@sjcrh/proteinpaint-client 2.187.0 → 2.188.1

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 (963) hide show
  1. package/dist/2dmaf-6YIEXAIG.js +1372 -0
  2. package/dist/AIProjectAdmin-5K5NIQNT.js +828 -0
  3. package/dist/AppHeader-4SN5M6SZ.js +834 -0
  4. package/dist/BoxPlot-DBJA6TQF.js +1218 -0
  5. package/dist/CorrelationVolcano-MDMTMTT5.js +618 -0
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  848. /package/dist/{leftlabel.sample-ZBI4NHCV.js.map → leftlabel.sample-JU7AIPZL.js.map} +0 -0
  849. /package/dist/{legacyDataset-PBCPC5I7.js.map → legacyDataset-TT4CHF23.js.map} +0 -0
  850. /package/dist/{lollipop-K7S6ASFE.js.map → lollipop-JG74M6PJ.js.map} +0 -0
  851. /package/dist/{maf-JEW6PPJB.js.map → maf-PDL2EGHI.js.map} +0 -0
  852. /package/dist/{maftimeline-7URL27MC.js.map → maftimeline-V43NQEEE.js.map} +0 -0
  853. /package/dist/{matrix-6EK5WGIG.js.map → matrix-EB2EFP4S.js.map} +0 -0
  854. /package/dist/{matrix-DKBD5RIL.js.map → matrix-Q57FU5FE.js.map} +0 -0
  855. /package/dist/{matrix.cells-KEIOXJQ7.js.map → matrix.cells-NJIMPD32.js.map} +0 -0
  856. /package/dist/{matrix.config-FGJB4VVM.js.map → matrix.config-GLDEQD3H.js.map} +0 -0
  857. /package/dist/{matrix.data-QGCGFLD7.js.map → matrix.data-6SHAKOQU.js.map} +0 -0
  858. /package/dist/{matrix.groups-HBPLZ2QX.js.map → matrix.groups-MTDEANQA.js.map} +0 -0
  859. /package/dist/{matrix.integration.spec-R4PF67KF.js.map → matrix.integration.spec-JCZ5VQJU.js.map} +0 -0
  860. /package/dist/{matrix.interactivity-M3SY33ET.js.map → matrix.interactivity-SVRNWL6V.js.map} +0 -0
  861. /package/dist/{matrix.layout-H6WQ3ZMW.js.map → matrix.layout-2HREO42N.js.map} +0 -0
  862. /package/dist/{matrix.legend-UCL7HM26.js.map → matrix.legend-QHVKT3MP.js.map} +0 -0
  863. /package/dist/{matrix.renderers-3PPFSS7Z.js.map → matrix.renderers-IYR3ZY6V.js.map} +0 -0
  864. /package/dist/{matrix.serieses-S2TJ3E6P.js.map → matrix.serieses-2VMTQXL2.js.map} +0 -0
  865. /package/dist/{matrix.sort-CFA4UWBJ.js.map → matrix.sort-PWA2RQQR.js.map} +0 -0
  866. /package/dist/{matrix.sort.unit.spec-562VIWDS.js.map → matrix.sort.unit.spec-3OYIPTFY.js.map} +0 -0
  867. /package/dist/{matrix.sorterUi-FT7K5664.js.map → matrix.sorterUi-Y5QLO75X.js.map} +0 -0
  868. /package/dist/{matrix.sorterUi.unit.spec-GAHHUN3K.js.map → matrix.sorterUi.unit.spec-BNEXQHLP.js.map} +0 -0
  869. /package/dist/{mavb-HPW5X55U.js.map → mavb-IZDDU4KK.js.map} +0 -0
  870. /package/dist/{mds.fimo-HSBKLIOX.js.map → mds.fimo-FWBL7JE6.js.map} +0 -0
  871. /package/dist/{mds.samplescatterplot-DE27OMJE.js.map → mds.samplescatterplot-T47C7DJB.js.map} +0 -0
  872. /package/dist/{mds.survivalplot-IW22UGCE.js.map → mds.survivalplot-MFZJCGS6.js.map} +0 -0
  873. /package/dist/{numericDictTermCluster-DOD66G3A.js.map → numericDictTermCluster-I2W67RGA.js.map} +0 -0
  874. /package/dist/{oncomatrix-BZCVCPR4.js.map → oncomatrix-6W7IBAED.js.map} +0 -0
  875. /package/dist/{oncomatrix.spec-IHYCIAP4.js.map → oncomatrix.spec-CEFH5IGH.js.map} +0 -0
  876. /package/dist/{plot.2dvaf-QLOZ54VC.js.map → plot.2dvaf-BN6CFLNU.js.map} +0 -0
  877. /package/dist/{plot.app-XDVDR23J.js.map → plot.app-7EYWUCZV.js.map} +0 -0
  878. /package/dist/{plot.barplot-XOESF7OQ.js.map → plot.barplot-MDIARSQD.js.map} +0 -0
  879. /package/dist/{plot.boxplot-VNOC2CHT.js.map → plot.boxplot-RUHGXC54.js.map} +0 -0
  880. /package/dist/{plot.brainImaging-7ZEOY4UR.js.map → plot.brainImaging-JEE32ZBV.js.map} +0 -0
  881. /package/dist/{plot.disco-6GVDYK7A.js.map → plot.disco-2RPNPX6E.js.map} +0 -0
  882. /package/dist/{plot.dzi-TEFPPPL6.js.map → plot.dzi-7VTYYGGW.js.map} +0 -0
  883. /package/dist/{plot.ssgq-OG4TODLO.js.map → plot.ssgq-FHE5KU5C.js.map} +0 -0
  884. /package/dist/{plot.vaf2cov-VMZRJULA.js.map → plot.vaf2cov-WDJJM5Q4.js.map} +0 -0
  885. /package/dist/{plot.wsi-2CHZZ7AC.js.map → plot.wsi-FQZWHNSF.js.map} +0 -0
  886. /package/dist/{polar-QUYQRQOQ.js.map → polar-M7EGINN4.js.map} +0 -0
  887. /package/dist/{polar2-OXXLAXJC.js.map → polar2-JFYY43K2.js.map} +0 -0
  888. /package/dist/{profile.spec-TI6PRHNJ.js.map → profile.spec-SIOHASOX.js.map} +0 -0
  889. /package/dist/{profileBarchart-GEK77XEB.js.map → profileBarchart-6JLEKVJV.js.map} +0 -0
  890. /package/dist/{profileForms-NR3VNHKM.js.map → profileForms-G6CH73RV.js.map} +0 -0
  891. /package/dist/{profilePlot-GGKO3IW5.js.map → profilePlot-NQYJOBVV.js.map} +0 -0
  892. /package/dist/{profileRadar-MN3LX5ER.js.map → profileRadar-4TNWIXDB.js.map} +0 -0
  893. /package/dist/{profileRadarFacility-3G2HWB2L.js.map → profileRadarFacility-XPH3LCBQ.js.map} +0 -0
  894. /package/dist/{proteomeAbundance-O4BB55O3.js.map → proteomeAbundance-NQ4635NL.js.map} +0 -0
  895. /package/dist/{qualitative-Q3TT73O7.js.map → qualitative-DL4WJG3O.js.map} +0 -0
  896. /package/dist/{radar2-LSD3VPZT.js.map → radar2-YNOQWHBT.js.map} +0 -0
  897. /package/dist/{radarFacility2-LZGIXY7A.js.map → radarFacility2-24UPSI7S.js.map} +0 -0
  898. /package/dist/{regression-J3XDAPAZ.js.map → regression-URAUTLTD.js.map} +0 -0
  899. /package/dist/{regression.inputs-BBZYI5OI.js.map → regression.inputs-UDVOU7FB.js.map} +0 -0
  900. /package/dist/{regression.inputs.term-7BW6XGLG.js.map → regression.inputs.term-BWW6W34R.js.map} +0 -0
  901. /package/dist/{regression.inputs.values.table-DYX2YU4H.js.map → regression.inputs.values.table-UKGIZTXG.js.map} +0 -0
  902. /package/dist/{regression.integration.spec-WLXZYKWW.js.map → regression.integration.spec-EBHQTNA3.js.map} +0 -0
  903. /package/dist/{regression.results-K5Q2N2KW.js.map → regression.results-XTOSWIP6.js.map} +0 -0
  904. /package/dist/{regression.spec-VT7T6KBY.js.map → regression.spec-KG2I53VR.js.map} +0 -0
  905. /package/dist/{report-3D3L573D.js.map → report-KH7SNPVF.js.map} +0 -0
  906. /package/dist/{sampleScatter.spec-6IPJQLM2.js.map → sampleScatter.spec-PIXGS3LG.js.map} +0 -0
  907. /package/dist/{sampleView-5JMFI4HF.js.map → sampleView-TWS6VT55.js.map} +0 -0
  908. /package/dist/{samplelst-SUCB5WOZ.js.map → samplelst-6AB5Y4WR.js.map} +0 -0
  909. /package/dist/{samplematrix-A5SZBKO6.js.map → samplematrix-AJAF555E.js.map} +0 -0
  910. /package/dist/{sc-NAA6ESO6.js.map → sc-PMNYZKXA.js.map} +0 -0
  911. /package/dist/{scatter-EQCN2HYE.js.map → scatter-Q2GH3ZJD.js.map} +0 -0
  912. /package/dist/{scatter.integration.spec-7NXIYS67.js.map → scatter.integration.spec-SMMYKWH3.js.map} +0 -0
  913. /package/dist/{selectGenomeWithTklst-KXODNCY6.js.map → selectGenomeWithTklst-VE4SDYY7.js.map} +0 -0
  914. /package/dist/{singleCellCellType-HMIW76YB.js.map → singleCellCellType-S324GCKW.js.map} +0 -0
  915. /package/dist/{singleCellCellType.unit.spec-ZCZET56X.js.map → singleCellCellType.unit.spec-NXC2GELH.js.map} +0 -0
  916. /package/dist/{singleCellGeneExpression-IUCUHF6R.js.map → singleCellGeneExpression-6H4HRKIA.js.map} +0 -0
  917. /package/dist/{singleCellGeneExpression.unit.spec-J4D6F2N3.js.map → singleCellGeneExpression.unit.spec-HIJXVUWJ.js.map} +0 -0
  918. /package/dist/{singleCellPlot-L6W3MDGG.js.map → singleCellPlot-H7PCZ2DP.js.map} +0 -0
  919. /package/dist/{singlecell-A6ECAAPI.js.map → singlecell-4LH3MQVL.js.map} +0 -0
  920. /package/dist/{singlecell-KBABNXC5.js.map → singlecell-MOSYT3RI.js.map} +0 -0
  921. /package/dist/{snp-RO7ATG6E.js.map → snp-IKLGTD4Q.js.map} +0 -0
  922. /package/dist/{snp.unit.spec-ZJLRGJD4.js.map → snp.unit.spec-GC74MUVM.js.map} +0 -0
  923. /package/dist/{snplocus-N3CU6NRP.js.map → snplocus-RIABFSBQ.js.map} +0 -0
  924. /package/dist/{spliceevent.a53ss.diagram-7PHT4COB.js.map → spliceevent.a53ss.diagram-4E2IYYHL.js.map} +0 -0
  925. /package/dist/{spliceevent.exonskip.diagram-3CZTY6QD.js.map → spliceevent.exonskip.diagram-C56R6XLQ.js.map} +0 -0
  926. /package/dist/{spliceevent.noeventdiagram-GQE256DT.js.map → spliceevent.noeventdiagram-SIPMAKXI.js.map} +0 -0
  927. /package/dist/{ssGSEA-4I3L5MX2.js.map → ssGSEA-5QNHLSOI.js.map} +0 -0
  928. /package/dist/{ssGSEA.unit.spec-PZCC5YU7.js.map → ssGSEA.unit.spec-KVPN553B.js.map} +0 -0
  929. /package/dist/{summarizeCnvGeneexp-ASXUQW56.js.map → summarizeCnvGeneexp-K4VGJSW6.js.map} +0 -0
  930. /package/dist/{summarizeGeneexpSurvival-ULGUOW5V.js.map → summarizeGeneexpSurvival-HGHX65FN.js.map} +0 -0
  931. /package/dist/{summarizeMutationCnv-VDUCIUGM.js.map → summarizeMutationCnv-3K4Z6R2X.js.map} +0 -0
  932. /package/dist/{summarizeMutationDiagnosis-FMAAMCZC.js.map → summarizeMutationDiagnosis-M2MHUPRT.js.map} +0 -0
  933. /package/dist/{summarizeMutationSurvival-GZ4NGDJT.js.map → summarizeMutationSurvival-WVBUP3GA.js.map} +0 -0
  934. /package/dist/{summary-2WNZ6JSB.js.map → summary-RZHZXCU5.js.map} +0 -0
  935. /package/dist/{summary.integration.spec-XPMYB6GM.js.map → summary.integration.spec-FGZP7DY7.js.map} +0 -0
  936. /package/dist/{summaryInput-2UGXEA5C.js.map → summaryInput-UGM7MMCR.js.map} +0 -0
  937. /package/dist/{sunburst-76WCQLTT.js.map → sunburst-L27U7LV7.js.map} +0 -0
  938. /package/dist/{survival-3EAMPHSX.js.map → survival-5ZMEBV6O.js.map} +0 -0
  939. /package/dist/{survival-23IZM4ML.js.map → survival-JWRRGTJT.js.map} +0 -0
  940. /package/dist/{survival.integration.spec-YNVAKBV3.js.map → survival.integration.spec-Z5542I4V.js.map} +0 -0
  941. /package/dist/{svgraph-G2M5LXEP.js.map → svgraph-O6ZVLNNN.js.map} +0 -0
  942. /package/dist/{svmr-BUDBVU34.js.map → svmr-ULFV7OSH.js.map} +0 -0
  943. /package/dist/{table-QJSZ6YFK.js.map → table-CHRQH2GH.js.map} +0 -0
  944. /package/dist/{termCollection-2YAY3RLZ.js.map → termCollection-FAO6ZA6F.js.map} +0 -0
  945. /package/dist/{termCollection-MAMDMEDD.js.map → termCollection-GBXS3GOY.js.map} +0 -0
  946. /package/dist/{termCollection.unit.spec-UY7G2BHG.js.map → termCollection.unit.spec-4WRTOV6E.js.map} +0 -0
  947. /package/dist/{tk-GFGP3F76.js.map → tk-KNUBWRNK.js.map} +0 -0
  948. /package/dist/{tp.ui-OQ757UIE.js.map → tp.ui-2PPYOQYL.js.map} +0 -0
  949. /package/dist/{tvs.density-BJK23JYJ.js.map → tvs.density-BZ5SKDQS.js.map} +0 -0
  950. /package/dist/{tvs.dt-TOYEFKNT.js.map → tvs.dt-TDNSTGQR.js.map} +0 -0
  951. /package/dist/{tvs.dtcnv.categorical-EO2VLFL2.js.map → tvs.dtcnv.categorical-P2IGIE4I.js.map} +0 -0
  952. /package/dist/{tvs.dtcnv.continuous-ZAHTKZ4Y.js.map → tvs.dtcnv.continuous-2XUCRBDR.js.map} +0 -0
  953. /package/dist/{tvs.dtfusion-BY3AHBL3.js.map → tvs.dtfusion-PRHZVMOG.js.map} +0 -0
  954. /package/dist/{tvs.dtsnvindel-UM5LQ4FR.js.map → tvs.dtsnvindel-KGKBW5JS.js.map} +0 -0
  955. /package/dist/{tvs.dtsv-H7ZVHLS5.js.map → tvs.dtsv-M3CY5TZF.js.map} +0 -0
  956. /package/dist/{tvs.numeric-66FP6RRH.js.map → tvs.numeric-W74JCC5P.js.map} +0 -0
  957. /package/dist/{tvs.samplelst-Q5ECTZOY.js.map → tvs.samplelst-BTWFBBAN.js.map} +0 -0
  958. /package/dist/{tvs.termCollection-FYNMKZTR.js.map → tvs.termCollection-Y64QIKOA.js.map} +0 -0
  959. /package/dist/{violin-EGWLAJVM.js.map → violin-3LLHHV3L.js.map} +0 -0
  960. /package/dist/{violin.integration.spec-3P4TYHBR.js.map → violin.integration.spec-6NF5FDLQ.js.map} +0 -0
  961. /package/dist/{violin.interactivity-VWDR4LYB.js.map → violin.interactivity-W2AKZ24D.js.map} +0 -0
  962. /package/dist/{violin.renderer-WWTU6J7X.js.map → violin.renderer-CRFYYZRI.js.map} +0 -0
  963. /package/dist/{vocabulary-JG4ZITOH.js.map → vocabulary-AUJOAVYS.js.map} +0 -0
@@ -0,0 +1,592 @@
1
+ import {
2
+ axisstyle,
3
+ bulk_badline,
4
+ disappear2 as disappear,
5
+ make_table_2col,
6
+ newpane,
7
+ newpane3,
8
+ renderSandboxFormDiv,
9
+ to_svg
10
+ } from "./chunk-2XPDA6NL.js";
11
+ import "./chunk-HJ6L54YS.js";
12
+ import "./chunk-LSEFWW72.js";
13
+ import "./chunk-GHWHLSUX.js";
14
+ import {
15
+ Menu
16
+ } from "./chunk-HYOEWQ5P.js";
17
+ import "./chunk-HBW42TDT.js";
18
+ import "./chunk-G6O3URDN.js";
19
+ import "./chunk-FN5XPUPH.js";
20
+ import "./chunk-KWM6B3NL.js";
21
+ import "./chunk-UCLS2SVB.js";
22
+ import "./chunk-AY4UBGLC.js";
23
+ import "./chunk-2P6Z7JFC.js";
24
+ import "./chunk-MYWJQRTD.js";
25
+ import "./chunk-MVTCBVSX.js";
26
+ import "./chunk-B43MTEYB.js";
27
+ import "./chunk-2T7VYQLY.js";
28
+ import "./chunk-FDK4UJMN.js";
29
+ import "./chunk-X7GDCYND.js";
30
+ import "./chunk-SJC2C77V.js";
31
+ import "./chunk-C3SYSMNE.js";
32
+ import {
33
+ category10_default
34
+ } from "./chunk-KSGA62R2.js";
35
+ import {
36
+ axisBottom,
37
+ axisLeft
38
+ } from "./chunk-LOZEKOES.js";
39
+ import "./chunk-TOU7EVFQ.js";
40
+ import {
41
+ format,
42
+ linear,
43
+ log,
44
+ ordinal,
45
+ time,
46
+ timeParse
47
+ } from "./chunk-OAWQ6LOO.js";
48
+ import "./chunk-NMBIT4IK.js";
49
+ import "./chunk-KYBIQBXE.js";
50
+ import {
51
+ select_default
52
+ } from "./chunk-I6Y4O3RR.js";
53
+ import "./chunk-OMR2DT66.js";
54
+ import "./chunk-DQC5FFGV.js";
55
+ import "./chunk-HFNDKYVF.js";
56
+
57
+ // src/maftimeline.js
58
+ var zerovalue = 1e-5;
59
+ var showcircle = true;
60
+ var maflogscale = true;
61
+ var tip = new Menu();
62
+ function maftimelineui(genomes, holder, sandbox_header) {
63
+ let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
64
+ if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
65
+ else {
66
+ ;
67
+ [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
68
+ pane.header.text("MAF timeline plot");
69
+ }
70
+ inputdiv.append("p").html(
71
+ "<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
72
+ );
73
+ inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
74
+ {
75
+ const id = Math.random().toString();
76
+ const p = inputdiv.append("p");
77
+ p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
78
+ maflogscale = !maflogscale;
79
+ });
80
+ p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
81
+ }
82
+ const fileui = () => {
83
+ filediv.selectAll("*").remove();
84
+ const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
85
+ saydiv.text("");
86
+ const file = event.target.files[0];
87
+ if (!file) {
88
+ fileui();
89
+ return;
90
+ }
91
+ if (file.size == 0) {
92
+ saydiv.text("Wrong file: " + file.name);
93
+ fileui();
94
+ return;
95
+ }
96
+ const reader = new FileReader();
97
+ reader.onload = (event2) => {
98
+ const lines = event2.target.result.trim().split(/\r?\n/);
99
+ const [err, header] = parseheader(lines[0].trim());
100
+ if (err) {
101
+ saydiv.text("File header error: " + err);
102
+ fileui();
103
+ return;
104
+ }
105
+ const badlines = [];
106
+ const data = {};
107
+ let good = 0;
108
+ for (let i = 1; i < lines.length; i++) {
109
+ if (lines[i] == "") continue;
110
+ if (lines[i][0] == "#") continue;
111
+ const m = parseline(i, lines[i], header, badlines, data);
112
+ if (m) {
113
+ good++;
114
+ }
115
+ }
116
+ if (badlines.length) {
117
+ bulk_badline(header, badlines);
118
+ }
119
+ if (good == 0) {
120
+ fileui();
121
+ return;
122
+ }
123
+ let visual_holder;
124
+ if (pane) {
125
+ disappear(pane.pane);
126
+ const pane2 = newpane({ x: 100, y: 100, toshrink: true });
127
+ pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
128
+ visual_holder = pane2.body;
129
+ }
130
+ if (holder !== void 0) {
131
+ visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
132
+ inputdiv.selectAll("*").remove();
133
+ saydiv.text("");
134
+ }
135
+ render(data, header, visual_holder);
136
+ };
137
+ reader.onerror = function() {
138
+ saydiv.text("Error reading file " + file.name);
139
+ fileui();
140
+ return;
141
+ };
142
+ saydiv.text("Parsing file " + file.name + " ...");
143
+ reader.readAsText(file, "utf8");
144
+ });
145
+ setTimeout(() => butt.node().focus(), 1100);
146
+ };
147
+ fileui();
148
+ }
149
+ function parseheader(line) {
150
+ const header = line.toLowerCase().split(" ");
151
+ if (header.length <= 1) return ["columns must be separated by tab"];
152
+ const htry = (...lst) => {
153
+ for (const i2 of lst) {
154
+ const j = header.indexOf(i2);
155
+ if (j != -1) return j;
156
+ }
157
+ return -1;
158
+ };
159
+ let i = htry("person", "patient", "caseid");
160
+ if (i == -1) return ["person missing"];
161
+ header[i] = "patient";
162
+ i = htry("sample", "sampleid");
163
+ if (i == -1) return ["sample missing"];
164
+ header[i] = "sample";
165
+ i = htry("snv4");
166
+ if (i == -1) return ["snv4 missing"];
167
+ header[i] = "snv4";
168
+ i = htry("date", "dateofsample");
169
+ if (i == -1) return ["date missing"];
170
+ header[i] = "date";
171
+ i = htry("mutant_readcount", "mutantcount");
172
+ if (i != -1) header[i] = "mutant_readcount";
173
+ i = htry("ref_readcount", "refcount");
174
+ if (i != -1) header[i] = "ref_readcount";
175
+ i = htry("total_readcount", "coveragecount");
176
+ if (i == -1) return ["total_readcount missing"];
177
+ header[i] = "coverage";
178
+ i = htry("maf");
179
+ if (i == -1) return ["maf missing"];
180
+ header[i] = "maf";
181
+ i = htry("call_manual");
182
+ if (i != -1) header[i] = "call_manual";
183
+ return [null, header];
184
+ }
185
+ function parseline(i, line, header, badlines, data) {
186
+ const lst = line.split(" ");
187
+ const m = {};
188
+ for (let j = 0; j < header.length; j++) {
189
+ m[header[j]] = lst[j];
190
+ }
191
+ if (!m.patient) {
192
+ badlines.push([i, "missing patient", lst]);
193
+ return;
194
+ }
195
+ if (!data[m.patient]) {
196
+ data[m.patient] = {
197
+ snv4: {},
198
+ show: false
199
+ };
200
+ }
201
+ if (!m.snv4) {
202
+ badlines.push([i, "missing snv4", lst]);
203
+ return;
204
+ }
205
+ if (!data[m.patient].snv4[m.snv4]) {
206
+ data[m.patient].snv4[m.snv4] = {
207
+ mutationname: m.snv4,
208
+ samples: [],
209
+ subidx: void 0
210
+ };
211
+ }
212
+ if (m.gene) {
213
+ data[m.patient].snv4[m.snv4].gene = m.gene;
214
+ }
215
+ if (!m.maf) {
216
+ badlines.push([i, "missing maf", lst]);
217
+ return;
218
+ }
219
+ let v = Number.parseFloat(m.maf);
220
+ if (Number.isNaN(v)) {
221
+ badlines.push([i, "invalid maf", lst]);
222
+ return;
223
+ }
224
+ if (v < zerovalue) {
225
+ v = zerovalue;
226
+ }
227
+ m.maf = v;
228
+ if (!m.coverage) {
229
+ badlines.push([i, "missing total_readcount", lst]);
230
+ return;
231
+ }
232
+ if (m.call_manual && m.call_manual == "wildtype") {
233
+ m.maf = zerovalue;
234
+ }
235
+ v = Number.parseInt(m.coverage);
236
+ if (Number.isNaN(v)) {
237
+ badlines.push([i, "invalid total_readcount", lst]);
238
+ return;
239
+ }
240
+ m.coverage = v;
241
+ let date;
242
+ if (m.date) {
243
+ const f = timeParse("%m/%d/%Y");
244
+ date = f(m.date);
245
+ m.Date = m.date;
246
+ } else {
247
+ badlines.push([i, "missing date", lst]);
248
+ return;
249
+ }
250
+ if (date == null) {
251
+ badlines.push([i, "cannot parse date", lst]);
252
+ return;
253
+ }
254
+ m.date = date;
255
+ if (!m.sample) {
256
+ badlines.push([i, "missing sample", lst]);
257
+ return;
258
+ }
259
+ data[m.patient].snv4[m.snv4].samples.push(m);
260
+ return true;
261
+ }
262
+ function render(data, header, holder) {
263
+ const table = holder.append("table").style("margin", "20px");
264
+ const tr1 = table.append("tr");
265
+ let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
266
+ td.append("button").text("Toggle circle visibility").on("click", () => {
267
+ showcircle = !showcircle;
268
+ for (const n in data) {
269
+ if (data[n].show) {
270
+ data[n].handle.node().click();
271
+ break;
272
+ }
273
+ }
274
+ });
275
+ const patientholder = td.append("div").style("margin-top", "10px");
276
+ const td1 = tr1.append("td").style("vertical-align", "top");
277
+ const graphholder = td1.append("div").style("display", "inline-block");
278
+ const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
279
+ const tr2 = table.append("tr");
280
+ const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
281
+ const gtr1 = tiantable.append("tr");
282
+ td = gtr1.append("td").style("vertical-align", "top");
283
+ td.append("div").text("Shared").style("font-size", "2em");
284
+ const graph1holder = td.append("div").style("border", "solid 1px black");
285
+ td = gtr1.append("td").style("vertical-align", "top");
286
+ td.append("div").text("Rising").style("font-size", "2em");
287
+ const graph2holder = td.append("div").style("border", "solid 1px black");
288
+ const gtr2 = tiantable.append("tr");
289
+ td = gtr2.append("td").style("vertical-align", "top");
290
+ td.append("div").text("Falling").style("font-size", "2em");
291
+ const graph3holder = td.append("div").style("border", "solid 1px black");
292
+ td = gtr2.append("td").style("vertical-align", "top");
293
+ td.append("div").text("R-only").style("font-size", "2em");
294
+ const graph4holder = td.append("div").style("border", "solid 1px black");
295
+ for (const patient in data) {
296
+ const snvlst = [];
297
+ const colors = ordinal(category10_default);
298
+ for (const x in data[patient].snv4) {
299
+ const snv = data[patient].snv4[x];
300
+ snv.show = true;
301
+ snv.color = colors(snv.mutationname);
302
+ snv.samples.sort((a, b) => a.date - b.date);
303
+ for (const s of snv.samples) {
304
+ s.color = snv.color;
305
+ }
306
+ snvlst.push(snv);
307
+ }
308
+ const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
309
+ for (const pn in data) {
310
+ data[pn].handle.style("color", "black");
311
+ data[pn].show = false;
312
+ }
313
+ data[patient].handle.style("color", "red");
314
+ data[patient].show = true;
315
+ makegraph(snvlst, header, graphholder);
316
+ makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
317
+ makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
318
+ });
319
+ data[patient].handle = div;
320
+ }
321
+ for (const n in data) {
322
+ data[n].handle.node().click();
323
+ break;
324
+ }
325
+ }
326
+ function makesubgraph(snvlst, g1, g2, g3, g4) {
327
+ g1.selectAll("*").remove();
328
+ g2.selectAll("*").remove();
329
+ g3.selectAll("*").remove();
330
+ g4.selectAll("*").remove();
331
+ const l1 = [];
332
+ const l2 = [];
333
+ const l3 = [];
334
+ const l4 = [];
335
+ for (const snv of snvlst) {
336
+ switch (snv.subidx) {
337
+ case 1:
338
+ l1.push(snv);
339
+ break;
340
+ case 2:
341
+ l2.push(snv);
342
+ break;
343
+ case 3:
344
+ l3.push(snv);
345
+ break;
346
+ case 4:
347
+ l4.push(snv);
348
+ break;
349
+ }
350
+ }
351
+ if (l1.length) {
352
+ makegraph(l1, null, g1, true);
353
+ } else {
354
+ g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
355
+ }
356
+ if (l2.length) {
357
+ makegraph(l2, null, g2, true);
358
+ } else {
359
+ g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
360
+ }
361
+ if (l3.length) {
362
+ makegraph(l3, null, g3, true);
363
+ } else {
364
+ g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
365
+ }
366
+ if (l4.length) {
367
+ makegraph(l4, null, g4, true);
368
+ } else {
369
+ g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
370
+ }
371
+ }
372
+ function makegraph(snvlst0, header, holder, issub) {
373
+ holder.selectAll("*").remove();
374
+ const samples = [];
375
+ const snvlst = [];
376
+ for (const snv of snvlst0) {
377
+ if (!issub && !snv.show) continue;
378
+ snvlst.push(snv);
379
+ for (const s of snv.samples) {
380
+ samples.push(s);
381
+ }
382
+ }
383
+ if (snvlst.length == 0) return;
384
+ let mindate = snvlst[0].samples[0].date;
385
+ let maxdate = snvlst[0].samples[0].date;
386
+ let maxmaf = snvlst[0].samples[0].maf;
387
+ let maxcoverage = snvlst[0].samples[0].coverage;
388
+ for (const snv of snvlst) {
389
+ for (const s of snv.samples) {
390
+ mindate = Math.min(mindate, s.date);
391
+ maxdate = Math.max(maxdate, s.date);
392
+ maxmaf = Math.max(maxmaf, s.maf);
393
+ maxcoverage = Math.max(maxcoverage, s.coverage);
394
+ }
395
+ }
396
+ const svg = holder.append("svg");
397
+ const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
398
+ let width = 600;
399
+ let height = 400;
400
+ let xpad, ypad, minradius;
401
+ const xaxisg = svg.append("g");
402
+ const yaxisg = svg.append("g");
403
+ const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
404
+ event.preventDefault();
405
+ const x = event.clientX;
406
+ const y = event.clientY;
407
+ const w0 = width;
408
+ const h0 = height;
409
+ const body = select_default(document.body);
410
+ body.on("mousemove", (event2) => {
411
+ setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
412
+ }).on("mouseup", () => {
413
+ body.on("mousemove", null).on("mouseup", null);
414
+ });
415
+ });
416
+ const xscale = time().domain([mindate, maxdate]);
417
+ const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
418
+ const rscale = linear().domain([1, maxcoverage]);
419
+ const g = svg.append("g");
420
+ const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
421
+ let circles;
422
+ if (showcircle) {
423
+ circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
424
+ event.target.setAttribute("fill-opacity", 0.4);
425
+ tip.clear();
426
+ tip.show(event.clientX, event.clientY);
427
+ const lst = [];
428
+ for (const k in d) {
429
+ if (k == "color") continue;
430
+ if (k == "gene") {
431
+ lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
432
+ continue;
433
+ }
434
+ if (k == "date") continue;
435
+ if (k == "url") {
436
+ lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
437
+ continue;
438
+ }
439
+ lst.push({ k, v: d[k] });
440
+ }
441
+ make_table_2col(tip.d, lst);
442
+ }).on("mouseout", (event) => {
443
+ event.target.setAttribute("fill-opacity", 0.1);
444
+ });
445
+ }
446
+ const legend = svg.append("g");
447
+ const setsize = (w, h) => {
448
+ width = w;
449
+ height = h;
450
+ minradius = 2;
451
+ const maxradius = Math.max(width, height) / 30;
452
+ xpad = maxradius;
453
+ ypad = maxradius;
454
+ rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
455
+ xscale.range([0, width]);
456
+ yscale.range([height, 0]);
457
+ svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
458
+ xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
459
+ yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
460
+ drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
461
+ axisstyle({
462
+ axis: xaxisg.call(axisBottom().scale(xscale)),
463
+ showline: true,
464
+ color: "black",
465
+ fontsize: Math.max(12, Math.min(20, width / 100))
466
+ });
467
+ axisstyle({
468
+ axis: yaxisg.call(
469
+ axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
470
+ ),
471
+ showline: true,
472
+ color: "black",
473
+ fontsize: Math.max(12, Math.min(20, height / 100))
474
+ });
475
+ g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
476
+ lines.attr("d", (d) => {
477
+ const lst = [];
478
+ for (let i = 0; i < d.samples.length; i++) {
479
+ const s = d.samples[i];
480
+ lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
481
+ }
482
+ return lst.join(" ");
483
+ });
484
+ if (showcircle) {
485
+ circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
486
+ }
487
+ legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
488
+ legend.selectAll("*").remove();
489
+ let y = minradius;
490
+ if (showcircle) {
491
+ legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
492
+ legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
493
+ y += 5 + minradius + maxradius;
494
+ legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
495
+ legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
496
+ y += 15 + maxradius;
497
+ }
498
+ const fontsize = 12;
499
+ for (const snv of snvlst) {
500
+ legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
501
+ if (showcircle) {
502
+ legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
503
+ }
504
+ legend.append("text").text(snv.gene).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("x", 30 + 10).attr("y", y).attr("fill", snv.color).style("cursor", "default").on("mouseover", (event) => {
505
+ event.target.setAttribute("font-weight", "bold");
506
+ lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
507
+ }).on("mouseout", (event) => {
508
+ event.target.setAttribute("font-weight", "normal");
509
+ lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
510
+ });
511
+ y += fontsize + 10;
512
+ }
513
+ };
514
+ setsize(width, height);
515
+ holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
516
+ to_svg(svg.node(), "maf-timeline");
517
+ });
518
+ }
519
+ function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
520
+ holder.selectAll("*").remove();
521
+ const table = holder.append("table");
522
+ for (const snv of snvlst) {
523
+ const tr = table.append("tr");
524
+ const td1 = tr.append("td");
525
+ td1.text(snv.gene).style("color", snv.color);
526
+ const td2 = tr.append("td");
527
+ const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
528
+ snv.checkbox = checkbox;
529
+ checkbox.on("change", (event) => {
530
+ snv.show = event.target.checked;
531
+ makegraph(snvlst, header, graphholder);
532
+ });
533
+ const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
534
+ for (const s2 of snvlst) {
535
+ s2.show = false;
536
+ s2.checkbox.property("checked", false);
537
+ }
538
+ snv.show = true;
539
+ snv.checkbox.property("checked", true);
540
+ makegraph(snvlst, header, graphholder);
541
+ });
542
+ let cname = Math.random();
543
+ const td11 = tr.append("td");
544
+ const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
545
+ td11.append("label").html("&nbsp;shared").attr("for", cname);
546
+ cname = Math.random();
547
+ const td22 = tr.append("td");
548
+ const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
549
+ td22.append("label").html("&nbsp;rising").attr("for", cname);
550
+ cname = Math.random();
551
+ const td33 = tr.append("td");
552
+ const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
553
+ td33.append("label").html("&nbsp;falling").attr("for", cname);
554
+ cname = Math.random();
555
+ const td44 = tr.append("td");
556
+ const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
557
+ td44.append("label").html("&nbsp;R-only").attr("for", cname);
558
+ if (snv.subidx == 1) c1.property("checked", true);
559
+ if (snv.subidx == 2) c2.property("checked", true);
560
+ if (snv.subidx == 3) c3.property("checked", true);
561
+ if (snv.subidx == 4) c4.property("checked", true);
562
+ const cchange = (which, check) => {
563
+ if (!check.checked) {
564
+ snv.subidx = -1;
565
+ } else {
566
+ snv.subidx = which;
567
+ if (which == 1) {
568
+ c2.property("checked", false);
569
+ c3.property("checked", false);
570
+ c4.property("checked", false);
571
+ } else if (which == 2) {
572
+ c1.property("checked", false);
573
+ c3.property("checked", false);
574
+ c4.property("checked", false);
575
+ } else if (which == 3) {
576
+ c1.property("checked", false);
577
+ c2.property("checked", false);
578
+ c4.property("checked", false);
579
+ } else {
580
+ c1.property("checked", false);
581
+ c2.property("checked", false);
582
+ c3.property("checked", false);
583
+ }
584
+ }
585
+ makesubgraph(snvlst, g1, g2, g3, g4);
586
+ };
587
+ }
588
+ }
589
+ export {
590
+ maftimelineui as default
591
+ };
592
+ //# sourceMappingURL=maftimeline-V43NQEEE.js.map
@@ -0,0 +1,57 @@
1
+ import {
2
+ Matrix,
3
+ componentInit,
4
+ makeChartBtnMenu,
5
+ matrixInit
6
+ } from "./chunk-YLDE3PVC.js";
7
+ import "./chunk-YBIZRASR.js";
8
+ import "./chunk-AROMXWCY.js";
9
+ import "./chunk-6ATE2TRC.js";
10
+ import "./chunk-FUSVXQ6C.js";
11
+ import "./chunk-DDKS3MV3.js";
12
+ import "./chunk-42Q53PXE.js";
13
+ import "./chunk-JUIPCWAM.js";
14
+ import "./chunk-QX3GF2IA.js";
15
+ import "./chunk-ALW5XXVW.js";
16
+ import "./chunk-46ASPS5Y.js";
17
+ import "./chunk-WP22GYZ2.js";
18
+ import "./chunk-HUBO743S.js";
19
+ import "./chunk-2QQO4RRD.js";
20
+ import "./chunk-V2OJLJSK.js";
21
+ import "./chunk-2XPDA6NL.js";
22
+ import "./chunk-HJ6L54YS.js";
23
+ import "./chunk-LSEFWW72.js";
24
+ import "./chunk-GHWHLSUX.js";
25
+ import "./chunk-HYOEWQ5P.js";
26
+ import "./chunk-HBW42TDT.js";
27
+ import "./chunk-G6O3URDN.js";
28
+ import "./chunk-FN5XPUPH.js";
29
+ import "./chunk-KWM6B3NL.js";
30
+ import "./chunk-UCLS2SVB.js";
31
+ import "./chunk-AY4UBGLC.js";
32
+ import "./chunk-2P6Z7JFC.js";
33
+ import "./chunk-MYWJQRTD.js";
34
+ import "./chunk-MVTCBVSX.js";
35
+ import "./chunk-B43MTEYB.js";
36
+ import "./chunk-2T7VYQLY.js";
37
+ import "./chunk-FDK4UJMN.js";
38
+ import "./chunk-X7GDCYND.js";
39
+ import "./chunk-SJC2C77V.js";
40
+ import "./chunk-C3SYSMNE.js";
41
+ import "./chunk-KSGA62R2.js";
42
+ import "./chunk-LOZEKOES.js";
43
+ import "./chunk-TOU7EVFQ.js";
44
+ import "./chunk-OAWQ6LOO.js";
45
+ import "./chunk-NMBIT4IK.js";
46
+ import "./chunk-KYBIQBXE.js";
47
+ import "./chunk-I6Y4O3RR.js";
48
+ import "./chunk-OMR2DT66.js";
49
+ import "./chunk-DQC5FFGV.js";
50
+ import "./chunk-HFNDKYVF.js";
51
+ export {
52
+ Matrix,
53
+ componentInit,
54
+ makeChartBtnMenu,
55
+ matrixInit
56
+ };
57
+ //# sourceMappingURL=matrix-EB2EFP4S.js.map