@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (977) hide show
  1. package/dist/2dmaf-BZWQ4YZF.js +1362 -0
  2. package/dist/AggMatrixInput-OXUENYYF.js +402 -0
  3. package/dist/AggregateMatrix-7PYLWY3X.js +37 -0
  4. package/dist/AppHeader-QOLLABH4.js +826 -0
  5. package/dist/BoxPlot-PDRYKWXF.js +1233 -0
  6. package/dist/CorrelationVolcano-Z3ABRHL6.js +613 -0
  7. package/dist/Cuminc-ATQT3KDO.js +1217 -0
  8. package/dist/DE-5LMMF5QB.js +85 -0
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  11. package/dist/DifferentialAnalysis-23WQKT6I.js +235 -0
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  18. package/dist/GeneExpInput-PW6HP5LO.js +38 -0
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  168. package/dist/condition-QROUALBG.js +323 -0
  169. package/dist/controls-GH37YWOP.js +30 -0
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  176. package/dist/dnaMethylation-2YU2HDD4.js +29 -0
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  849. /package/dist/{hierCluster-BJ5VBPXR.js.map → hierCluster-SU4BDK6I.js.map} +0 -0
  850. /package/dist/{hierCluster.config-4EERP4KK.js.map → hierCluster.config-4OZ65GKH.js.map} +0 -0
  851. /package/dist/{hierCluster.integration.spec-VR4GULRV.js.map → hierCluster.integration.spec-CHNSKZD4.js.map} +0 -0
  852. /package/dist/{hierCluster.interactivity-SMTQOKUY.js.map → hierCluster.interactivity-M72CEGCW.js.map} +0 -0
  853. /package/dist/{hierCluster.renderers-PAME7BWU.js.map → hierCluster.renderers-RM43G7ZR.js.map} +0 -0
  854. /package/dist/{imagePlot-4LMIKBVE.js.map → imagePlot-UYMWFNI4.js.map} +0 -0
  855. /package/dist/{importPlot-3CG6ASNH.js.map → importPlot-W3HPE4LZ.js.map} +0 -0
  856. /package/dist/{isoformExpression-VCDNKTZ6.js.map → isoformExpression-JEMJE5WY.js.map} +0 -0
  857. /package/dist/{isoformExpression.unit.spec-ZXYY37TA.js.map → isoformExpression.unit.spec-GOK5LFME.js.map} +0 -0
  858. /package/dist/{jspdf.es.min-V7ONHJJV.js.map → jspdf.es.min-KB3HW45U.js.map} +0 -0
  859. /package/dist/{junction-5DXJO4PS.js.map → junction-2X4AS47T.js.map} +0 -0
  860. /package/dist/{junction.customTerm-UOPUSEOE.js.map → junction.customTerm-MVSIUY66.js.map} +0 -0
  861. /package/dist/{junction.unit.spec-F35E3GJW.js.map → junction.unit.spec-HA74XQYV.js.map} +0 -0
  862. /package/dist/{launch.adhoc-V2HTCQGD.js.map → launch.adhoc-PZAJ6J2S.js.map} +0 -0
  863. /package/dist/{leftlabel.sample-V7O2EC36.js.map → leftlabel.sample-7BZKFB3I.js.map} +0 -0
  864. /package/dist/{lollipop-RNRZLG64.js.map → lollipop-URSFH4ZE.js.map} +0 -0
  865. /package/dist/{maf-W6SF6BJS.js.map → maf-CM3ETF4N.js.map} +0 -0
  866. /package/dist/{maftimeline-NABCAMHG.js.map → maftimeline-CRQEUTRY.js.map} +0 -0
  867. /package/dist/{matrix-JC6AJT2N.js.map → matrix-IBWB4A3Z.js.map} +0 -0
  868. /package/dist/{matrix-UCHESWVK.js.map → matrix-SOBGWBTY.js.map} +0 -0
  869. /package/dist/{matrix.cells-B4L42TBM.js.map → matrix.cells-GSKC6FXI.js.map} +0 -0
  870. /package/dist/{matrix.config-6US3AAH7.js.map → matrix.config-4KU5X3LQ.js.map} +0 -0
  871. /package/dist/{matrix.data-FYFXYDA3.js.map → matrix.data-XC2OTBTR.js.map} +0 -0
  872. /package/dist/{matrix.groups-Y7DEG3GS.js.map → matrix.groups-THXKRQSD.js.map} +0 -0
  873. /package/dist/{matrix.integration.spec-KXX7SFX5.js.map → matrix.integration.spec-GKHH4RSR.js.map} +0 -0
  874. /package/dist/{matrix.interactivity-NHWG4WCC.js.map → matrix.interactivity-ITXMM2ZP.js.map} +0 -0
  875. /package/dist/{matrix.layout-5DQNT7DD.js.map → matrix.layout-D6SRLAXS.js.map} +0 -0
  876. /package/dist/{matrix.legend-OY7IF6AS.js.map → matrix.legend-OWQAMHI2.js.map} +0 -0
  877. /package/dist/{matrix.renderers-GYOXGHPU.js.map → matrix.renderers-J66OAQUZ.js.map} +0 -0
  878. /package/dist/{matrix.serieses-657TLDAV.js.map → matrix.serieses-P5I4E2NB.js.map} +0 -0
  879. /package/dist/{matrix.sort-IMA2ES3T.js.map → matrix.sort-CXBXF75N.js.map} +0 -0
  880. /package/dist/{matrix.sort.unit.spec-S6BAFYPR.js.map → matrix.sort.unit.spec-RSXBKXC5.js.map} +0 -0
  881. /package/dist/{matrix.sorterUi-77F36Q5H.js.map → matrix.sorterUi-WEZRKU63.js.map} +0 -0
  882. /package/dist/{matrix.sorterUi.unit.spec-V5NVQGD5.js.map → matrix.sorterUi.unit.spec-6EULDV43.js.map} +0 -0
  883. /package/dist/{matrix.unit.spec-R4NMTZYQ.js.map → matrix.unit.spec-D4ZLDVDT.js.map} +0 -0
  884. /package/dist/{mds.fimo-5DCH5BEM.js.map → mds.fimo-CQFREH3A.js.map} +0 -0
  885. /package/dist/{mds.samplescatterplot-VIBCS5M6.js.map → mds.samplescatterplot-XLJITURG.js.map} +0 -0
  886. /package/dist/{mds.survivalplot-AZ7LJDZZ.js.map → mds.survivalplot-MLRD27QP.js.map} +0 -0
  887. /package/dist/{multivalue-4QKGYYW2.js.map → multivalue-KJQCYBHA.js.map} +0 -0
  888. /package/dist/{numericDictTermCluster-GLLG6IK2.js.map → numericDictTermCluster-ZOU6R4XP.js.map} +0 -0
  889. /package/dist/{oncomatrix-R32ZPMX7.js.map → oncomatrix-4RHDDJDC.js.map} +0 -0
  890. /package/dist/{oncomatrix.spec-BMK6LMBS.js.map → oncomatrix.spec-JA6DT4PP.js.map} +0 -0
  891. /package/dist/{plot.2dvaf-46FT53MF.js.map → plot.2dvaf-VJWPWCOY.js.map} +0 -0
  892. /package/dist/{plot.app-7EE4YCV4.js.map → plot.app-JNEOGNVW.js.map} +0 -0
  893. /package/dist/{plot.barplot-FK4J2G7K.js.map → plot.barplot-YELRBXUB.js.map} +0 -0
  894. /package/dist/{plot.boxplot-ATY4LK3X.js.map → plot.boxplot-HNFOB3TV.js.map} +0 -0
  895. /package/dist/{plot.brainImaging-S7B547V4.js.map → plot.brainImaging-AZYEGF3U.js.map} +0 -0
  896. /package/dist/{plot.disco-K5MMC2GD.js.map → plot.disco-L6PGGZJI.js.map} +0 -0
  897. /package/dist/{plot.ssgq-B3OVMZFD.js.map → plot.ssgq-UM64SSXW.js.map} +0 -0
  898. /package/dist/{plot.vaf2cov-RBHDQULW.js.map → plot.vaf2cov-DKUKJRUP.js.map} +0 -0
  899. /package/dist/{polar2-GECELCTG.js.map → polar2-4YHPENAV.js.map} +0 -0
  900. /package/dist/{profileForms-2USYOA34.js.map → profileForms-KMECFO3K.js.map} +0 -0
  901. /package/dist/{profilePlot-YGD2CF6P.js.map → profilePlot-3AXSIXCK.js.map} +0 -0
  902. /package/dist/{proteinView-FCPWJLGU.js.map → proteinView-QWHOTL35.js.map} +0 -0
  903. /package/dist/{proteomeCohortCompare-TYYUF5A5.js.map → proteomeCohortCompare-DL2QLFL3.js.map} +0 -0
  904. /package/dist/{pseudbulk.unit.spec-UVVRP6NR.js.map → pseudbulk.unit.spec-IWR7EZ7O.js.map} +0 -0
  905. /package/dist/{pseudobulk-ZIN5VJGB.js.map → pseudobulk-IC525IZ2.js.map} +0 -0
  906. /package/dist/{qualitative-27BZGASV.js.map → qualitative-LK2QEYHU.js.map} +0 -0
  907. /package/dist/{qualitative-N4F6NITI.js.map → qualitative-YY4NQGO5.js.map} +0 -0
  908. /package/dist/{radar2-X465RPJX.js.map → radar2-TJUPENQF.js.map} +0 -0
  909. /package/dist/{radarFacility2-AE7BA62N.js.map → radarFacility2-Q7LBWLCV.js.map} +0 -0
  910. /package/dist/{rememberedGvQ.unit.spec-4PDIU5RY.js.map → rememberedGvQ.unit.spec-2GBLM5AO.js.map} +0 -0
  911. /package/dist/{render-TD2QWOHT.js.map → render-AHR6SCQX.js.map} +0 -0
  912. /package/dist/{report-3Y2OWDF7.js.map → report-BPHJTRTO.js.map} +0 -0
  913. /package/dist/{sampleView-BUMMYRHJ.js.map → sampleView-CS2FB3K3.js.map} +0 -0
  914. /package/dist/{samplelst-BWK53BLI.js.map → samplelst-A3DHKP6U.js.map} +0 -0
  915. /package/dist/{samplematrix-RQU43UYR.js.map → samplematrix-5X7MFT3G.js.map} +0 -0
  916. /package/dist/{sc-LCBFWCZZ.js.map → sc-RCYXZMN6.js.map} +0 -0
  917. /package/dist/{scatter-6S5I7OW3.js.map → scatter-2ITGMX5N.js.map} +0 -0
  918. /package/dist/{scatter-MJELX75N.js.map → scatter-OAL4YOCA.js.map} +0 -0
  919. /package/dist/{selectGenomeWithTklst-WAVXHXR5.js.map → selectGenomeWithTklst-PB5KDW2N.js.map} +0 -0
  920. /package/dist/{singleCellCellType-WMCAJ7JF.js.map → singleCellCellType-FEFNOHOP.js.map} +0 -0
  921. /package/dist/{singleCellCellType.unit.spec-4Z46ZT5Q.js.map → singleCellCellType.unit.spec-V2I32V23.js.map} +0 -0
  922. /package/dist/{singleCellGeneExpression-7Q5ZJT4R.js.map → singleCellGeneExpression-RUQQMKDE.js.map} +0 -0
  923. /package/dist/{singleCellGeneExpression.unit.spec-6C7PDGRH.js.map → singleCellGeneExpression.unit.spec-VCMJRMT7.js.map} +0 -0
  924. /package/dist/{singleCellNumericValue-QGYITZRC.js.map → singleCellNumericValue-JLXZQWNT.js.map} +0 -0
  925. /package/dist/{singleCellNumericValue.unit.spec-MQUKPEZJ.js.map → singleCellNumericValue.unit.spec-XVCZEN5K.js.map} +0 -0
  926. /package/dist/{singleCellPlot-JJMFJ2KQ.js.map → singleCellPlot-4EBYWOJ2.js.map} +0 -0
  927. /package/dist/{singlecell-J23S3JR2.js.map → singlecell-UKZJAYVH.js.map} +0 -0
  928. /package/dist/{singlecell-Y4OGUWEC.js.map → singlecell-VNRWPXGV.js.map} +0 -0
  929. /package/dist/{snp-IO6TKWGD.js.map → snp-2RJDJQZC.js.map} +0 -0
  930. /package/dist/{snp.unit.spec-X7ILEEPO.js.map → snp.unit.spec-Z4DNBFAH.js.map} +0 -0
  931. /package/dist/{snplocus-Z2NGIKMO.js.map → snplocus-OZLIZ7R7.js.map} +0 -0
  932. /package/dist/{snplst-XCS2FCQV.js.map → snplst-EVRJ4OCL.js.map} +0 -0
  933. /package/dist/{spliceevent.a53ss.diagram-F3S4BRVG.js.map → spliceevent.a53ss.diagram-N5UXX4OX.js.map} +0 -0
  934. /package/dist/{spliceevent.exonskip.diagram-AXCDJKH4.js.map → spliceevent.exonskip.diagram-WBNFLW4V.js.map} +0 -0
  935. /package/dist/{spliceevent.noeventdiagram-UK3X667E.js.map → spliceevent.noeventdiagram-EI72A6L3.js.map} +0 -0
  936. /package/dist/{ssGSEA-ZRPNQKJ5.js.map → ssGSEA-NONMMNF7.js.map} +0 -0
  937. /package/dist/{ssGSEA.unit.spec-DG5ZHLC7.js.map → ssGSEA.unit.spec-7JDPNLZA.js.map} +0 -0
  938. /package/dist/{stattable-XYSC3CYU.js.map → stattable-NNUHKPF4.js.map} +0 -0
  939. /package/dist/{studyCatalog-Y75LMI62.js.map → studyCatalog-KMLE7Q55.js.map} +0 -0
  940. /package/dist/{summarizeCnvGeneexp-H2NP7VLU.js.map → summarizeCnvGeneexp-AHCGPQLE.js.map} +0 -0
  941. /package/dist/{summarizeGeneexpSurvival-HTCD3VQQ.js.map → summarizeGeneexpSurvival-NCST7HDQ.js.map} +0 -0
  942. /package/dist/{summarizeMutationCnv-UEGXWK2P.js.map → summarizeMutationCnv-VUTQYXO6.js.map} +0 -0
  943. /package/dist/{summarizeMutationDiagnosis-MJGWP7IT.js.map → summarizeMutationDiagnosis-TFU2HUHQ.js.map} +0 -0
  944. /package/dist/{summarizeMutationSurvival-55JW5LA6.js.map → summarizeMutationSurvival-F4CJILS3.js.map} +0 -0
  945. /package/dist/{summary-HJO23RGB.js.map → summary-QQZW7BEE.js.map} +0 -0
  946. /package/dist/{summary.integration.spec-OWI2C2N5.js.map → summary.integration.spec-FILIPD3W.js.map} +0 -0
  947. /package/dist/{summaryInput-RL2JXRDE.js.map → summaryInput-RMY226Y3.js.map} +0 -0
  948. /package/dist/{sunburst-JFY6V5E2.js.map → sunburst-Y4LNCKMR.js.map} +0 -0
  949. /package/dist/{survival-PBBU6PA5.js.map → survival-4FYQHQHX.js.map} +0 -0
  950. /package/dist/{survival-6FLR4YCJ.js.map → survival-6GC267GY.js.map} +0 -0
  951. /package/dist/{survival.integration.spec-WAKTGYGP.js.map → survival.integration.spec-5ERXR6MG.js.map} +0 -0
  952. /package/dist/{svg2pdf.es.min-NIFE2BIE.js.map → svg2pdf.es.min-KKHWPFWG.js.map} +0 -0
  953. /package/dist/{svgraph-WD3DUZV7.js.map → svgraph-XIQIA7OJ.js.map} +0 -0
  954. /package/dist/{swimmer-VPKSBV6V.js.map → swimmer-643B5Q6F.js.map} +0 -0
  955. /package/dist/{table-GX3VJLPZ.js.map → table-JQIBRXTJ.js.map} +0 -0
  956. /package/dist/{termCollection-YQ332WKB.js.map → termCollection-LU5NW6KT.js.map} +0 -0
  957. /package/dist/{termCollection-QE7U5QBD.js.map → termCollection-XZCPBXRV.js.map} +0 -0
  958. /package/dist/{termCollection.unit.spec-ELLN7VRA.js.map → termCollection.unit.spec-H5LBV3N4.js.map} +0 -0
  959. /package/dist/{termCollectionFractionSelection-V3RP5KAT.js.map → termCollectionFractionSelection-3YHOFXEL.js.map} +0 -0
  960. /package/dist/{termCollectionFractionSelection.unit.spec-JR7Q7TJI.js.map → termCollectionFractionSelection.unit.spec-G5X3Y5YI.js.map} +0 -0
  961. /package/dist/{tk-J5VPFEX6.js.map → tk-NPWNBXLB.js.map} +0 -0
  962. /package/dist/{tk-GD2KJM5W.js.map → tk-YSW5NPW2.js.map} +0 -0
  963. /package/dist/{tvs.categorical-RPACB4VU.js.map → tvs.categorical-TUX6KRZI.js.map} +0 -0
  964. /package/dist/{tvs.condition-O6JBUM6D.js.map → tvs.condition-2CH25PLO.js.map} +0 -0
  965. /package/dist/{tvs.dt-5EVBSRX3.js.map → tvs.dt-YKP3F75O.js.map} +0 -0
  966. /package/dist/{tvs.dtcnv.categorical-Y5YHBZNC.js.map → tvs.dtcnv.categorical-QBJWJNHZ.js.map} +0 -0
  967. /package/dist/{tvs.dtcnv.continuous-WP322QUP.js.map → tvs.dtcnv.continuous-MV25OLBD.js.map} +0 -0
  968. /package/dist/{tvs.dtfusion-CCMUFDMQ.js.map → tvs.dtfusion-SJ64HNKE.js.map} +0 -0
  969. /package/dist/{tvs.dtitd-P3ED3MWA.js.map → tvs.dtitd-WQLHZK2P.js.map} +0 -0
  970. /package/dist/{tvs.dtsnvindel-X2MXPLC6.js.map → tvs.dtsnvindel-WMFJ7W7U.js.map} +0 -0
  971. /package/dist/{tvs.dtsv-4FOWFNVV.js.map → tvs.dtsv-GKEC5OGA.js.map} +0 -0
  972. /package/dist/{tvs.multivalue-IRF467ZK.js.map → tvs.multivalue-LFWMQETN.js.map} +0 -0
  973. /package/dist/{tvs.numeric-C7FDCGCS.js.map → tvs.numeric-63NVZG7U.js.map} +0 -0
  974. /package/dist/{tvs.samplelst-CBU6ATI5.js.map → tvs.samplelst-DEMMYRKK.js.map} +0 -0
  975. /package/dist/{tvs.survival-3K5ASAXV.js.map → tvs.survival-M4QUVP5L.js.map} +0 -0
  976. /package/dist/{tvs.termCollection-MXEWO6KJ.js.map → tvs.termCollection-J367GZY3.js.map} +0 -0
  977. /package/dist/{vocabulary-GQBHDP3K.js.map → vocabulary-RAVWS5IS.js.map} +0 -0
@@ -0,0 +1,80 @@
1
+ import {
2
+ addGeneSearchbox,
3
+ getGEunit,
4
+ getSampleTypeLabelByTerms,
5
+ getSelectedSampleTypes,
6
+ getSelectedSampleTypesByTerms,
7
+ renderSampleTypeSelect,
8
+ renderSampleTypesByTermsSelect,
9
+ table2col
10
+ } from "./chunk-YS7Y257H.js";
11
+ import {
12
+ Menu
13
+ } from "./chunk-CNFTQSNE.js";
14
+ import {
15
+ TermTypes
16
+ } from "./chunk-LMG7Y5IN.js";
17
+
18
+ // termdb/handlers/geneExpression.ts
19
+ var SearchHandler = class {
20
+ init(opts) {
21
+ this.callback = opts.callback;
22
+ this.app = opts.app;
23
+ this.dom = {};
24
+ const holder = opts.holder.append("div").style("padding", "10px 0px");
25
+ this.dom.sampleTypeDiv = holder.append("div");
26
+ this.mayRenderSampleTypeSelect();
27
+ const geneSearch = addGeneSearchbox({
28
+ tip: new Menu({ padding: "0px" }),
29
+ genome: opts.genomeObj,
30
+ row: holder,
31
+ searchOnly: "gene",
32
+ callback: () => this.selectGene(geneSearch)
33
+ });
34
+ holder.select(".sja_genesearchinput").style("margin", "0px");
35
+ }
36
+ mayRenderSampleTypeSelect() {
37
+ this.dom.sampleTypeDiv.selectAll("*").remove();
38
+ this.querySampleTypes = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypes;
39
+ this.querySampleTypesByTerms = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypesByTerms;
40
+ if (Array.isArray(this.querySampleTypes) && this.querySampleTypes.length >= 2 || this.querySampleTypesByTerms) {
41
+ const table = table2col({ holder: this.dom.sampleTypeDiv, margin: "0px 0px 15px 0px" });
42
+ const [td1, td2] = table.addRow();
43
+ td1.text("Sample Type");
44
+ td2.style("padding-left", "10px");
45
+ if (this.querySampleTypesByTerms) {
46
+ this.sampleTypeSelect = renderSampleTypesByTermsSelect(
47
+ td2,
48
+ this.querySampleTypesByTerms,
49
+ this.app.vocabApi.termdbConfig
50
+ );
51
+ } else {
52
+ this.sampleTypeSelect = renderSampleTypeSelect(td2, this.querySampleTypes, this.app.vocabApi.termdbConfig);
53
+ }
54
+ }
55
+ }
56
+ async selectGene(geneSearch) {
57
+ const gene = geneSearch?.geneSymbol;
58
+ if (!gene) throw new Error("No gene selected");
59
+ const sampleTypes = this.querySampleTypesByTerms ? getSelectedSampleTypesByTerms(this.sampleTypeSelect, this.querySampleTypesByTerms) : getSelectedSampleTypes(this.sampleTypeSelect) || this.querySampleTypes;
60
+ if (this.sampleTypeSelect && !sampleTypes?.length) {
61
+ return;
62
+ }
63
+ const unit = getGEunit(this.app.vocabApi);
64
+ const name = `${gene} ${unit}`;
65
+ const term = { gene, name, type: TermTypes.GENE_EXPRESSION, sampleTypes };
66
+ if (this.querySampleTypesByTerms) {
67
+ const sampleTypeLabel = getSampleTypeLabelByTerms(this.sampleTypeSelect);
68
+ if (sampleTypeLabel) {
69
+ term.sampleTypeLabel = sampleTypeLabel;
70
+ term.name += ` (${sampleTypeLabel})`;
71
+ }
72
+ }
73
+ this.callback(term);
74
+ }
75
+ };
76
+
77
+ export {
78
+ SearchHandler
79
+ };
80
+ //# sourceMappingURL=chunk-HKXBGMUT.js.map
@@ -0,0 +1,38 @@
1
+ import {
2
+ plotColor
3
+ } from "./chunk-LMG7Y5IN.js";
4
+
5
+ // plots/violin/settings/defaults.ts
6
+ function getDefaultViolinSettings(app, overrides = {}) {
7
+ const defaults = {
8
+ orientation: "horizontal",
9
+ rowlabelw: 250,
10
+ brushRange: null,
11
+ //object with start and end if there is a brush selection
12
+ svgw: 500,
13
+ // span length of a plot/svg, not including margin
14
+ datasymbol: "rug",
15
+ radius: 10,
16
+ axisHeight: 60,
17
+ rightMargin: 50,
18
+ lines: [],
19
+ isLogScale: false,
20
+ // false: linear scale, true: log scale
21
+ rowSpace: 10,
22
+ medianLength: 7,
23
+ medianColor: "#FF0000",
24
+ medianThickness: 3,
25
+ ticks: 15,
26
+ defaultColor: plotColor,
27
+ method: 0,
28
+ orderByMedian: false,
29
+ showStats: true,
30
+ showAssociationTests: true
31
+ };
32
+ return Object.assign(defaults, overrides);
33
+ }
34
+
35
+ export {
36
+ getDefaultViolinSettings
37
+ };
38
+ //# sourceMappingURL=chunk-HNMKK33Y.js.map
@@ -0,0 +1,480 @@
1
+ import {
2
+ renderTable
3
+ } from "./chunk-YS7Y257H.js";
4
+ import {
5
+ clusterMethodLst,
6
+ distanceMethodLst
7
+ } from "./chunk-XJYVMXMZ.js";
8
+ import {
9
+ termType2label
10
+ } from "./chunk-ET2KFCXK.js";
11
+ import {
12
+ select_default
13
+ } from "./chunk-I6Y4O3RR.js";
14
+ import {
15
+ __export
16
+ } from "./chunk-HS5PO5ZQ.js";
17
+
18
+ // plots/matrix/hierCluster.interactivity.js
19
+ var hierCluster_interactivity_exports = {};
20
+ __export(hierCluster_interactivity_exports, {
21
+ addSelectedRowsOptions: () => addSelectedRowsOptions,
22
+ addSelectedSamplesOptions: () => addSelectedSamplesOptions,
23
+ getAllChildrenClusterIds: () => getAllChildrenClusterIds,
24
+ getClusterFromLeftDendrogram: () => getClusterFromLeftDendrogram,
25
+ getClusterFromTopDendrogram: () => getClusterFromTopDendrogram,
26
+ setClusteringBtn: () => setClusteringBtn,
27
+ showTable4selectedRows: () => showTable4selectedRows,
28
+ showTable4selectedSamples: () => showTable4selectedSamples,
29
+ triggerZoomBranch: () => triggerZoomBranch
30
+ });
31
+ function getAllChildrenClusterIds(clickedClusterId, left) {
32
+ const mergedClusters = left ? this.hierClusterData.clustering.row.mergedClusters : this.hierClusterData.clustering.col.mergedClusters;
33
+ const children = mergedClusters.get(clickedClusterId).childrenClusters || [];
34
+ let allChildren = [...children];
35
+ for (const child of children) {
36
+ allChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left));
37
+ }
38
+ return allChildren;
39
+ }
40
+ function addSelectedSamplesOptions(clickedSampleNames, event) {
41
+ const l = this.settings.matrix.controlLabels;
42
+ const ss = this.opts.allow2selectSamples;
43
+ const optionArr = [
44
+ {
45
+ label: "Zoom in",
46
+ callback: () => {
47
+ this.triggerZoomBranch(this, clickedSampleNames);
48
+ }
49
+ },
50
+ {
51
+ label: `List ${clickedSampleNames.length} ${l.samples}`,
52
+ callback: () => this.showTable4selectedSamples(clickedSampleNames)
53
+ }
54
+ ];
55
+ if (ss) {
56
+ optionArr.push({
57
+ label: ss.buttonText || `Select ${l.samples}`,
58
+ callback: async () => {
59
+ const samples = clickedSampleNames.map((c) => this.data.samples[c]);
60
+ ss.callback({
61
+ samples: await this.app.vocabApi.convertSampleId(samples, ss.attributes),
62
+ source: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`
63
+ });
64
+ }
65
+ });
66
+ } else {
67
+ if (this.state.nav && this.state.nav.header_mode !== "hidden") {
68
+ const samples = clickedSampleNames.map((c) => this.sampleOrder.find((s) => s.row.sample == c).row);
69
+ for (const s of samples) {
70
+ if (!s.sampleId) s.sampleId = s.sample;
71
+ }
72
+ optionArr.push({
73
+ label: "Add to a group",
74
+ callback: async () => {
75
+ const group = {
76
+ name: "Group",
77
+ items: samples
78
+ };
79
+ this.addGroup(group);
80
+ }
81
+ });
82
+ }
83
+ }
84
+ this.mouseout();
85
+ this.dom.tip.hide();
86
+ this.dom.dendroClickMenu.d.selectAll("*").remove();
87
+ this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", "sja_menuoption").style("border-radius", "0px").html((d) => d.label).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
88
+ this.dom.dendroClickMenu.d.selectAll("*").remove();
89
+ event2.target.__data__.callback();
90
+ });
91
+ this.dom.dendroClickMenu.show(event.clientX, event.clientY);
92
+ }
93
+ function addSelectedRowsOptions(clickedRowNames, event) {
94
+ const rowType = this.config.settings.matrix.controlLabels.terms;
95
+ const optionArr = [
96
+ {
97
+ label: `List ${clickedRowNames.length} ${rowType}`,
98
+ callback: () => this.showTable4selectedRows(clickedRowNames, rowType)
99
+ }
100
+ ];
101
+ if (this.config.dataType == "geneExpression" && this.app.opts.genome.termdbs) {
102
+ const minGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.minCutoff;
103
+ const maxGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.maxCutoff;
104
+ optionArr.push({
105
+ label: `Gene set overrepresentation analysis`,
106
+ disabled: clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff,
107
+ callback: () => {
108
+ if (clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff) return;
109
+ this.dom.dendroClickMenu.d.selectAll("*").remove();
110
+ const lst = [];
111
+ for (const x of clickedRowNames) {
112
+ const j = this.terms?.find?.((t) => t.tw.$id == x);
113
+ if (j) {
114
+ const n = j.tw?.term?.gene;
115
+ if (n) lst.push(n);
116
+ }
117
+ }
118
+ const config = {
119
+ chartType: "geneORA",
120
+ geneORAparams: {
121
+ sample_genes: lst.join(","),
122
+ genome: this.app.vocabApi.opts.state.vocab.genome
123
+ }
124
+ };
125
+ this.app.dispatch({
126
+ type: "plot_create",
127
+ config
128
+ });
129
+ }
130
+ });
131
+ }
132
+ this.mouseout();
133
+ this.dom.tip.hide();
134
+ this.dom.dendroClickMenu.d.selectAll("*").remove();
135
+ this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", (d) => d.disabled ? "sja_menuoption_not_interactive" : "sja_menuoption").style("opacity", (d) => d.disabled ? 0.5 : 1).style("border-radius", "0px").html(
136
+ (d) => d.disabled ? `${d.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>` : d.label
137
+ ).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
138
+ if (event2.target.__data__?.callback) event2.target.__data__.callback();
139
+ });
140
+ this.dom.dendroClickMenu.show(event.clientX, event.clientY);
141
+ }
142
+ function triggerZoomBranch(self, clickedSampleNames) {
143
+ if (self.zoomArea) {
144
+ self.zoomArea.remove();
145
+ delete self.zoomArea;
146
+ }
147
+ const c = {
148
+ startCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[0]),
149
+ endCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[clickedSampleNames.length - 1])
150
+ };
151
+ const s = self.settings.matrix;
152
+ const d = self.dimensions;
153
+ const start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell;
154
+ const zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2);
155
+ const centerCell = self.sampleOrder[zoomIndex];
156
+ const colw = self.computedSettings.colw || self.settings.matrix.colw;
157
+ const maxZoomLevel = s.colwMax / colw;
158
+ const minZoomLevel = s.colwMin / colw;
159
+ const tentativeZoomLevel = Math.max(
160
+ 1,
161
+ s.zoomLevel * d.mainw / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw) * 0.7
162
+ );
163
+ const zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel));
164
+ self.app.dispatch({
165
+ type: "plot_edit",
166
+ id: self.id,
167
+ config: {
168
+ settings: {
169
+ matrix: {
170
+ zoomLevel,
171
+ zoomCenterPct: 0.5,
172
+ //zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,
173
+ zoomIndex,
174
+ zoomGrpIndex: centerCell.grpIndex
175
+ }
176
+ }
177
+ }
178
+ });
179
+ self.resetInteractions();
180
+ }
181
+ function showTable4selectedSamples(clickedSampleNames) {
182
+ const templates = this.state.termdbConfig.urlTemplates;
183
+ const rows = templates?.sample ? clickedSampleNames.map((c) => [
184
+ { value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }
185
+ ]) : clickedSampleNames.map((c) => [{ value: this.hierClusterData.bySampleId[c].label }]);
186
+ const columns = [{ label: this.settings.matrix.controlLabels.Sample }];
187
+ renderTable({
188
+ rows,
189
+ columns,
190
+ div: this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px"),
191
+ showLines: true,
192
+ maxHeight: "35vh",
193
+ resize: true
194
+ });
195
+ }
196
+ function showTable4selectedRows(clickedRowNames, rowType) {
197
+ const templates = this.state.termdbConfig.urlTemplates;
198
+ const rows = [];
199
+ if (templates?.gene && this.config.dataType == "geneExpression" && this.hierClusterData.byTermId) {
200
+ for (const i of clickedRowNames) {
201
+ const genesymbol = this.terms.find((t) => t.tw?.$id == i)?.tw?.term?.gene;
202
+ if (!genesymbol) continue;
203
+ const gencode = this.hierClusterData.byTermId[i]?.gencodeId;
204
+ if (gencode) {
205
+ rows.push([{ value: genesymbol, url: `${templates.gene.base}${gencode}` }]);
206
+ } else {
207
+ rows.push([{ value: genesymbol }]);
208
+ }
209
+ }
210
+ } else {
211
+ for (const i of clickedRowNames) {
212
+ const tw = this.terms.find((t) => t.tw?.$id == i)?.tw;
213
+ if (!tw) continue;
214
+ const n = tw.term?.gene || tw.term?.name;
215
+ if (!n) continue;
216
+ rows.push([{ value: n }]);
217
+ }
218
+ }
219
+ const div = this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px");
220
+ const buttonDiv = div.append("div").style("padding", "5px");
221
+ const copyButton = buttonDiv.append("button").html(`Copy ${rowType}`).attr("class", ".sja_menu_div button").style("margin-top", "2px").style("padding", "5px").on("click", () => {
222
+ const geneNames = rows.map((row) => row[0].value).join("\n");
223
+ navigator.clipboard.writeText(geneNames).then(() => {
224
+ }, console.warn);
225
+ copyButton.html(`Copy ${rowType}&nbsp;&check;`);
226
+ });
227
+ renderTable({
228
+ rows,
229
+ columns: [{ label: rowType }],
230
+ div: div.append("div"),
231
+ showLines: true,
232
+ maxHeight: "35vh",
233
+ resize: true
234
+ });
235
+ }
236
+ function getClusterFromTopDendrogram(event) {
237
+ if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
238
+ else return;
239
+ const y = event.clientY - this.imgBox.y - event.target.clientTop;
240
+ const xMin = this.dimensions.xMin;
241
+ const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
242
+ for (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {
243
+ const { x1, y1, x2, y2, clusterY } = cluster.clusterPosition;
244
+ if (x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5 || clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5 || clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5) {
245
+ return clusterId;
246
+ }
247
+ }
248
+ }
249
+ function getClusterFromLeftDendrogram(event) {
250
+ if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
251
+ else return;
252
+ const y = event.clientY - this.imgBox.y - event.target.clientTop;
253
+ const xMin = this.dimensions.xMin;
254
+ const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
255
+ for (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {
256
+ const { x1, y1, x2, y2, clusterX } = cluster.clusterPosition;
257
+ if (y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5 || clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5 || clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5) {
258
+ return clusterId;
259
+ }
260
+ }
261
+ }
262
+ function setClusteringBtn(holder, callback) {
263
+ const cl = this.config.settings.matrix.controlLabels;
264
+ const dataType = this.config.dataType;
265
+ const clusterRowLabel = cl.Terms;
266
+ const cluteringButtonLabel = `${termType2label(dataType)} Clustering`;
267
+ holder.append("button").datum({
268
+ label: cluteringButtonLabel,
269
+ getCount: () => this.hcTermGroup?.lst.length || 0,
270
+ showCount: "hide",
271
+ rows: [
272
+ {
273
+ label: `Cluster ${cl.Samples}`,
274
+ title: `Option to enable ${cl.samples} clustering, instead of enabling ${cl.samples} sorting.`,
275
+ type: "checkbox",
276
+ chartType: "hierCluster",
277
+ settingsKey: "clusterSamples",
278
+ boxLabel: `Cluster ${cl.Samples} (Disable ${cl.Samples} Sorting)`,
279
+ callback: (checked) => {
280
+ if (!checked) {
281
+ this.config.settings.hierCluster.yDendrogramHeight = 0;
282
+ this.config.settings.hierCluster.clusterSamples = false;
283
+ } else {
284
+ this.config.divideBy = null;
285
+ this.config.settings.hierCluster.yDendrogramHeight = 200;
286
+ this.config.settings.hierCluster.clusterSamples = true;
287
+ }
288
+ this.app.dispatch({
289
+ type: "plot_edit",
290
+ id: this.id,
291
+ config: this.config
292
+ });
293
+ }
294
+ },
295
+ {
296
+ label: `Cluster ${clusterRowLabel}`,
297
+ title: `Option to enable ${clusterRowLabel} clustering, instead of enabling ${clusterRowLabel} sorting.`,
298
+ type: "checkbox",
299
+ chartType: "hierCluster",
300
+ settingsKey: "clusterRows",
301
+ boxLabel: `Cluster ${clusterRowLabel} (Disable ${clusterRowLabel} Sorting)`,
302
+ callback: (checked) => {
303
+ if (!checked) {
304
+ this.config.settings.hierCluster.clusterRows = false;
305
+ this.config.settings.hierCluster.sortClusterRows = "asListed";
306
+ } else {
307
+ this.config.settings.hierCluster.clusterRows = true;
308
+ this.config.settings.hierCluster.sortClusterRows = void 0;
309
+ }
310
+ this.app.dispatch({
311
+ type: "plot_edit",
312
+ id: this.id,
313
+ config: this.config
314
+ });
315
+ }
316
+ },
317
+ {
318
+ label: `Sort ${clusterRowLabel}`,
319
+ title: `Set how to order the ${clusterRowLabel} as rows`,
320
+ type: "radio",
321
+ chartType: "hierCluster",
322
+ settingsKey: "sortClusterRows",
323
+ options: [
324
+ { label: `By input ${clusterRowLabel} order`, value: "asListed" },
325
+ { label: `By ${clusterRowLabel} name`, value: "byName" }
326
+ ],
327
+ styles: { padding: 0, "padding-right": "10px", margin: 0, display: "inline-block" },
328
+ getDisplayStyle(plot) {
329
+ return plot.settings.hierCluster.clusterRows ? "none" : "table-row";
330
+ }
331
+ },
332
+ {
333
+ label: "Z-score Transformation",
334
+ title: `Option to do Z-score transformation`,
335
+ type: "checkbox",
336
+ chartType: "hierCluster",
337
+ settingsKey: "zScoreTransformation",
338
+ boxLabel: `Perform Z-score Transformation`,
339
+ callback: (checked) => {
340
+ if (!checked) {
341
+ this.config.settings.hierCluster.zScoreTransformation = false;
342
+ this.config.settings.hierCluster.colorScale = "whiteRed";
343
+ } else {
344
+ this.config.settings.hierCluster.zScoreTransformation = true;
345
+ this.config.settings.hierCluster.colorScale = "blueWhiteRed";
346
+ }
347
+ this.app.dispatch({
348
+ type: "plot_edit",
349
+ id: this.id,
350
+ config: this.config
351
+ });
352
+ }
353
+ },
354
+ {
355
+ label: `Clustering Method`,
356
+ title: `Sets which clustering method to use`,
357
+ type: "radio",
358
+ chartType: "hierCluster",
359
+ settingsKey: "clusterMethod",
360
+ options: clusterMethodLst
361
+ },
362
+ {
363
+ label: `Distance Method`,
364
+ title: `Sets which distance method to use for clustering`,
365
+ type: "radio",
366
+ chartType: "hierCluster",
367
+ settingsKey: "distanceMethod",
368
+ options: distanceMethodLst
369
+ },
370
+ {
371
+ label: `Column Dendrogram Height`,
372
+ title: `The maximum height to render the column dendrogram`,
373
+ type: "number",
374
+ chartType: "hierCluster",
375
+ settingsKey: "yDendrogramHeight",
376
+ getDisplayStyle(plot) {
377
+ return plot.settings.hierCluster.clusterSamples ? "table-row" : "none";
378
+ }
379
+ },
380
+ {
381
+ label: `Row Dendrogram Width`,
382
+ title: `The maximum width to render the row dendrogram`,
383
+ type: "number",
384
+ chartType: "hierCluster",
385
+ settingsKey: "xDendrogramHeight",
386
+ getDisplayStyle(plot) {
387
+ return plot.settings.hierCluster.clusterRows ? "table-row" : "none";
388
+ }
389
+ },
390
+ {
391
+ label: `Z-score Cap`,
392
+ title: `Cap the Z-score scale to not exceed this absolute value`,
393
+ type: "number",
394
+ chartType: "hierCluster",
395
+ settingsKey: "zScoreCap"
396
+ },
397
+ {
398
+ label: `Color Scheme`,
399
+ title: `Sets which color scheme to use`,
400
+ type: "radio",
401
+ chartType: "hierCluster",
402
+ settingsKey: "colorScale",
403
+ options: [
404
+ {
405
+ label: "Blue-White-Red",
406
+ value: "blueWhiteRed",
407
+ title: `color scheme Blue-White-Red`
408
+ },
409
+ {
410
+ label: "Green-Black-Red",
411
+ value: "greenBlackRed",
412
+ title: `color scheme Green-Black-Red`
413
+ },
414
+ {
415
+ label: "Blue-Yellow-Red",
416
+ value: "blueYellowRed",
417
+ title: `color scheme Blue-Yellow-Red`
418
+ },
419
+ {
420
+ label: "Green-White-Red",
421
+ value: "greenWhiteRed",
422
+ title: `color scheme Green-White-Red`
423
+ },
424
+ {
425
+ label: "Blue-Black-Yellow",
426
+ value: "blueBlackYellow",
427
+ title: `color scheme Blue-Black-Yellow`
428
+ }
429
+ ]
430
+ }
431
+ ],
432
+ customInputs: updateClusteringControls
433
+ }).html((d) => d.label).style("margin", "2px 0").on("click", callback);
434
+ }
435
+ function updateClusteringControls(self, app, parent, table) {
436
+ if (parent.chartType == "hierCluster" && !parent.config.settings.hierCluster.zScoreTransformation) {
437
+ const zScoreCapControl = select_default(
438
+ table.selectAll("td").filter(function() {
439
+ return select_default(this).text() == "Z-score Cap";
440
+ }).node().closest("tr")
441
+ );
442
+ zScoreCapControl.style("display", "none");
443
+ const colorSchemeControl = select_default(
444
+ table.selectAll("td").filter(function() {
445
+ return select_default(this).text() == "Color Scheme";
446
+ }).node().closest("tr")
447
+ );
448
+ colorSchemeControl.style("display", "none");
449
+ }
450
+ if (parent.chartType == "hierCluster" && parent.config.dataType !== "geneExpression") {
451
+ const geneInputTr = table.insert("tr", () => table.select("tr").node());
452
+ geneInputTr.append("td").attr("class", "sja-termdb-config-row-label").html("Hierarchical Clustering Term Set");
453
+ const td1 = geneInputTr.append("td").style("display", "block").style("padding", "5px 0px");
454
+ const editGrpDiv = td1.append("div").append("label");
455
+ const clusteringBtn = self.btns.node();
456
+ editGrpDiv.append("button").html("Edit Set").on("click", () => {
457
+ app.tip.clear();
458
+ const backDiv = app.tip.d.append("div").style("padding", "5px");
459
+ backDiv.attr("tabindex", 0).style("padding", "5px").style("text-decoration", "underline").style("cursor", "pointer").style("margin-bottom", "12px").html(`&#171; Back`).on("click", () => clusteringBtn.click()).on("keyup", (event) => {
460
+ if (event.key == "Enter") event.target.click();
461
+ });
462
+ const setEdiUiHolder = app.tip.d.append("div");
463
+ parent.showDictTermSelection(setEdiUiHolder);
464
+ });
465
+ }
466
+ }
467
+
468
+ export {
469
+ getAllChildrenClusterIds,
470
+ addSelectedSamplesOptions,
471
+ addSelectedRowsOptions,
472
+ triggerZoomBranch,
473
+ showTable4selectedSamples,
474
+ showTable4selectedRows,
475
+ getClusterFromTopDendrogram,
476
+ getClusterFromLeftDendrogram,
477
+ setClusteringBtn,
478
+ hierCluster_interactivity_exports
479
+ };
480
+ //# sourceMappingURL=chunk-IKZAWD7P.js.map