@sjcrh/proteinpaint-client 2.205.0 → 2.206.1

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.
Files changed (928) hide show
  1. package/dist/2dmaf-XWKIQYRN.js +1367 -0
  2. package/dist/AggMatrixInput-D3HJXDOD.js +277 -0
  3. package/dist/AggregateMatrix-E2JZY5N5.js +41 -0
  4. package/dist/AppHeader-SR6LMFTW.js +830 -0
  5. package/dist/BoxPlot-G2LRWABH.js +1211 -0
  6. package/dist/CorrelationVolcano-CCQGOSR7.js +614 -0
  7. package/dist/Cuminc-QB6GE5MI.js +1219 -0
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  166. package/dist/databrowser.ui-O7KNP5RH.js +425 -0
  167. package/dist/dictionary-LLGX2XNU.js +113 -0
  168. package/dist/dnaMethylation-MXRMFWGM.js +33 -0
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  170. package/dist/dofetch-F5XSHQIS.js +48 -0
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  829. /package/dist/{matrix-EXNYXYLK.js.map → matrix-NEEZS7HQ.js.map} +0 -0
  830. /package/dist/{matrix.cells-DVPWSLJW.js.map → matrix.cells-ZFKVIPDC.js.map} +0 -0
  831. /package/dist/{matrix.config-RLSTWDXC.js.map → matrix.config-37V4NZU2.js.map} +0 -0
  832. /package/dist/{matrix.data-Z6GUACVZ.js.map → matrix.data-NCGZPNWR.js.map} +0 -0
  833. /package/dist/{matrix.groups-3ZSTUWRK.js.map → matrix.groups-XQJTGM6M.js.map} +0 -0
  834. /package/dist/{matrix.integration.spec-4U2R3UB2.js.map → matrix.integration.spec-MRQUAGQN.js.map} +0 -0
  835. /package/dist/{matrix.interactivity-DJZFQ7DN.js.map → matrix.interactivity-NR2KH4CG.js.map} +0 -0
  836. /package/dist/{matrix.layout-RQJ6VB4P.js.map → matrix.layout-7FXNBXWB.js.map} +0 -0
  837. /package/dist/{matrix.legend-YQ36NWKW.js.map → matrix.legend-U36VCS46.js.map} +0 -0
  838. /package/dist/{matrix.renderers-MWDFI6HW.js.map → matrix.renderers-TKNU75PG.js.map} +0 -0
  839. /package/dist/{matrix.serieses-LTC4RLYD.js.map → matrix.serieses-AW7XBXLJ.js.map} +0 -0
  840. /package/dist/{matrix.sort-5VFYLABY.js.map → matrix.sort-7PMECLOE.js.map} +0 -0
  841. /package/dist/{matrix.sort.unit.spec-2RUEKUT4.js.map → matrix.sort.unit.spec-S7Z2HDDD.js.map} +0 -0
  842. /package/dist/{matrix.sorterUi-EEMYZLPI.js.map → matrix.sorterUi-J6PRUT6J.js.map} +0 -0
  843. /package/dist/{matrix.sorterUi.unit.spec-ZXGSPRFZ.js.map → matrix.sorterUi.unit.spec-PCR7U67A.js.map} +0 -0
  844. /package/dist/{matrix.unit.spec-HTF6UV4L.js.map → matrix.unit.spec-GSOK3M34.js.map} +0 -0
  845. /package/dist/{mavb-GGQRDCO6.js.map → mavb-QP64LXJ5.js.map} +0 -0
  846. /package/dist/{mds.fimo-YKV5OIYV.js.map → mds.fimo-JS52GPE4.js.map} +0 -0
  847. /package/dist/{mds.samplescatterplot-RQOEW2AW.js.map → mds.samplescatterplot-RY5PA35G.js.map} +0 -0
  848. /package/dist/{mds.survivalplot-TN636DED.js.map → mds.survivalplot-PG5VHT4W.js.map} +0 -0
  849. /package/dist/{multivalue-MDQY64EH.js.map → multivalue-EG2OGEET.js.map} +0 -0
  850. /package/dist/{numericDictTermCluster-E73TJCLI.js.map → numericDictTermCluster-5AKP6ICC.js.map} +0 -0
  851. /package/dist/{oncomatrix-AENXQMLL.js.map → oncomatrix-JUGMZ7X7.js.map} +0 -0
  852. /package/dist/{oncomatrix.spec-UD6U462U.js.map → oncomatrix.spec-76PSNGCH.js.map} +0 -0
  853. /package/dist/{plot.2dvaf-XMRV6KEG.js.map → plot.2dvaf-WXOEUEE7.js.map} +0 -0
  854. /package/dist/{plot.app-A6JKLYQQ.js.map → plot.app-ON6AY4A3.js.map} +0 -0
  855. /package/dist/{plot.barplot-UIX7LVWR.js.map → plot.barplot-WX3KM6KS.js.map} +0 -0
  856. /package/dist/{plot.boxplot-DIFWVLMA.js.map → plot.boxplot-L4PT7YVS.js.map} +0 -0
  857. /package/dist/{plot.brainImaging-ZRPVE2UK.js.map → plot.brainImaging-4JY67ZEV.js.map} +0 -0
  858. /package/dist/{plot.disco-I56MT3PC.js.map → plot.disco-3NY3P37U.js.map} +0 -0
  859. /package/dist/{plot.ssgq-FCKFSZTV.js.map → plot.ssgq-3YHZPC4V.js.map} +0 -0
  860. /package/dist/{plot.vaf2cov-E5C7RJ7Z.js.map → plot.vaf2cov-PJJN2GCQ.js.map} +0 -0
  861. /package/dist/{polar2-SKVBB4FD.js.map → polar2-5WVM7HGK.js.map} +0 -0
  862. /package/dist/{profileForms-5B3MTUNP.js.map → profileForms-MZNIQSE5.js.map} +0 -0
  863. /package/dist/{profilePlot-MCYCGEWT.js.map → profilePlot-2F5KXRFX.js.map} +0 -0
  864. /package/dist/{pseudbulk.unit.spec-Q4YTIPH7.js.map → pseudbulk.unit.spec-AHI6LHZY.js.map} +0 -0
  865. /package/dist/{pseudobulk-3UIWCCCQ.js.map → pseudobulk-I4I733CJ.js.map} +0 -0
  866. /package/dist/{qualitative-6TJRXZFV.js.map → qualitative-G7MKJJNX.js.map} +0 -0
  867. /package/dist/{radar2-6X4XW5IZ.js.map → radar2-XJCS6ZUN.js.map} +0 -0
  868. /package/dist/{radarFacility2-UVPXWPV5.js.map → radarFacility2-GDTKB4KP.js.map} +0 -0
  869. /package/dist/{rememberedGvQ.unit.spec-GVRFRVSO.js.map → rememberedGvQ.unit.spec-N43O4YTF.js.map} +0 -0
  870. /package/dist/{render-G7V6R4PV.js.map → render-G7TGAAPN.js.map} +0 -0
  871. /package/dist/{report-O7D46EKQ.js.map → report-PKYTJRKJ.js.map} +0 -0
  872. /package/dist/{sampleView-6Y3OOOMW.js.map → sampleView-QSB3PW33.js.map} +0 -0
  873. /package/dist/{samplelst-JRVC4GYC.js.map → samplelst-N33FNNIM.js.map} +0 -0
  874. /package/dist/{samplematrix-VP5RQVRH.js.map → samplematrix-4CVVIXWR.js.map} +0 -0
  875. /package/dist/{sc-BPHVEP6N.js.map → sc-LENH35VN.js.map} +0 -0
  876. /package/dist/{scatter-2YYRZCSW.js.map → scatter-5G272VMO.js.map} +0 -0
  877. /package/dist/{scatter-Y4BIG2PW.js.map → scatter-A3TK5TR5.js.map} +0 -0
  878. /package/dist/{selectGenomeWithTklst-2BVZU5SW.js.map → selectGenomeWithTklst-CP25JXDJ.js.map} +0 -0
  879. /package/dist/{singleCellCellType-XBGCSIQT.js.map → singleCellCellType-5ZLTPHVY.js.map} +0 -0
  880. /package/dist/{singleCellCellType.unit.spec-T4GFRLVZ.js.map → singleCellCellType.unit.spec-3JIUZS6Z.js.map} +0 -0
  881. /package/dist/{singleCellGeneExpression-5ZPWLSVW.js.map → singleCellGeneExpression-UTUK4JAM.js.map} +0 -0
  882. /package/dist/{singleCellGeneExpression.unit.spec-4O5UBUDU.js.map → singleCellGeneExpression.unit.spec-LRRBT5YG.js.map} +0 -0
  883. /package/dist/{singleCellPlot-CZLQBGVU.js.map → singleCellPlot-QXTJCGSI.js.map} +0 -0
  884. /package/dist/{singlecell-O3P5BLWT.js.map → singlecell-BS2HYXK2.js.map} +0 -0
  885. /package/dist/{singlecell-IIUYX7OG.js.map → singlecell-KG4WCPCW.js.map} +0 -0
  886. /package/dist/{snp-ZCYBF3ZQ.js.map → snp-X7AVONSN.js.map} +0 -0
  887. /package/dist/{snp.unit.spec-TAGD2DRL.js.map → snp.unit.spec-RNOIV6IA.js.map} +0 -0
  888. /package/dist/{snplocus-TL25OOPE.js.map → snplocus-DS6E47B6.js.map} +0 -0
  889. /package/dist/{spliceevent.a53ss.diagram-I7J4PQZT.js.map → spliceevent.a53ss.diagram-MUB6Y74Z.js.map} +0 -0
  890. /package/dist/{spliceevent.exonskip.diagram-SB4454HB.js.map → spliceevent.exonskip.diagram-47IHL2WK.js.map} +0 -0
  891. /package/dist/{spliceevent.noeventdiagram-FOSDNYLH.js.map → spliceevent.noeventdiagram-EMHYY3LK.js.map} +0 -0
  892. /package/dist/{ssGSEA-WANB2X5L.js.map → ssGSEA-XJVB4KXR.js.map} +0 -0
  893. /package/dist/{ssGSEA.unit.spec-4XXWU4XV.js.map → ssGSEA.unit.spec-DV6XJRPZ.js.map} +0 -0
  894. /package/dist/{stattable-FNTJLVNB.js.map → stattable-45LHJWVF.js.map} +0 -0
  895. /package/dist/{summarizeCnvGeneexp-P4AFZMKD.js.map → summarizeCnvGeneexp-RBFYEF4F.js.map} +0 -0
  896. /package/dist/{summarizeGeneexpSurvival-YL2J7F4R.js.map → summarizeGeneexpSurvival-2MTLML7E.js.map} +0 -0
  897. /package/dist/{summarizeMutationCnv-BHBHST5F.js.map → summarizeMutationCnv-6YEOAUA6.js.map} +0 -0
  898. /package/dist/{summarizeMutationDiagnosis-Z7ZHTV27.js.map → summarizeMutationDiagnosis-GMGPKNVC.js.map} +0 -0
  899. /package/dist/{summarizeMutationSurvival-PZ4TYHT7.js.map → summarizeMutationSurvival-63LEMNOV.js.map} +0 -0
  900. /package/dist/{summary-ZMNPO65S.js.map → summary-TUL6Z35N.js.map} +0 -0
  901. /package/dist/{summary.integration.spec-DPJR2ZBE.js.map → summary.integration.spec-X22T3LB4.js.map} +0 -0
  902. /package/dist/{summaryInput-6JUFJZ5P.js.map → summaryInput-YBMESKTV.js.map} +0 -0
  903. /package/dist/{sunburst-OWAUI3HC.js.map → sunburst-QVK3JOKT.js.map} +0 -0
  904. /package/dist/{survival-7EXICNK7.js.map → survival-WQR2JVXU.js.map} +0 -0
  905. /package/dist/{survival-6JPKG3VA.js.map → survival-ZDWBE2JO.js.map} +0 -0
  906. /package/dist/{svgraph-34IKFHUS.js.map → svgraph-XFA7GFTF.js.map} +0 -0
  907. /package/dist/{svmr-4XNPSVVQ.js.map → svmr-WCNU5AM4.js.map} +0 -0
  908. /package/dist/{table-LPZATFLC.js.map → table-FT7OWBPC.js.map} +0 -0
  909. /package/dist/{termCollection-DYY5FXU5.js.map → termCollection-JIBZNZS6.js.map} +0 -0
  910. /package/dist/{termCollection-WOAUFFIC.js.map → termCollection-MGMWCQ2O.js.map} +0 -0
  911. /package/dist/{termCollection.unit.spec-WTICTZ7H.js.map → termCollection.unit.spec-4OI4OIHR.js.map} +0 -0
  912. /package/dist/{termCollectionFractionSelection-K5HPDEFP.js.map → termCollectionFractionSelection-AFIJHB3Z.js.map} +0 -0
  913. /package/dist/{termCollectionFractionSelection.unit.spec-D7DG2HOI.js.map → termCollectionFractionSelection.unit.spec-MG7W4M7F.js.map} +0 -0
  914. /package/dist/{tk-NV7NBLT6.js.map → tk-23G2PAGW.js.map} +0 -0
  915. /package/dist/{tk-DD2LWVGM.js.map → tk-OQ72O2QL.js.map} +0 -0
  916. /package/dist/{tp.ui-B5J3UUVB.js.map → tp.ui-M5D3MNIR.js.map} +0 -0
  917. /package/dist/{tvs.dt-XLKQT64T.js.map → tvs.dt-T7EQO547.js.map} +0 -0
  918. /package/dist/{tvs.dtcnv.categorical-XIC3RH2D.js.map → tvs.dtcnv.categorical-4HIP3F24.js.map} +0 -0
  919. /package/dist/{tvs.dtcnv.continuous-OA2K4LHF.js.map → tvs.dtcnv.continuous-KVJWKU7Q.js.map} +0 -0
  920. /package/dist/{tvs.dtfusion-ZGNKALZB.js.map → tvs.dtfusion-C4AXERQA.js.map} +0 -0
  921. /package/dist/{tvs.dtitd-6QSG4E34.js.map → tvs.dtitd-KUZRPWA3.js.map} +0 -0
  922. /package/dist/{tvs.dtsnvindel-5CXXOGPH.js.map → tvs.dtsnvindel-DJYY7MG3.js.map} +0 -0
  923. /package/dist/{tvs.dtsv-QYYEYUD3.js.map → tvs.dtsv-RRO45ITI.js.map} +0 -0
  924. /package/dist/{tvs.numeric-3UXW4JHJ.js.map → tvs.numeric-22AHXO5K.js.map} +0 -0
  925. /package/dist/{tvs.samplelst-X77ODFFR.js.map → tvs.samplelst-M27QVSNU.js.map} +0 -0
  926. /package/dist/{tvs.termCollection-VXROWAPS.js.map → tvs.termCollection-6S2524FW.js.map} +0 -0
  927. /package/dist/{vocabulary-DKWYTZRC.js.map → vocabulary-YGPUDI4D.js.map} +0 -0
  928. /package/dist/{wsi.direct-C3HQEC2V.js.map → wsi.direct-SGGSZTWZ.js.map} +0 -0
@@ -0,0 +1,480 @@
1
+ import {
2
+ renderTable
3
+ } from "./chunk-XDLCPJCK.js";
4
+ import {
5
+ clusterMethodLst,
6
+ distanceMethodLst
7
+ } from "./chunk-RPDVFM7E.js";
8
+ import {
9
+ termType2label
10
+ } from "./chunk-5ILEFNXJ.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-GUH5IG5N.js.map
@@ -0,0 +1,102 @@
1
+ import {
2
+ getPlotConfig
3
+ } from "./chunk-A3JOQX4P.js";
4
+ import {
5
+ fillTermWrapper
6
+ } from "./chunk-XDLCPJCK.js";
7
+ import {
8
+ dictionaryNumericTypes,
9
+ numericTypes
10
+ } from "./chunk-5ILEFNXJ.js";
11
+ import {
12
+ copyMerge
13
+ } from "./chunk-WINIL2KN.js";
14
+
15
+ // plots/matrix/hierCluster.config.js
16
+ async function getPlotConfig2(opts = {}, app) {
17
+ opts.chartType = "hierCluster";
18
+ if (dictionaryNumericTypes.has(opts.dataType) || opts.dataType == "numericDictTerm") {
19
+ const grp = opts.termgroups?.find((g) => g.type == "hierCluster");
20
+ for (const tw of grp?.lst || []) tw.q = { ...tw.q, mode: "continuous" };
21
+ }
22
+ const config = await getPlotConfig(opts, app);
23
+ delete config.genes;
24
+ if (config.dataType == "numericDictTerm") {
25
+ const lst = config.termgroups?.find((g) => g.type == "hierCluster")?.lst;
26
+ config.dataType = lst?.[0]?.term?.type || "float";
27
+ }
28
+ config.settings.hierCluster = {
29
+ /* type of data used for clustering
30
+ exciting todo: (to introduce new dt values)
31
+ - gene dependency
32
+ - numeric dic term
33
+ - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
34
+ - metabolite
35
+ */
36
+ dataType: config.dataType,
37
+ // adjust the default group name based on automatically detected term types
38
+ // Done in matrix.cells.js: setHierClusterCellProps
39
+ // termGroupName: 'Expression',
40
+ clusterSamples: true,
41
+ clusterRows: true,
42
+ clusterMethod: "average",
43
+ // complete
44
+ distanceMethod: "euclidean",
45
+ zScoreCap: 5,
46
+ zScoreTransformation: true,
47
+ xDendrogramHeight: 100,
48
+ yDendrogramHeight: 200,
49
+ colorScale: "blueWhiteRed"
50
+ };
51
+ const overrides = app.vocabApi.termdbConfig.hierCluster || {};
52
+ const numericDictTermClusterOverrides = dictionaryNumericTypes.has(config.dataType) && app.vocabApi.termdbConfig.numericDictTermCluster ? app.vocabApi.termdbConfig.numericDictTermCluster : {};
53
+ copyMerge(
54
+ config.settings.hierCluster,
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-HMJOZAKA.js.map