
-
controls: this.dom.plotControls
|
|
119
|
-
});
|
|
120
|
-
this.components.plots[plot.id] = plotApi;
|
|
121
|
-
}
|
|
122
|
-
}
|
|
123
|
-
}
|
|
124
|
-
printError(e) {
|
|
125
|
-
sayerror(this.dom.errdiv, "Error: " + (e.message || e));
|
|
126
|
-
if (e.stack) console.log(e.stack);
|
|
127
|
-
this.bus.emit("error");
|
|
128
|
-
}
|
|
129
|
-
skipPrevActionAbort(action) {
|
|
130
|
-
return skipPrevActionAbort(action);
|
|
131
|
-
}
|
|
132
|
-
destroy() {
|
|
133
|
-
if (this.dom?.holder) this.dom.holder.selectAll("*").remove();
|
|
134
|
-
}
|
|
135
|
-
};
|
|
136
|
-
var appInit = AppApi.getInitFxn(PlotApp);
|
|
137
|
-
|
|
138
|
-
export {
|
|
139
|
-
appInit
|
|
140
|
-
};
|
|
141
|
-
//# sourceMappingURL=chunk-W46Q37IZ.js.map
|
package/dist/chunk-WHF2BXCF.js
DELETED
|
@@ -1,56 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
sayerror
|
|
3
|
-
} from "./chunk-U45YALDI.js";
|
|
4
|
-
import {
|
|
5
|
-
TermTypeGroups
|
|
6
|
-
} from "./chunk-WJLRU5OF.js";
|
|
7
|
-
|
|
8
|
-
// termdb/handlers/singleCellCellType.ts
|
|
9
|
-
var SearchHandler = class {
|
|
10
|
-
async init(opts) {
|
|
11
|
-
this.validateOpts(opts);
|
|
12
|
-
this.callback = opts.callback;
|
|
13
|
-
this.app = opts.app;
|
|
14
|
-
const holder = opts.holder.append("div").style("padding", "10px 0px");
|
|
15
|
-
const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
|
|
16
|
-
if (!scctTerms?.length) {
|
|
17
|
-
sayerror(
|
|
18
|
-
holder,
|
|
19
|
-
`termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
|
|
20
|
-
);
|
|
21
|
-
return;
|
|
22
|
-
}
|
|
23
|
-
const usecaseConfig = opts.usecase?.specialCase?.config;
|
|
24
|
-
const plots = usecaseConfig?.sample?.plots;
|
|
25
|
-
const isMeta = usecaseConfig?.sample?.isMetaResult;
|
|
26
|
-
const filtered = plots ? scctTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scctTerms.filter((t) => t.plot === usecaseConfig.name) : scctTerms;
|
|
27
|
-
const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
|
|
28
|
-
const filteredTerms = new Set(
|
|
29
|
-
plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
|
|
30
|
-
);
|
|
31
|
-
for (const t of Array.from(filteredTerms)) {
|
|
32
|
-
holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
|
|
33
|
-
const term = this.makeTerm(t, usecaseConfig);
|
|
34
|
-
this.callback(term);
|
|
35
|
-
});
|
|
36
|
-
}
|
|
37
|
-
}
|
|
38
|
-
makeTerm(_term, usecaseConfig) {
|
|
39
|
-
const term = { ..._term };
|
|
40
|
-
if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
|
|
41
|
-
return term;
|
|
42
|
-
}
|
|
43
|
-
validateOpts(opts) {
|
|
44
|
-
if (opts.callback == null) throw new Error("callback is required");
|
|
45
|
-
if (opts.app == null) throw new Error("app is required");
|
|
46
|
-
if (opts.holder == null) throw new Error("holder is required");
|
|
47
|
-
if (opts.usecase == null) throw new Error("usecase is required");
|
|
48
|
-
if (!opts.app.vocabApi.termdbConfig?.termType2terms)
|
|
49
|
-
throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
|
|
50
|
-
}
|
|
51
|
-
};
|
|
52
|
-
|
|
53
|
-
export {
|
|
54
|
-
SearchHandler
|
|
55
|
-
};
|
|
56
|
-
//# sourceMappingURL=chunk-WHF2BXCF.js.map
|