@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

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 (937) hide show
  1. package/dist/2dmaf-PBJ3POZQ.js +1371 -0
  2. package/dist/AIProjectAdmin-5IAXCACJ.js +830 -0
  3. package/dist/AppHeader-HLUE2IQT.js +833 -0
  4. package/dist/BoxPlot-NAQS5MHV.js +1217 -0
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  174. package/dist/dnaMethylation-4VDQBBGJ.js +36 -0
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  835. /package/dist/{matrix.integration.spec-PQH67KRM.js.map → matrix.integration.spec-XHGSEBYM.js.map} +0 -0
  836. /package/dist/{matrix.interactivity-JW4AXAWO.js.map → matrix.interactivity-OZS7R32Z.js.map} +0 -0
  837. /package/dist/{matrix.layout-I56KRVCO.js.map → matrix.layout-GBQJ7O3H.js.map} +0 -0
  838. /package/dist/{matrix.legend-42LQGAGX.js.map → matrix.legend-AGTC5JPS.js.map} +0 -0
  839. /package/dist/{matrix.renderers-IX3FCNBK.js.map → matrix.renderers-L5D5NLLR.js.map} +0 -0
  840. /package/dist/{matrix.serieses-4B2WB526.js.map → matrix.serieses-DDQOSCL4.js.map} +0 -0
  841. /package/dist/{matrix.sort-BJACNR7G.js.map → matrix.sort-6VF7VNFX.js.map} +0 -0
  842. /package/dist/{matrix.sort.unit.spec-3KKDKIPY.js.map → matrix.sort.unit.spec-QGJBVO3X.js.map} +0 -0
  843. /package/dist/{matrix.sorterUi-W6XFYZY2.js.map → matrix.sorterUi-UE7CBIUP.js.map} +0 -0
  844. /package/dist/{matrix.sorterUi.unit.spec-CMJ7EBIW.js.map → matrix.sorterUi.unit.spec-CTLTVJCO.js.map} +0 -0
  845. /package/dist/{mavb-ROAE6WYA.js.map → mavb-MU7H7YWY.js.map} +0 -0
  846. /package/dist/{mds.fimo-UGK5OWCF.js.map → mds.fimo-ELCNQMNR.js.map} +0 -0
  847. /package/dist/{mds.samplescatterplot-5KFUAYSB.js.map → mds.samplescatterplot-P7N4SXYT.js.map} +0 -0
  848. /package/dist/{mds.survivalplot-2EVNZUX5.js.map → mds.survivalplot-KJFW4IRT.js.map} +0 -0
  849. /package/dist/{oncomatrix-UGFXSXQJ.js.map → oncomatrix-Q5X3O65P.js.map} +0 -0
  850. /package/dist/{oncomatrix.spec-FEP7BR7L.js.map → oncomatrix.spec-CJGXXI3U.js.map} +0 -0
  851. /package/dist/{plot.2dvaf-WXGLWCOC.js.map → plot.2dvaf-CDPVMUPX.js.map} +0 -0
  852. /package/dist/{plot.app-IZAFRTBU.js.map → plot.app-BSPQMQCI.js.map} +0 -0
  853. /package/dist/{plot.barplot-Z4VWOPFJ.js.map → plot.barplot-C33LEV4Q.js.map} +0 -0
  854. /package/dist/{plot.boxplot-QU2KZSB7.js.map → plot.boxplot-XH7FN6PC.js.map} +0 -0
  855. /package/dist/{plot.brainImaging-U643YIK7.js.map → plot.brainImaging-5BB455FT.js.map} +0 -0
  856. /package/dist/{plot.disco-3BV6YEBC.js.map → plot.disco-3YUN6XAY.js.map} +0 -0
  857. /package/dist/{plot.dzi-DWXPOOQE.js.map → plot.dzi-RZWAL5UC.js.map} +0 -0
  858. /package/dist/{plot.ssgq-GXB2GZO3.js.map → plot.ssgq-M763HWMN.js.map} +0 -0
  859. /package/dist/{plot.vaf2cov-EKRIADPB.js.map → plot.vaf2cov-EAHQV6FD.js.map} +0 -0
  860. /package/dist/{plot.wsi-E2LLE6HI.js.map → plot.wsi-2BDC3RJS.js.map} +0 -0
  861. /package/dist/{polar-MZLIUXHO.js.map → polar-3SJ5SUNJ.js.map} +0 -0
  862. /package/dist/{polar2-IUVHNQM4.js.map → polar2-3GTEGZUL.js.map} +0 -0
  863. /package/dist/{profile.spec-JRW6KYUI.js.map → profile.spec-AR7JLQYT.js.map} +0 -0
  864. /package/dist/{profileBarchart-N7HJMYZ5.js.map → profileBarchart-GLTPPW2O.js.map} +0 -0
  865. /package/dist/{profileForms-Q5TPGPQP.js.map → profileForms-FE4GHA2T.js.map} +0 -0
  866. /package/dist/{profilePlot-TXTUYDVE.js.map → profilePlot-3JXEZUX5.js.map} +0 -0
  867. /package/dist/{profileRadar-ICEASI7W.js.map → profileRadar-NA2WUSHG.js.map} +0 -0
  868. /package/dist/{profileRadarFacility-NFMRNJYX.js.map → profileRadarFacility-6UNT4GPM.js.map} +0 -0
  869. /package/dist/{proteinView-K3JFNORQ.js.map → proteinView-ESTBC3K2.js.map} +0 -0
  870. /package/dist/{proteomeAbundance-LTB3QR3G.js.map → proteomeAbundance-GDK5EIE7.js.map} +0 -0
  871. /package/dist/{proteomeAbundance-DE4NVBCN.js.map → proteomeAbundance-NVLYQRKI.js.map} +0 -0
  872. /package/dist/{qualitative-DFGWQURY.js.map → qualitative-TUNIICQ4.js.map} +0 -0
  873. /package/dist/{regression-TTQTAEGD.js.map → regression-22IF77A7.js.map} +0 -0
  874. /package/dist/{regression.inputs-2LU2XRGC.js.map → regression.inputs-VCVMUBA7.js.map} +0 -0
  875. /package/dist/{regression.inputs.term-G57GL57T.js.map → regression.inputs.term-6FWVBNJT.js.map} +0 -0
  876. /package/dist/{regression.inputs.values.table-JSEM3PXL.js.map → regression.inputs.values.table-2FXOWLKN.js.map} +0 -0
  877. /package/dist/{regression.integration.spec-XJQJAIC3.js.map → regression.integration.spec-2UMB7EIG.js.map} +0 -0
  878. /package/dist/{regression.results-3YNM6LLQ.js.map → regression.results-27XHC5GE.js.map} +0 -0
  879. /package/dist/{regression.spec-S6WFCPSW.js.map → regression.spec-5Q4J7TJZ.js.map} +0 -0
  880. /package/dist/{report-YRAV4MY4.js.map → report-B4RRLC7Q.js.map} +0 -0
  881. /package/dist/{sampleScatter.spec-MBJ4XNTX.js.map → sampleScatter.spec-TXZYLGM7.js.map} +0 -0
  882. /package/dist/{sampleView-IUR3ZEN7.js.map → sampleView-2WKGJUSX.js.map} +0 -0
  883. /package/dist/{samplelst-C2NBFGH6.js.map → samplelst-NJZOPYYJ.js.map} +0 -0
  884. /package/dist/{samplematrix-AOK2HHSB.js.map → samplematrix-ZXOLANI5.js.map} +0 -0
  885. /package/dist/{sc-XT3Z5XJI.js.map → sc-4IYYVV2I.js.map} +0 -0
  886. /package/dist/{scatter-SAHKZRFL.js.map → scatter-UBF4N6ON.js.map} +0 -0
  887. /package/dist/{scatter.integration.spec-6KRDNHHH.js.map → scatter.integration.spec-JNGJ4BU5.js.map} +0 -0
  888. /package/dist/{selectGenomeWithTklst-2YVZ4JWV.js.map → selectGenomeWithTklst-7ICTRJNK.js.map} +0 -0
  889. /package/dist/{singleCellCellType-NFN5GQJM.js.map → singleCellCellType-Y5ETQYDC.js.map} +0 -0
  890. /package/dist/{singleCellCellType.unit.spec-CR4IJ4DA.js.map → singleCellCellType.unit.spec-TLLZRMD7.js.map} +0 -0
  891. /package/dist/{singleCellGeneExpression-7AQGLXTR.js.map → singleCellGeneExpression-HZRIE2XT.js.map} +0 -0
  892. /package/dist/{singleCellGeneExpression.unit.spec-QYNWSV2G.js.map → singleCellGeneExpression.unit.spec-K435LTFJ.js.map} +0 -0
  893. /package/dist/{singleCellPlot-IWFEG44C.js.map → singleCellPlot-T7MKCAAW.js.map} +0 -0
  894. /package/dist/{singlecell-EATPLH66.js.map → singlecell-K662WWCH.js.map} +0 -0
  895. /package/dist/{singlecell-3QNV4OMZ.js.map → singlecell-KVLDYQ36.js.map} +0 -0
  896. /package/dist/{snp-UP7WL7WG.js.map → snp-JNV3DX5W.js.map} +0 -0
  897. /package/dist/{snp.unit.spec-Y5NWQ442.js.map → snp.unit.spec-7KFVZUWR.js.map} +0 -0
  898. /package/dist/{snplocus-WAQK2AZG.js.map → snplocus-VJLA35TV.js.map} +0 -0
  899. /package/dist/{spliceevent.a53ss.diagram-FFK27UIB.js.map → spliceevent.a53ss.diagram-MZPU6IBF.js.map} +0 -0
  900. /package/dist/{spliceevent.exonskip.diagram-KWEF2OZJ.js.map → spliceevent.exonskip.diagram-OOYBJT4F.js.map} +0 -0
  901. /package/dist/{spliceevent.noeventdiagram-PU4TI7OM.js.map → spliceevent.noeventdiagram-KPEZVRFS.js.map} +0 -0
  902. /package/dist/{ssGSEA-N6QOAVLW.js.map → ssGSEA-GPPPUU2J.js.map} +0 -0
  903. /package/dist/{ssGSEA.unit.spec-KQBNZNNP.js.map → ssGSEA.unit.spec-4SRZ4NRN.js.map} +0 -0
  904. /package/dist/{summarizeCnvGeneexp-NWX4M6LZ.js.map → summarizeCnvGeneexp-NRLEM4X4.js.map} +0 -0
  905. /package/dist/{summarizeGeneexpSurvival-N5VTE2G6.js.map → summarizeGeneexpSurvival-BJLP43OZ.js.map} +0 -0
  906. /package/dist/{summarizeMutationCnv-VV7CVAA7.js.map → summarizeMutationCnv-7DCCBY5U.js.map} +0 -0
  907. /package/dist/{summarizeMutationDiagnosis-5RHSG7L6.js.map → summarizeMutationDiagnosis-HATSCOMG.js.map} +0 -0
  908. /package/dist/{summarizeMutationSurvival-22YYXGS5.js.map → summarizeMutationSurvival-XIRZFWDJ.js.map} +0 -0
  909. /package/dist/{summary-P3WIKJS7.js.map → summary-VOFTJ76P.js.map} +0 -0
  910. /package/dist/{summary.integration.spec-ULGRPICW.js.map → summary.integration.spec-2C5RCIY4.js.map} +0 -0
  911. /package/dist/{summaryInput-IH4EVNF5.js.map → summaryInput-DIIECI4W.js.map} +0 -0
  912. /package/dist/{sunburst-VJJ3UVYC.js.map → sunburst-CYROEYTG.js.map} +0 -0
  913. /package/dist/{survival-2ZE3N62A.js.map → survival-5Y3DFIES.js.map} +0 -0
  914. /package/dist/{survival-ASCLKIII.js.map → survival-WCPGEHW5.js.map} +0 -0
  915. /package/dist/{svgraph-AYR2UPNK.js.map → svgraph-3T6XL7TR.js.map} +0 -0
  916. /package/dist/{svmr-MOMW5DNY.js.map → svmr-GUBPSOID.js.map} +0 -0
  917. /package/dist/{table-PQB6KCEY.js.map → table-NTS6ROT7.js.map} +0 -0
  918. /package/dist/{termCollection-OQMUUTW6.js.map → termCollection-EE72SAHN.js.map} +0 -0
  919. /package/dist/{termCollection-5AY2AWT4.js.map → termCollection-ZZXLZ3UE.js.map} +0 -0
  920. /package/dist/{termCollection.unit.spec-BUAXYIJK.js.map → termCollection.unit.spec-3CTEJRTX.js.map} +0 -0
  921. /package/dist/{tk-EJLFFA5H.js.map → tk-6FIXPXTM.js.map} +0 -0
  922. /package/dist/{tp.ui-WUW6A7KP.js.map → tp.ui-4ESL6SCH.js.map} +0 -0
  923. /package/dist/{tvs.density-HSVPDDGA.js.map → tvs.density-AQ5GD437.js.map} +0 -0
  924. /package/dist/{tvs.dt-MVJXQMNU.js.map → tvs.dt-G5FMPWPL.js.map} +0 -0
  925. /package/dist/{tvs.dtcnv.categorical-FIIDWVK7.js.map → tvs.dtcnv.categorical-EYQ6RTHD.js.map} +0 -0
  926. /package/dist/{tvs.dtcnv.continuous-JPQU3JA2.js.map → tvs.dtcnv.continuous-PSQMFFNX.js.map} +0 -0
  927. /package/dist/{tvs.dtfusion-BW35GOQM.js.map → tvs.dtfusion-4F6627GK.js.map} +0 -0
  928. /package/dist/{tvs.dtsnvindel-AEMFZ4EH.js.map → tvs.dtsnvindel-YNYVLJEI.js.map} +0 -0
  929. /package/dist/{tvs.dtsv-JHTU7UFD.js.map → tvs.dtsv-X2K4K4RN.js.map} +0 -0
  930. /package/dist/{tvs.numeric-ICUGA4WY.js.map → tvs.numeric-ZN2R7BH3.js.map} +0 -0
  931. /package/dist/{tvs.samplelst-VD2NFFFS.js.map → tvs.samplelst-XZK4BE3H.js.map} +0 -0
  932. /package/dist/{tvs.termCollection-IKE5Q74D.js.map → tvs.termCollection-ZAX57TN4.js.map} +0 -0
  933. /package/dist/{violin-DPMJLHQG.js.map → violin-YEMSGTYF.js.map} +0 -0
  934. /package/dist/{violin.integration.spec-A4PNR4ES.js.map → violin.integration.spec-TULH2DWL.js.map} +0 -0
  935. /package/dist/{violin.interactivity-TS4DYUE5.js.map → violin.interactivity-RX2CDFVC.js.map} +0 -0
  936. /package/dist/{violin.renderer-53L4PXUT.js.map → violin.renderer-OJJDZFMZ.js.map} +0 -0
  937. /package/dist/{vocabulary-4MPFHKYC.js.map → vocabulary-726CSMNM.js.map} +0 -0
@@ -0,0 +1,368 @@
1
+ import {
2
+ fillTermWrapper,
3
+ termsettingInit
4
+ } from "./chunk-2LCTMDCS.js";
5
+ import {
6
+ isNumericTerm
7
+ } from "./chunk-SOED2SLH.js";
8
+ import {
9
+ select_default
10
+ } from "./chunk-NDWTN4U5.js";
11
+
12
+ // plots/matrix/matrix.renderers.js
13
+ function setRenderers(self) {
14
+ self.render = function() {
15
+ const s = self.settings.matrix;
16
+ const l = self.layout;
17
+ const d = self.dimensions;
18
+ const duration = self.dom.svg.attr("width") ? s.duration : 0;
19
+ self.dom.clipRect.attr("x", d.xOffset - 1).attr("y", 0).attr("width", d.mainw + 3).attr("height", d.mainh + 500);
20
+ self.renderSerieses(s, l, d, duration);
21
+ self.renderLabels(s, l, d, duration);
22
+ self.renderDivideByLabel(s, l, d, duration);
23
+ self.dom.colBeam.attr("width", d.dx).attr("height", d.mainh).style("stroke", s.beamStroke);
24
+ self.dom.rowBeam.attr("width", d.zoomedMainW).attr("height", s.rowh).style("stroke", s.beamStroke);
25
+ };
26
+ self.renderSerieses = function(s, l, d, duration) {
27
+ if (self.prevUseCanvas != s.useCanvas) {
28
+ self.dom.seriesesG.selectAll("g").remove();
29
+ }
30
+ if (s.useCanvas) {
31
+ const _g = self.dom.seriesesG.selectAll("g");
32
+ const g = (
33
+ /*(_g.size() && _g) ||*/
34
+ self.dom.seriesesG.append("g").datum(this.serieses)
35
+ );
36
+ self.renderCanvas(this.serieses, g, d, s, _g, duration);
37
+ } else {
38
+ self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
39
+ const sg = self.dom.seriesesG.selectAll(".sjpp-mass-series-g").data(this.serieses, (series) => series.tw.$id);
40
+ sg.exit().remove();
41
+ sg.each(self.renderSeries);
42
+ sg.enter().append("g").attr("class", "sjpp-mass-series-g").style("opacity", 1e-3).each(self.renderSeries);
43
+ self.mouseout();
44
+ }
45
+ self.prevUseCanvas = s.useCanvas;
46
+ };
47
+ self.renderSeries = async function(series) {
48
+ const s = self.settings.matrix;
49
+ const d = self.dimensions;
50
+ const g = select_default(this);
51
+ const duration = g.attr("transform") ? s.duration : 0;
52
+ g.attr("transform", `translate(${series.x},${series.y})`).style("opacity", 1);
53
+ const last = series.cells[series.cells.length - 1];
54
+ const height = series.y + last?.y + s.rowh;
55
+ const rects = g.selectAll("rect").data(series.cells, (cell) => cell.sample + ";;" + cell.tw.$id + ";;" + cell.valueIndex);
56
+ rects.exit().remove();
57
+ rects.each(self.renderCell);
58
+ rects.enter().append("rect").each(self.renderCell);
59
+ };
60
+ self.renderCanvas = async function(serieses, g, d, s, _g, duration) {
61
+ const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
62
+ g.selectAll("*").remove();
63
+ const width = d.imgW;
64
+ const height = self.dimensions.mainh;
65
+ const canvas = window.OffscreenCanvas ? new OffscreenCanvas(width * pxr, height * pxr) : (
66
+ // TODO: no need to support older browser versions???
67
+ self.dom.holder.append("canvas").attr("width", pxr * width).attr("height", pxr * height).style("opacity", 0).node()
68
+ );
69
+ const ctx = canvas.getContext("2d");
70
+ ctx.imageSmoothingEnabled = false;
71
+ ctx.imageSmoothingQuality = "high";
72
+ ctx.scale(pxr, pxr);
73
+ for (const series of serieses) {
74
+ for (const cell of series.cells) {
75
+ self.renderCellWithCanvas(ctx, cell, series, s, d, series.y);
76
+ }
77
+ }
78
+ if (window.OffscreenCanvas) {
79
+ const reader = new FileReader();
80
+ reader.addEventListener(
81
+ "load",
82
+ () => {
83
+ _g?.remove();
84
+ self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
85
+ g.selectAll("image").remove();
86
+ g.append("image").attr("xlink:href", reader.result).attr("x", d.xMin).attr("width", width).attr("height", height);
87
+ },
88
+ false
89
+ );
90
+ const blob = await canvas.convertToBlob({ quality: 1 });
91
+ const dataURL = reader.readAsDataURL(blob);
92
+ } else {
93
+ _g?.remove();
94
+ self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
95
+ const dataURL = canvas.toDataURL();
96
+ const ratio = window.devicePixelRatio * window.devicePixelRatio;
97
+ g.append("image").attr("width", width).attr("height", height).attr("xlink:href", dataURL);
98
+ if (!window.OffscreenCanvas) canvas.remove();
99
+ }
100
+ self.mouseout();
101
+ };
102
+ self.renderCellWithCanvas = function(ctx, cell, series, s, d, _y) {
103
+ if (!cell.fill)
104
+ cell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell);
105
+ const x = cell.x ? cell.x - d.xMin : 0;
106
+ const y = _y ? _y + cell.y : cell.y || 0;
107
+ const width = s.useMinPixelWidth ? Math.max(cell.width || d.colw, d.pxw) : cell.width || d.colw;
108
+ const height = "height" in cell ? cell.height : s.rowh;
109
+ ctx.fillStyle = cell.fill;
110
+ ctx.fillRect(x, y, width, height);
111
+ const borderWidth = Math.min(width, height) * 0.1;
112
+ if (cell.border) {
113
+ ctx.lineWidth = borderWidth;
114
+ ctx.strokeStyle = "white";
115
+ ctx.strokeRect(x, y, width, height);
116
+ }
117
+ };
118
+ self.renderCell = function(cell) {
119
+ if (!cell.fill)
120
+ cell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell);
121
+ const s = self.settings.matrix;
122
+ const rect = select_default(this).attr("x", cell.x || 0).attr("y", cell.y || 0).attr("width", cell.width || self.dimensions.colw).attr("height", "height" in cell ? Math.max(0, cell.height) : s.rowh).attr("shape-rendering", "crispEdges").attr("fill", cell.fill);
123
+ if (cell.border) {
124
+ rect.attr("stroke", "white").attr("stroke-width", 0.8);
125
+ }
126
+ };
127
+ self.renderLabels = function(s, l, d, duration) {
128
+ for (const direction of ["top", "btm", "left", "right"]) {
129
+ let renderLabel2 = function(lab) {
130
+ const g = select_default(this);
131
+ g.attr("transform", side.attr.labelGTransform);
132
+ if (!g.select(":scope>text").size()) g.append("text");
133
+ const showContAxis = !side.isGroup && lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous";
134
+ const labelText = side.label(lab);
135
+ const text = g.select(":scope>text").attr("fill", "#000");
136
+ let continuousBarHAdjust;
137
+ const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
138
+ const twSettingsBarH = twSpecificSettings[lab.tw?.$id]?.contBarH;
139
+ if (twSettingsBarH && s.barh) continuousBarHAdjust = (twSettingsBarH - s.barh) * 0.5;
140
+ text.attr(
141
+ "display",
142
+ lab.grp?.type === "hierCluster" && s.clusterRowh < 6 ? "none" : side.attr.fontSize < 6 || labelText === "configure" ? "none" : ""
143
+ ).attr("font-size", lab.grp?.type === "hierCluster" ? Math.max(4, s.clusterRowh - 4) : side.attr.fontSize).attr("text-anchor", side.attr.labelAnchor).attr(
144
+ "transform",
145
+ side.attr.labelTransform + (continuousBarHAdjust ? ` translate(0,${continuousBarHAdjust})` : "")
146
+ ).attr("cursor", "pointer").attr(side.attr.textpos.coord, side.attr.textpos.factor * (showContAxis ? 30 : 0));
147
+ if (!Array.isArray(labelText)) {
148
+ text.text(labelText);
149
+ text.attr(
150
+ "y",
151
+ lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous" ? 10 : lab.grp?.type === "hierCluster" ? 0.1 * s.clusterRowh : 0
152
+ );
153
+ if (lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous") text.attr("x", -20);
154
+ } else {
155
+ text.text("");
156
+ const tspan = text.selectAll("tspan").data(labelText);
157
+ tspan.enter().append("tspan").attr("class", getTspanCls2).attr("dx", getTspanDx2).attr("font-size", getTspanFontSize2).text(getTspanText2);
158
+ }
159
+ text.on("mouseover", labelText === "configure" ? () => text.attr("opacity", 0.5) : null).on("mouseout", labelText === "configure" ? () => text.attr("opacity", 0) : null);
160
+ const hasAxis = g.select(".sjpp-matrix-cell-axis").size() && true;
161
+ if (showContAxis && labelText) {
162
+ if (!hasAxis) {
163
+ g.append("g").attr("class", "sjpp-matrix-cell-axis").attr("shape-rendering", "crispEdges");
164
+ }
165
+ const axisg = g.select(".sjpp-matrix-cell-axis");
166
+ axisg.selectAll("*").remove();
167
+ const domain = [lab.counts.maxval, lab.counts.minval];
168
+ if (s.transpose) domain.reverse();
169
+ const twSpecificSettings2 = self.config.settings.matrix.twSpecificSettings;
170
+ const twSettings = twSpecificSettings2[lab.tw.$id];
171
+ const x = !s.transpose ? 0 : twSettings.contBarGap - 1 - lab.labelOffset;
172
+ const y = !s.transpose ? twSettings.contBarGap - 1 - lab.labelOffset : 0;
173
+ axisg.attr("shape-rendering", "crispEdges").attr("transform", `translate(${x},${y})`).call(side.attr.axisFxn(lab.scales.full.domain(lab.scales.tickValues)).tickValues(lab.scales.tickValues));
174
+ } else if (hasAxis) {
175
+ g.select(".sjpp-matrix-cell-axis").remove();
176
+ }
177
+ }, getTspanCls2 = function(d2) {
178
+ return d2.cls;
179
+ }, getTspanDx2 = function(d2) {
180
+ return d2.dx;
181
+ }, getTspanFontSize2 = function(d2) {
182
+ return d2.fontSize || side.attr.fontSize;
183
+ }, getTspanText2 = function(d2) {
184
+ return d2.text;
185
+ };
186
+ var renderLabel = renderLabel2, getTspanCls = getTspanCls2, getTspanDx = getTspanDx2, getTspanFontSize = getTspanFontSize2, getTspanText = getTspanText2;
187
+ const side = l[direction];
188
+ side.box.style("display", side.display || "").attr("transform", side.attr.boxTransform);
189
+ const labels = side.box.selectAll(".sjpp-matrix-label").data(side.data, side.key);
190
+ labels.exit().remove();
191
+ labels.each(renderLabel2);
192
+ labels.enter().append("g").attr("class", "sjpp-matrix-label").each(renderLabel2);
193
+ }
194
+ };
195
+ self.colLabelGTransform = (lab, grpIndex) => {
196
+ const s = self.settings.matrix;
197
+ const d = self.dimensions;
198
+ lab.labelOffset = 0.8 * d.colw;
199
+ const x = lab.grpIndex * s.colgspace + lab.totalIndex * d.dx + lab.labelOffset + lab.totalHtAdjustments;
200
+ const y = 0;
201
+ return `translate(${x + d.seriesXoffset},${y})`;
202
+ };
203
+ self.colGrpLabelGTransform = (lab, grpIndex) => {
204
+ const s = self.settings.matrix;
205
+ const d = self.dimensions;
206
+ const len = (lab.processedLst || lab.grp.lst).length;
207
+ const x = lab.grpIndex * s.colgspace + lab.prevGrpTotalIndex * d.dx + len * d.dx / 2 + s.grpLabelFontSize / 2 + lab.totalHtAdjustments;
208
+ return `translate(${x + d.seriesXoffset},0)`;
209
+ };
210
+ self.rowLabelGTransform = (lab, grpIndex) => {
211
+ const s = self.settings.matrix;
212
+ const d = self.dimensions;
213
+ const x = 0;
214
+ lab.labelOffset = 0.7 * (lab.grp.type == "hierCluster" ? s.clusterRowh : s.rowh);
215
+ const y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + lab.labelOffset + lab.totalHtAdjustments;
216
+ return `translate(${x},${y})`;
217
+ };
218
+ self.rowGrpLabelGTransform = (lab, grpIndex) => {
219
+ const s = self.settings.matrix;
220
+ const d = self.dimensions;
221
+ const len = (lab.processedLst || lab.grp.lst).length;
222
+ const x = lab.tw?.q?.mode == "continuous" ? 20 : 0;
223
+ const y = lab.grpIndex * s.rowgspace + lab.prevGrpTotalIndex * d.dy + len * d.dy / 2 + s.grpLabelFontSize / 2 + lab.totalHtAdjustments;
224
+ return `translate(${x},${y})`;
225
+ };
226
+ self.rowAxisGTransform = (lab, grpIndex) => {
227
+ const s = self.settings.matrix;
228
+ const d = self.dimensions;
229
+ const x = 0;
230
+ const y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + 0.7 * s.rowh + lab.totalHtAdjustments;
231
+ return `translate(${x},${y})`;
232
+ };
233
+ self.renderDivideByLabel = async (s, l, d) => {
234
+ self.dom.mainG.selectAll(".sjpp-matrix-divide-by-label").remove();
235
+ if (!self.config.divideBy) return;
236
+ const name = self.config.divideBy?.term.name || "";
237
+ const text = name.length <= s.rowlabelmaxchars ? name : name.slice(0, s.rowlabelmaxchars) + "\u2026";
238
+ const sides = !s.transpose ? [l.left, l.right] : [l.top, l.bottom];
239
+ const box = sides.find((d2) => !d2.isGroup)?.box;
240
+ const y = (s.collabelpos == "top" ? d.mainh + s.collabelmaxchars : -s.collabelmaxchars) + 8;
241
+ const anchor = s.rowlabelpos == "left" ? "end" : "start";
242
+ const cl = s.controlLabels;
243
+ const gNote = box.append("g").attr("class", "sjpp-matrix-divide-by-label").attr("transform", `translate(0, ${y})`);
244
+ gNote.append("text").attr("text-anchor", anchor).attr("font-style", "italic").attr("y", -20).text(`${cl.Samples} grouped by`);
245
+ const g = box.datum({ tw: self.config.divideBy }).append("g").attr("class", "sjpp-matrix-divide-by-label").attr("transform", `translate(0, ${y})`).on("click", (event, d2) => {
246
+ pill.showMenu(event, textElem.node());
247
+ });
248
+ const textElem = g.append("text").attr("text-anchor", anchor).attr("font-weight", 600).text(text);
249
+ g.append("title").text(`${cl.Samples} are grouped by this gene or variable. Click to edit.`);
250
+ const customMenuOptions = [];
251
+ const tvsKey = isNumericTerm(self.config.divideBy.term) ? "ranges" : "values";
252
+ if (self.config.legendValueFilter.lst?.find(
253
+ (l2) => l2.legendGrpName == self.config.divideBy.term.id || l2.legendGrpName == self.config.divideBy.term.name
254
+ )?.tvs[tvsKey]?.length) {
255
+ customMenuOptions.push({ label: `Show filtered ${cl.samples}`, callback: self.showDeletedSampleGroups });
256
+ }
257
+ const pill = await termsettingInit({
258
+ menuOptions: "{edit,replace,remove}",
259
+ //numericEditMenuVersion: opts.numericEditMenuVersion,
260
+ customMenuOptions,
261
+ //custom menu options other than menuOptions
262
+ vocabApi: self.app.vocabApi,
263
+ vocab: self.state.vocab,
264
+ //activeCohort: opts.state?.activeCohort,
265
+ holder: g,
266
+ debug: self.opts.debug,
267
+ usecase: { target: "matrix" },
268
+ getBodyParams: () => {
269
+ const currentGeneNames = self.termOrder.filter((t) => t.tw.term.type === "geneVariant").map(
270
+ (t) => t.tw.term.chr ? `${t.tw.term.chr}:${t.tw.term.start}-${t.tw.term.stop}` : t.tw.term.gene || t.tw.term.name
271
+ );
272
+ if (currentGeneNames.length) return { currentGeneNames };
273
+ return {};
274
+ },
275
+ callback: async (tw) => {
276
+ if (self.dom.loadingDiv && self.dom.svg) {
277
+ self.dom.loadingDiv.selectAll("*").remove();
278
+ self.dom.loadingDiv.html("").style("display", "").style("position", "relative").style("left", "45%");
279
+ self.dom.loadingDiv.html("Processing data ...");
280
+ self.dom.svg.style("opacity", 0.1).style("pointer-events", "none");
281
+ }
282
+ if (tw && !tw.q) throw "data.q{} missing from pill callback";
283
+ if (tw?.term && isNumericTerm(tw.term)) {
284
+ tw.q = { ...tw.q, mode: "discrete" };
285
+ }
286
+ if (tw) await fillTermWrapper(tw, self.app.vocabApi);
287
+ await pill.main(tw ? tw : { term: null, q: null });
288
+ box.datum({ tw });
289
+ self.app.dispatch({
290
+ type: "plot_edit",
291
+ id: self.id,
292
+ config: {
293
+ divideBy: tw,
294
+ legendValueFilter: self.mayRemoveTvsEntry(self.config.divideBy)
295
+ }
296
+ });
297
+ }
298
+ });
299
+ const arg = {
300
+ term: self.config.divideBy.term,
301
+ q: self.config.divideBy.q
302
+ };
303
+ if (self.config.divideBy.$id) arg.$id = self.config.divideBy.$id;
304
+ pill.main(arg);
305
+ };
306
+ self.adjustSvgDimensions = async function(prevTranspose) {
307
+ const s = self.settings.matrix;
308
+ const hc = self.settings.hierCluster || {};
309
+ const l = self.layout;
310
+ const hcHeight = !hc.yDendrogramHeight ? 0 : hc.yDendrogramHeight + (l.top.display === "none" ? 0 : 10);
311
+ const hcWidth = hc.xDendrogramHeight || 0;
312
+ const d = self.dimensions;
313
+ const duration = self.dom.svg.attr("width") ? s.duration : 0;
314
+ await sleep(prevTranspose == s.transpose ? duration : s.duration);
315
+ const topBox = l.top.box.node().getBBox();
316
+ const btmBox = l.btm.box.node().getBBox();
317
+ const leftBox = l.left.box.node().getBBox();
318
+ const rtBox = l.right.box.node().getBBox();
319
+ const legendBox = self.dom.legendG.node().getBBox();
320
+ const seriesBox = self.dom.seriesesG.node().getBBox();
321
+ d.extraWidth = leftBox.width + rtBox.width + s.margin.left + s.margin.right + s.rowlabelgap * 2;
322
+ d.extraHeight = topBox.height + btmBox.height + s.margin.top + s.margin.bottom + s.collabelgap * 2;
323
+ d.svgw = d.mainw + d.extraWidth + hcWidth;
324
+ d.svgh = d.mainh + d.extraHeight + legendBox.height + 20 + s.scrollHeight + hcHeight;
325
+ self.dom.svg.attr("width", d.svgw).attr("height", d.svgh);
326
+ let maxLabelWidth = self.type == "hierCluster" ? 0 : leftBox.width, maxLabelNumChars = 0;
327
+ if (hc.xDendrogramHeight) {
328
+ self.dom.termLabelG.selectAll(".sjpp-matrix-label").each(function(d2) {
329
+ if (d2.grp.type !== "hierCluster") return;
330
+ const box = this.getBBox();
331
+ if (box.width > maxLabelWidth) {
332
+ maxLabelWidth = box.width;
333
+ maxLabelNumChars = d2.label.length;
334
+ }
335
+ });
336
+ }
337
+ const x = -l.left.offset + hcWidth + maxLabelWidth;
338
+ const xAdjust = !hc.xDendrogramHeight ? 0 : Math.max(leftBox.width - (hc.xDendrogramHeight + maxLabelWidth), 0);
339
+ const y = (l.top.display == "none" ? 0 : topBox.height) - l.top.offset + hcHeight;
340
+ self.dom.mainG.attr("transform", `translate(${x + xAdjust},${y})`);
341
+ self.dom.clipRect.attr("y", -y).attr("height", d.mainh + 500 + y);
342
+ const legendX = d.xOffset + (s.transpose ? 20 : 0);
343
+ const legendY = d.yOffset + d.mainh + s.collabelgap + (l.btm.display == "none" ? 0 : btmBox.height) + 20;
344
+ self.dom.legendG.attr("transform", `translate(${legendX},${legendY})`);
345
+ if (hc.xDendrogramHeight) {
346
+ const dendroX = maxLabelWidth + xAdjust - l.left.offset + d.xOffset - d.dx / 2;
347
+ self.dom.hcClipRect.attr("x", dendroX + hcWidth + d.dx / 2).attr("y", 0).attr("width", d.mainw + 3).attr("height", d.mainh + hc.yDendrogramHeight + 500);
348
+ self.topDendroX = dendroX + d.seriesXoffset;
349
+ self.dom.topDendrogram.attr("transform", `translate(${self.topDendroX}, 0)`);
350
+ const y2 = l.top.display == "none" ? 0 : topBox.height + s.collabelgap;
351
+ self.dom.leftDendrogram.attr("transform", `translate(${dendroX - maxLabelWidth - 10}, ${y2})`);
352
+ }
353
+ };
354
+ }
355
+ function getRectFill(d) {
356
+ if (d.fill) return d.fill;
357
+ const cls = d.class || Array.isArray(d.values) && d.values[0].class;
358
+ if (!cls) console.log;
359
+ return cls ? mclass[cls].color : "#555";
360
+ }
361
+ function sleep(ms) {
362
+ return new Promise((resolve) => setTimeout(resolve, ms));
363
+ }
364
+
365
+ export {
366
+ setRenderers
367
+ };
368
+ //# sourceMappingURL=chunk-RH573XZP.js.map
@@ -0,0 +1,257 @@
1
+ import {
2
+ TermTypeGroups,
3
+ dtTerms,
4
+ dtdnamethylation,
5
+ dtgeneexpression,
6
+ dtmetaboliteintensity,
7
+ dtproteomeabundance,
8
+ dtssgsea
9
+ } from "./chunk-XRVBHNCW.js";
10
+
11
+ // ../shared/utils/src/terms.js
12
+ var ROOT_SAMPLE_TYPE = 1;
13
+ var DEFAULT_SAMPLE_TYPE = 2;
14
+ var NumericModes = {
15
+ continuous: "continuous",
16
+ discrete: "discrete"
17
+ };
18
+ var CATEGORICAL = "categorical";
19
+ var CONDITION = "condition";
20
+ var DATE = "date";
21
+ var DNA_METHYLATION = "dnaMethylation";
22
+ var FLOAT = "float";
23
+ var GENE_VARIANT = "geneVariant";
24
+ var GENE_EXPRESSION = "geneExpression";
25
+ var ISOFORM_EXPRESSION = "isoformExpression";
26
+ var INTEGER = "integer";
27
+ var METABOLITE_INTENSITY = "metaboliteIntensity";
28
+ var MULTIVALUE = "multivalue";
29
+ var SAMPLELST = "samplelst";
30
+ var SINGLECELL_CELLTYPE = "singleCellCellType";
31
+ var SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression";
32
+ var SNP = "snp";
33
+ var SNP_LIST = "snplst";
34
+ var SNP_LOCUS = "snplocus";
35
+ var SSGSEA = "ssGSEA";
36
+ var SURVIVAL = "survival";
37
+ var TERM_COLLECTION = "termCollection";
38
+ var PROTEOME_ABUNDANCE = "proteomeAbundance";
39
+ var TermTypes = {
40
+ GENE_VARIANT,
41
+ GENE_EXPRESSION,
42
+ ISOFORM_EXPRESSION,
43
+ SSGSEA,
44
+ DNA_METHYLATION,
45
+ CATEGORICAL,
46
+ INTEGER,
47
+ FLOAT,
48
+ SNP,
49
+ SNP_LIST,
50
+ SNP_LOCUS,
51
+ CONDITION,
52
+ SURVIVAL,
53
+ SAMPLELST,
54
+ METABOLITE_INTENSITY,
55
+ PROTEOME_ABUNDANCE,
56
+ SINGLECELL_CELLTYPE,
57
+ SINGLECELL_GENE_EXPRESSION,
58
+ MULTIVALUE,
59
+ DATE,
60
+ TERM_COLLECTION
61
+ };
62
+ var dtTermTypes = new Set(dtTerms.map((t) => t.type));
63
+ for (const dtTermType of dtTermTypes) {
64
+ TermTypes[dtTermType.toUpperCase()] = dtTermType;
65
+ }
66
+ var TermTypes2Dt = {
67
+ [GENE_EXPRESSION]: dtgeneexpression,
68
+ [SSGSEA]: dtssgsea,
69
+ [DNA_METHYLATION]: dtdnamethylation,
70
+ [METABOLITE_INTENSITY]: dtmetaboliteintensity,
71
+ [PROTEOME_ABUNDANCE]: dtproteomeabundance
72
+ };
73
+ var typeGroup = {
74
+ [CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,
75
+ [CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,
76
+ [FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,
77
+ [INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,
78
+ [SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,
79
+ [SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,
80
+ [DATE]: TermTypeGroups.DICTIONARY_VARIABLES,
81
+ [MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,
82
+ [GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,
83
+ [SNP]: TermTypeGroups.SNP,
84
+ [SNP_LIST]: TermTypeGroups.SNP_LIST,
85
+ [SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
86
+ [GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
87
+ [ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,
88
+ [SSGSEA]: TermTypeGroups.SSGSEA,
89
+ [DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
90
+ [METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
91
+ [PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,
92
+ [TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
93
+ [SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
94
+ [SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION
95
+ };
96
+ var nonDictTypes = /* @__PURE__ */ new Set([
97
+ SNP,
98
+ SNP_LIST,
99
+ SNP_LOCUS,
100
+ GENE_EXPRESSION,
101
+ ISOFORM_EXPRESSION,
102
+ SSGSEA,
103
+ DNA_METHYLATION,
104
+ GENE_VARIANT,
105
+ METABOLITE_INTENSITY,
106
+ PROTEOME_ABUNDANCE,
107
+ SINGLECELL_CELLTYPE,
108
+ SINGLECELL_GENE_EXPRESSION
109
+ ]);
110
+ for (const dtTermType of dtTermTypes) {
111
+ nonDictTypes.add(TermTypes[dtTermType.toUpperCase()]);
112
+ }
113
+ var numericTypes = /* @__PURE__ */ new Set([
114
+ INTEGER,
115
+ FLOAT,
116
+ GENE_EXPRESSION,
117
+ ISOFORM_EXPRESSION,
118
+ SSGSEA,
119
+ DNA_METHYLATION,
120
+ METABOLITE_INTENSITY,
121
+ PROTEOME_ABUNDANCE,
122
+ SINGLECELL_GENE_EXPRESSION,
123
+ DATE
124
+ ]);
125
+ var categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
126
+ var singleCellTerms = /* @__PURE__ */ new Set([SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION]);
127
+ function isSingleCellTerm(term) {
128
+ if (!term) return false;
129
+ return singleCellTerms.has(term.type);
130
+ }
131
+ function isNumericTerm(term) {
132
+ if (!term) return false;
133
+ return numericTypes.has(term.type);
134
+ }
135
+ function isCategoricalTerm(term) {
136
+ if (!term) return false;
137
+ return categoricalTypes.has(term.type);
138
+ }
139
+ function isDictionaryType(type) {
140
+ return !isNonDictionaryType(type);
141
+ }
142
+ function isNonDictionaryType(type) {
143
+ if (!type) throw new Error("Type is not defined");
144
+ return nonDictTypes.has(type);
145
+ }
146
+ function isNumTermCollection(term) {
147
+ if (!term || !term.type) throw new Error("Term or term type is not defined");
148
+ return term.type === TERM_COLLECTION;
149
+ }
150
+ function equals(t1, t2) {
151
+ if (!t1) throw new Error("First term is not defined ");
152
+ if (!t2) throw new Error("Second term is not defined ");
153
+ if (t1.type !== t2.type) return false;
154
+ if (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST) return t1.id === t2.id;
155
+ switch (t1.type) {
156
+ case GENE_EXPRESSION:
157
+ return t1.gene == t2.gene;
158
+ case ISOFORM_EXPRESSION:
159
+ return t1.isoform == t2.isoform;
160
+ case SSGSEA:
161
+ return t1.id == t2.id;
162
+ case DNA_METHYLATION:
163
+ return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
164
+ case METABOLITE_INTENSITY:
165
+ case PROTEOME_ABUNDANCE:
166
+ return t1.name == t2.name;
167
+ case GENE_VARIANT:
168
+ return t1.gene == t2.gene || t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
169
+ // TO DO: Add more cases
170
+ // case SNP_LIST:
171
+ // case SNP_LOCUS:
172
+ // case SAMPLELST:
173
+ default:
174
+ return false;
175
+ }
176
+ }
177
+ var typeMap = {
178
+ categorical: "Categorical",
179
+ condition: "Condition",
180
+ float: "Numerical",
181
+ integer: "Numerical",
182
+ geneExpression: "Gene Expression",
183
+ isoformExpression: "Isoform Expression",
184
+ ssGSEA: "Geneset Expression",
185
+ dnaMethylation: "DNA Methylation",
186
+ geneVariant: "Gene Variant",
187
+ metaboliteIntensity: "Metabolite Intensity",
188
+ proteomeAbundance: "Proteome Abundance",
189
+ multivalue: "Multi Value",
190
+ singleCellGeneExpression: "Single Cell, Gene Expression",
191
+ singleCellCellType: "Single Cell, Cell Type",
192
+ snplocus: "SNP Locus",
193
+ snp: "SNP",
194
+ snplst: "SNP List",
195
+ termCollection: "Term Collection"
196
+ };
197
+ function termType2label(type) {
198
+ return typeMap[type] || "Unknown term type";
199
+ }
200
+ function getDateFromNumber(value) {
201
+ const year = Math.floor(value);
202
+ const january1st = new Date(year, 0, 1);
203
+ const totalDays = getDaysInYear(year);
204
+ const time = Math.round((value - year) * totalDays) * oneDayTime;
205
+ const date = new Date(january1st.getTime() + time);
206
+ return date;
207
+ }
208
+ var oneDayTime = 24 * 60 * 60 * 1e3;
209
+ function getDateStrFromNumber(value) {
210
+ const date = getDateFromNumber(value);
211
+ return date.toLocaleDateString("en-US", {
212
+ year: "numeric",
213
+ month: "long"
214
+ });
215
+ }
216
+ function getDaysInYear(year) {
217
+ const isLeap = new Date(year, 1, 29).getMonth() === 1;
218
+ const days = isLeap ? 366 : 365;
219
+ return days;
220
+ }
221
+
222
+ export {
223
+ ROOT_SAMPLE_TYPE,
224
+ DEFAULT_SAMPLE_TYPE,
225
+ NumericModes,
226
+ CATEGORICAL,
227
+ DATE,
228
+ DNA_METHYLATION,
229
+ FLOAT,
230
+ GENE_VARIANT,
231
+ GENE_EXPRESSION,
232
+ ISOFORM_EXPRESSION,
233
+ INTEGER,
234
+ METABOLITE_INTENSITY,
235
+ SINGLECELL_CELLTYPE,
236
+ SINGLECELL_GENE_EXPRESSION,
237
+ SNP,
238
+ SSGSEA,
239
+ TERM_COLLECTION,
240
+ PROTEOME_ABUNDANCE,
241
+ TermTypes,
242
+ dtTermTypes,
243
+ TermTypes2Dt,
244
+ typeGroup,
245
+ numericTypes,
246
+ isSingleCellTerm,
247
+ isNumericTerm,
248
+ isCategoricalTerm,
249
+ isDictionaryType,
250
+ isNonDictionaryType,
251
+ isNumTermCollection,
252
+ equals,
253
+ termType2label,
254
+ getDateFromNumber,
255
+ getDateStrFromNumber
256
+ };
257
+ //# sourceMappingURL=chunk-SOED2SLH.js.map
@@ -0,0 +1,7 @@
1
+ {
2
+ "version": 3,
3
+ "sources": ["../../shared/utils/src/terms.js"],
4
+ "sourcesContent": ["import {\n\tdtgeneexpression,\n\tdtssgsea,\n\tdtdnamethylation,\n\tdtmetaboliteintensity,\n\tdtproteomeabundance,\n\tTermTypeGroups,\n\tdtTerms\n} from './common.js'\nimport { TermTypeGroups as TermTypeGroups2 } from './common.js'\nconst ROOT_SAMPLE_TYPE = 1\nconst DEFAULT_SAMPLE_TYPE = 2\nconst NumericModes = {\n\tcontinuous: 'continuous',\n\tdiscrete: 'discrete'\n}\nconst CATEGORICAL = 'categorical'\nconst CONDITION = 'condition'\nconst DATE = 'date'\nconst DNA_METHYLATION = 'dnaMethylation'\nconst FLOAT = 'float'\nconst GENE_VARIANT = 'geneVariant'\nconst GENE_EXPRESSION = 'geneExpression'\nconst ISOFORM_EXPRESSION = 'isoformExpression'\nconst INTEGER = 'integer'\nconst METABOLITE_INTENSITY = 'metaboliteIntensity'\nconst MULTIVALUE = 'multivalue'\nconst SAMPLELST = 'samplelst'\nconst SINGLECELL_CELLTYPE = 'singleCellCellType'\nconst SINGLECELL_GENE_EXPRESSION = 'singleCellGeneExpression'\nconst SNP = 'snp'\nconst SNP_LIST = 'snplst'\nconst SNP_LOCUS = 'snplocus'\nconst SSGSEA = 'ssGSEA'\nconst SURVIVAL = 'survival'\nconst TERM_COLLECTION = 'termCollection'\nconst PROTEOME_ABUNDANCE = 'proteomeAbundance'\nconst TermTypes = {\n\tGENE_VARIANT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tCONDITION,\n\tSURVIVAL,\n\tSAMPLELST,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tMULTIVALUE,\n\tDATE,\n\tTERM_COLLECTION\n}\nconst dtTermTypes = new Set(dtTerms.map(t => t.type))\nfor (const dtTermType of dtTermTypes) {\n\tTermTypes[dtTermType.toUpperCase()] = dtTermType\n}\nconst TermTypes2Dt = {\n\t[GENE_EXPRESSION]: dtgeneexpression,\n\t[SSGSEA]: dtssgsea,\n\t[DNA_METHYLATION]: dtdnamethylation,\n\t[METABOLITE_INTENSITY]: dtmetaboliteintensity,\n\t[PROTEOME_ABUNDANCE]: dtproteomeabundance\n}\nconst typeGroup = {\n\t[CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[DATE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,\n\t[SNP]: TermTypeGroups.SNP,\n\t[SNP_LIST]: TermTypeGroups.SNP_LIST,\n\t[SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,\n\t[GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,\n\t[ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,\n\t[SSGSEA]: TermTypeGroups.SSGSEA,\n\t[DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,\n\t[METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,\n\t[PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,\n\t[TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,\n\t[SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,\n\t[SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION\n}\nconst nonDictTypes = /* @__PURE__ */ new Set([\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tGENE_VARIANT,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION\n])\nfor (const dtTermType of dtTermTypes) {\n\tnonDictTypes.add(TermTypes[dtTermType.toUpperCase()])\n}\nconst numericTypes = /* @__PURE__ */ new Set([\n\tINTEGER,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tDATE\n])\nconst annoNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE])\nconst categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP])\nconst singleCellTerms = /* @__PURE__ */ new Set([SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION])\nfunction isSingleCellTerm(term) {\n\tif (!term) return false\n\treturn singleCellTerms.has(term.type)\n}\nfunction isNumericTerm(term) {\n\tif (!term) return false\n\treturn numericTypes.has(term.type)\n}\nfunction isCategoricalTerm(term) {\n\tif (!term) return false\n\treturn categoricalTypes.has(term.type)\n}\nfunction isDictionaryType(type) {\n\treturn !isNonDictionaryType(type)\n}\nfunction isNonDictionaryType(type) {\n\tif (!type) throw new Error('Type is not defined')\n\treturn nonDictTypes.has(type)\n}\nfunction isNumTermCollection(term) {\n\tif (!term || !term.type) throw new Error('Term or term type is not defined')\n\treturn term.type === TERM_COLLECTION\n}\nfunction equals(t1, t2) {\n\tif (!t1) throw new Error('First term is not defined ')\n\tif (!t2) throw new Error('Second term is not defined ')\n\tif (t1.type !== t2.type) return false\n\tif (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST) return t1.id === t2.id\n\tswitch (t1.type) {\n\t\tcase GENE_EXPRESSION:\n\t\t\treturn t1.gene == t2.gene\n\t\tcase ISOFORM_EXPRESSION:\n\t\t\treturn t1.isoform == t2.isoform\n\t\tcase SSGSEA:\n\t\t\treturn t1.id == t2.id\n\t\tcase DNA_METHYLATION:\n\t\t\treturn t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop\n\t\tcase METABOLITE_INTENSITY:\n\t\tcase PROTEOME_ABUNDANCE:\n\t\t\treturn t1.name == t2.name\n\t\tcase GENE_VARIANT:\n\t\t\treturn t1.gene == t2.gene || (t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop)\n\t\t// TO DO: Add more cases\n\t\t// case SNP_LIST:\n\t\t// case SNP_LOCUS:\n\t\t// case SAMPLELST:\n\t\tdefault:\n\t\t\treturn false\n\t}\n}\nfunction getBin(lst, value) {\n\tlet bin = lst.findIndex(\n\t\tb => (b.startunbounded && value < b.stop) || (b.startunbounded && b.stopinclusive && value == b.stop)\n\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\tb => (b.stopunbounded && value > b.start) || (b.stopunbounded && b.startinclusive && value == b.start)\n\t\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\tb =>\n\t\t\t\t(value > b.start && value < b.stop) ||\n\t\t\t\t(b.startinclusive && value == b.start) ||\n\t\t\t\t(b.stopinclusive && value == b.stop)\n\t\t)\n\treturn bin\n}\nfunction getSampleType(term, ds) {\n\tif (!term) return null\n\tif (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE\n\tif (term.id) return ds.cohort.termdb.term2SampleType.get(term.id)\n\tif (term.type == 'samplelst') {\n\t\tconst key = Object.keys(term.values)[0]\n\t\tconst sampleId = term.values[key].list[0]?.sampleId\n\t\tif (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId)\n\t\telse return DEFAULT_SAMPLE_TYPE\n\t}\n\treturn DEFAULT_SAMPLE_TYPE\n}\nfunction getParentType(types, ds) {\n\tif (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null\n\tconst ids = Array.from(types)\n\tif (!ids || ids.length == 0) return null\n\tfor (const id of ids) {\n\t\tconst typeObj = ds.cohort.termdb.sampleTypes[id]\n\t\tif (!typeObj) continue\n\t\tif (typeObj.parent_id == null) return id\n\t\tif (ids.includes(typeObj.parent_id)) continue\n\t\telse return typeObj.parent_id\n\t}\n\treturn null\n}\nconst typeMap = {\n\tcategorical: 'Categorical',\n\tcondition: 'Condition',\n\tfloat: 'Numerical',\n\tinteger: 'Numerical',\n\tgeneExpression: 'Gene Expression',\n\tisoformExpression: 'Isoform Expression',\n\tssGSEA: 'Geneset Expression',\n\tdnaMethylation: 'DNA Methylation',\n\tgeneVariant: 'Gene Variant',\n\tmetaboliteIntensity: 'Metabolite Intensity',\n\tproteomeAbundance: 'Proteome Abundance',\n\tmultivalue: 'Multi Value',\n\tsingleCellGeneExpression: 'Single Cell, Gene Expression',\n\tsingleCellCellType: 'Single Cell, Cell Type',\n\tsnplocus: 'SNP Locus',\n\tsnp: 'SNP',\n\tsnplst: 'SNP List',\n\ttermCollection: 'Term Collection'\n}\nfunction termType2label(type) {\n\treturn typeMap[type] || 'Unknown term type'\n}\nfunction getDateFromNumber(value) {\n\tconst year = Math.floor(value)\n\tconst january1st = new Date(year, 0, 1)\n\tconst totalDays = getDaysInYear(year)\n\tconst time = Math.round((value - year) * totalDays) * oneDayTime\n\tconst date = new Date(january1st.getTime() + time)\n\treturn date\n}\nconst oneDayTime = 24 * 60 * 60 * 1e3\nfunction getDateStrFromNumber(value) {\n\tconst date = getDateFromNumber(value)\n\treturn date.toLocaleDateString('en-US', {\n\t\tyear: 'numeric',\n\t\tmonth: 'long'\n\t})\n}\nfunction getNumberFromDateStr(str) {\n\tconst date = new Date(str)\n\treturn getNumberFromDate(date)\n}\nfunction getNumberFromDate(date) {\n\tconst year = date.getFullYear()\n\tconst january1st = new Date(year, 0, 1)\n\tconst diffDays = (date.getTime() - january1st.getTime()) / oneDayTime\n\tconst daysTotal = getDaysInYear(year)\n\tconst decimal = diffDays / daysTotal\n\treturn year + decimal\n}\nfunction getDaysInYear(year) {\n\tconst isLeap = new Date(year, 1, 29).getMonth() === 1\n\tconst days = isLeap ? 366 : 365\n\treturn days\n}\nexport 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6
+ "names": []
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+ }