@sjcrh/proteinpaint-client 2.224.1 → 2.224.2

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 (980) hide show
  1. package/dist/2dmaf-OWA6REJ5.js +1362 -0
  2. package/dist/AggMatrixInput-5GC33U5A.js +402 -0
  3. package/dist/AggregateMatrix-CMJFO53B.js +37 -0
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  8. package/dist/Cuminc-HHBYFFFM.js +1217 -0
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  849. /package/dist/{hierCluster-C67VO3VF.js.map → hierCluster-POD3DRO4.js.map} +0 -0
  850. /package/dist/{hierCluster-CEJTROX7.js.map → hierCluster-QA7HXKRD.js.map} +0 -0
  851. /package/dist/{hierCluster.config-G3X5I72U.js.map → hierCluster.config-HQ3SVKCE.js.map} +0 -0
  852. /package/dist/{hierCluster.integration.spec-HTS2GNUR.js.map → hierCluster.integration.spec-MOYDWJL3.js.map} +0 -0
  853. /package/dist/{hierCluster.interactivity-4JVDLIPZ.js.map → hierCluster.interactivity-OZTNHXZQ.js.map} +0 -0
  854. /package/dist/{hierCluster.renderers-YGX6MZZW.js.map → hierCluster.renderers-46E37NL4.js.map} +0 -0
  855. /package/dist/{imagePlot-HNKJX6YK.js.map → imagePlot-HNAYBWY3.js.map} +0 -0
  856. /package/dist/{importPlot-XUL6XFBL.js.map → importPlot-XTW46VF4.js.map} +0 -0
  857. /package/dist/{isoformExpression-ZJJUXJDF.js.map → isoformExpression-2TMTILKG.js.map} +0 -0
  858. /package/dist/{isoformExpression.unit.spec-INU6WFAM.js.map → isoformExpression.unit.spec-SIJWP7TH.js.map} +0 -0
  859. /package/dist/{jspdf.es.min-THXUXEDC.js.map → jspdf.es.min-GSH2SAQO.js.map} +0 -0
  860. /package/dist/{junction-FKYIKDC4.js.map → junction-AICKHNXX.js.map} +0 -0
  861. /package/dist/{junction.customTerm-3R2GNE3A.js.map → junction.customTerm-5STKYZ4B.js.map} +0 -0
  862. /package/dist/{junction.unit.spec-VRFIOT4T.js.map → junction.unit.spec-EXFN4MLW.js.map} +0 -0
  863. /package/dist/{launch.adhoc-SDMXDSHS.js.map → launch.adhoc-PB6PGR7Q.js.map} +0 -0
  864. /package/dist/{leftlabel.sample-S33KB225.js.map → leftlabel.sample-ISUD4A7F.js.map} +0 -0
  865. /package/dist/{lollipop-WXQOGEY7.js.map → lollipop-5UXUAFYY.js.map} +0 -0
  866. /package/dist/{maf-K6ZUNABR.js.map → maf-L6YD25JK.js.map} +0 -0
  867. /package/dist/{maftimeline-Y2LETT7W.js.map → maftimeline-63YZDGJ3.js.map} +0 -0
  868. /package/dist/{matrix-LADX4K5W.js.map → matrix-OPEBHZCW.js.map} +0 -0
  869. /package/dist/{matrix-M63KP6IL.js.map → matrix-TLMWPG7C.js.map} +0 -0
  870. /package/dist/{matrix.cells-5RTZUJVN.js.map → matrix.cells-IELMNYC6.js.map} +0 -0
  871. /package/dist/{matrix.config-ZMT7A2D5.js.map → matrix.config-J7SVFXLM.js.map} +0 -0
  872. /package/dist/{matrix.data-Y5TPRGMW.js.map → matrix.data-DJTJCPO4.js.map} +0 -0
  873. /package/dist/{matrix.groups-6DXCAY4P.js.map → matrix.groups-2REICNZK.js.map} +0 -0
  874. /package/dist/{matrix.integration.spec-LJ5EQ65D.js.map → matrix.integration.spec-ZXU2OEFU.js.map} +0 -0
  875. /package/dist/{matrix.interactivity-2ISWFOK2.js.map → matrix.interactivity-SX3OR6OI.js.map} +0 -0
  876. /package/dist/{matrix.layout-EAYTUK2H.js.map → matrix.layout-ZJ6X5RON.js.map} +0 -0
  877. /package/dist/{matrix.legend-S3E76TVO.js.map → matrix.legend-ZOP72TIO.js.map} +0 -0
  878. /package/dist/{matrix.renderers-XUMZZUDW.js.map → matrix.renderers-YUSROXKN.js.map} +0 -0
  879. /package/dist/{matrix.serieses-3UGLZW25.js.map → matrix.serieses-UMAZNCMR.js.map} +0 -0
  880. /package/dist/{matrix.sort-A7CNLDUJ.js.map → matrix.sort-2JNIZHNL.js.map} +0 -0
  881. /package/dist/{matrix.sort.unit.spec-UPG3D6GE.js.map → matrix.sort.unit.spec-SNB643Y6.js.map} +0 -0
  882. /package/dist/{matrix.sorterUi-6PZR3YOD.js.map → matrix.sorterUi-JXEIY6UL.js.map} +0 -0
  883. /package/dist/{matrix.sorterUi.unit.spec-WPMREECT.js.map → matrix.sorterUi.unit.spec-LDAT4R3H.js.map} +0 -0
  884. /package/dist/{matrix.unit.spec-Z2HXOXM4.js.map → matrix.unit.spec-QBQIMDLD.js.map} +0 -0
  885. /package/dist/{mavb-WT4XM6U3.js.map → mavb-EQUF3VGG.js.map} +0 -0
  886. /package/dist/{mds.samplescatterplot-UTEBJF66.js.map → mds.samplescatterplot-73E45ZT7.js.map} +0 -0
  887. /package/dist/{mds.survivalplot-DXWJA4IJ.js.map → mds.survivalplot-DL53IRVD.js.map} +0 -0
  888. /package/dist/{multivalue-LR7Z3OLZ.js.map → multivalue-PQN75ENP.js.map} +0 -0
  889. /package/dist/{numericDictTermCluster-6XDVVWLE.js.map → numericDictTermCluster-FGMIOTBO.js.map} +0 -0
  890. /package/dist/{oncomatrix-WV2LSH3X.js.map → oncomatrix-CCHWOA3N.js.map} +0 -0
  891. /package/dist/{oncomatrix.spec-S7KHSJJG.js.map → oncomatrix.spec-GQT3UTCR.js.map} +0 -0
  892. /package/dist/{plot.2dvaf-FH7PMZ3U.js.map → plot.2dvaf-L6ZI5ROR.js.map} +0 -0
  893. /package/dist/{plot.app-DDB6YZJ3.js.map → plot.app-A73VXJCP.js.map} +0 -0
  894. /package/dist/{plot.barplot-XVSZDYKB.js.map → plot.barplot-HSCHPOO7.js.map} +0 -0
  895. /package/dist/{plot.boxplot-M6URTYED.js.map → plot.boxplot-AXBVNTNH.js.map} +0 -0
  896. /package/dist/{plot.brainImaging-GNIBY3XC.js.map → plot.brainImaging-PEMURKM3.js.map} +0 -0
  897. /package/dist/{plot.disco-EH4E7B3O.js.map → plot.disco-YKMYYVMV.js.map} +0 -0
  898. /package/dist/{plot.ssgq-7HIGQHOT.js.map → plot.ssgq-FGMQXKZU.js.map} +0 -0
  899. /package/dist/{plot.vaf2cov-MGJHP2PV.js.map → plot.vaf2cov-IBM7NQEB.js.map} +0 -0
  900. /package/dist/{polar2-VYUW5GZO.js.map → polar2-N7KWY36S.js.map} +0 -0
  901. /package/dist/{profileForms-LHJCFAP6.js.map → profileForms-Q4NN7653.js.map} +0 -0
  902. /package/dist/{profilePlot-UF2KERDD.js.map → profilePlot-SQ77M6LI.js.map} +0 -0
  903. /package/dist/{proteinView-5AF4I3PB.js.map → proteinView-KSIZRDNP.js.map} +0 -0
  904. /package/dist/{proteomeCohortCompare-4DYWZTLQ.js.map → proteomeCohortCompare-GYSBJSDY.js.map} +0 -0
  905. /package/dist/{pseudbulk.unit.spec-ZTAP2YYA.js.map → pseudbulk.unit.spec-XELPZVXM.js.map} +0 -0
  906. /package/dist/{pseudobulk-A2KE233U.js.map → pseudobulk-H3USXM5U.js.map} +0 -0
  907. /package/dist/{qualitative-3FDE4JUM.js.map → qualitative-ABXENRAF.js.map} +0 -0
  908. /package/dist/{qualitative-NVWG57TK.js.map → qualitative-OSEJTJ4D.js.map} +0 -0
  909. /package/dist/{radar2-3CQ7T5QY.js.map → radar2-VTDQGHWN.js.map} +0 -0
  910. /package/dist/{radarFacility2-ERBWZQFH.js.map → radarFacility2-BWGEC5A2.js.map} +0 -0
  911. /package/dist/{rememberedGvQ.unit.spec-SHTMMZGG.js.map → rememberedGvQ.unit.spec-TWUDSEDP.js.map} +0 -0
  912. /package/dist/{render-LIUPN5SK.js.map → render-C3XJQ2QY.js.map} +0 -0
  913. /package/dist/{report-JWNWR6NA.js.map → report-7ZZ44X4R.js.map} +0 -0
  914. /package/dist/{sampleView-BQ6HCCKT.js.map → sampleView-CUCNI65Q.js.map} +0 -0
  915. /package/dist/{samplelst-RQWH7WOX.js.map → samplelst-S7AJQ36J.js.map} +0 -0
  916. /package/dist/{samplematrix-7FDWXSZA.js.map → samplematrix-U7WM6GNB.js.map} +0 -0
  917. /package/dist/{sc-J2ZPQFGP.js.map → sc-FMJHN2SW.js.map} +0 -0
  918. /package/dist/{scatter-7FQLITP7.js.map → scatter-4UMCJNEH.js.map} +0 -0
  919. /package/dist/{scatter-BDIZX73F.js.map → scatter-KMAZ3ZNR.js.map} +0 -0
  920. /package/dist/{selectGenomeWithTklst-52BHWMVR.js.map → selectGenomeWithTklst-5SRM45BI.js.map} +0 -0
  921. /package/dist/{singleCellCellType-OC6QG6MU.js.map → singleCellCellType-GIIICJK5.js.map} +0 -0
  922. /package/dist/{singleCellCellType.unit.spec-R3QPRXVY.js.map → singleCellCellType.unit.spec-MVA7BMGL.js.map} +0 -0
  923. /package/dist/{singleCellGeneExpression-QDRIVFQ5.js.map → singleCellGeneExpression-2QFQHJJH.js.map} +0 -0
  924. /package/dist/{singleCellGeneExpression.unit.spec-FHUA6VWD.js.map → singleCellGeneExpression.unit.spec-SAIETYHV.js.map} +0 -0
  925. /package/dist/{singleCellNumericValue-2PKMS7NM.js.map → singleCellNumericValue-45H5EPIB.js.map} +0 -0
  926. /package/dist/{singleCellNumericValue.unit.spec-YXDYOFJ5.js.map → singleCellNumericValue.unit.spec-FNKEJ2WC.js.map} +0 -0
  927. /package/dist/{singleCellPlot-5RVA7KM7.js.map → singleCellPlot-SP7OEGYQ.js.map} +0 -0
  928. /package/dist/{singlecell-5OUPDXEQ.js.map → singlecell-AVZQX4AH.js.map} +0 -0
  929. /package/dist/{singlecell-MLKBNJAG.js.map → singlecell-JQKUHGIH.js.map} +0 -0
  930. /package/dist/{snp-ARLPF6ZU.js.map → snp-4SA7VABN.js.map} +0 -0
  931. /package/dist/{snp.unit.spec-MUB7YKMP.js.map → snp.unit.spec-YIYGR6GW.js.map} +0 -0
  932. /package/dist/{snplocus-EZ33TXDU.js.map → snplocus-TDGQ57ZJ.js.map} +0 -0
  933. /package/dist/{snplst-GLTNXAE5.js.map → snplst-SWBGRYPA.js.map} +0 -0
  934. /package/dist/{spliceevent.a53ss.diagram-FMP6CNCV.js.map → spliceevent.a53ss.diagram-YODOBS6U.js.map} +0 -0
  935. /package/dist/{spliceevent.exonskip.diagram-QRQ3DZ3I.js.map → spliceevent.exonskip.diagram-PMZIQ5UG.js.map} +0 -0
  936. /package/dist/{spliceevent.noeventdiagram-LAPCKJS3.js.map → spliceevent.noeventdiagram-A4T2PNUX.js.map} +0 -0
  937. /package/dist/{ssGSEA-WUE2PKUU.js.map → ssGSEA-U7D6HOIV.js.map} +0 -0
  938. /package/dist/{ssGSEA.unit.spec-Y7KCKEGK.js.map → ssGSEA.unit.spec-SMNAM5DJ.js.map} +0 -0
  939. /package/dist/{stattable-GZF4ZWTT.js.map → stattable-DBYMPJU6.js.map} +0 -0
  940. /package/dist/{studyCatalog-PPV7WB2O.js.map → studyCatalog-7RABX4W5.js.map} +0 -0
  941. /package/dist/{summarizeCnvGeneexp-LZ7UWWZS.js.map → summarizeCnvGeneexp-YVRW7LWY.js.map} +0 -0
  942. /package/dist/{summarizeGeneexpSurvival-VBRJFZR6.js.map → summarizeGeneexpSurvival-ZB7IWGPS.js.map} +0 -0
  943. /package/dist/{summarizeMutationCnv-6LUM4YR7.js.map → summarizeMutationCnv-CUSYURDK.js.map} +0 -0
  944. /package/dist/{summarizeMutationDiagnosis-B47HKNM6.js.map → summarizeMutationDiagnosis-NSPCT5WI.js.map} +0 -0
  945. /package/dist/{summarizeMutationSurvival-6GH3MTLN.js.map → summarizeMutationSurvival-2PZZCC4G.js.map} +0 -0
  946. /package/dist/{summary-BBI7MS3B.js.map → summary-CYDZSICI.js.map} +0 -0
  947. /package/dist/{summary.integration.spec-SYLP7X3F.js.map → summary.integration.spec-2TLKJS3X.js.map} +0 -0
  948. /package/dist/{summaryInput-5PPK7KRL.js.map → summaryInput-BRQ5JRGV.js.map} +0 -0
  949. /package/dist/{sunburst-BVPS44ZR.js.map → sunburst-435LKL2S.js.map} +0 -0
  950. /package/dist/{sunburst-H57DYWLE.js.map → sunburst-D5WAGHX6.js.map} +0 -0
  951. /package/dist/{survival-PRHRAD2T.js.map → survival-MHESSYWF.js.map} +0 -0
  952. /package/dist/{survival.integration.spec-KH6GPVZ4.js.map → survival.integration.spec-WMS3FTNR.js.map} +0 -0
  953. /package/dist/{svg2pdf.es.min-BRE45YLJ.js.map → svg2pdf.es.min-PHWTISHJ.js.map} +0 -0
  954. /package/dist/{svgraph-VVGRE672.js.map → svgraph-LYFGVTHI.js.map} +0 -0
  955. /package/dist/{svmr-OKTQIHLN.js.map → svmr-UR67QZIP.js.map} +0 -0
  956. /package/dist/{swimmer-U5COUOM6.js.map → swimmer-RP4SUEZS.js.map} +0 -0
  957. /package/dist/{table-I7SINEY4.js.map → table-V4OOMF3B.js.map} +0 -0
  958. /package/dist/{termCollection-QCSPDISY.js.map → termCollection-VHGVBSWW.js.map} +0 -0
  959. /package/dist/{termCollection-TFNI2VIX.js.map → termCollection-WSNM3YFK.js.map} +0 -0
  960. /package/dist/{termCollection.unit.spec-22E76H2W.js.map → termCollection.unit.spec-NCZUZL6P.js.map} +0 -0
  961. /package/dist/{termCollectionFractionSelection-VZ5JJ7KV.js.map → termCollectionFractionSelection-XM3FJWBQ.js.map} +0 -0
  962. /package/dist/{termCollectionFractionSelection.unit.spec-KCAQU2BV.js.map → termCollectionFractionSelection.unit.spec-VO4SAV72.js.map} +0 -0
  963. /package/dist/{tk-YOBCGYFC.js.map → tk-G5PKWSXJ.js.map} +0 -0
  964. /package/dist/{tk-GBNB42AI.js.map → tk-KIELQHVI.js.map} +0 -0
  965. /package/dist/{tp.ui-OEL4S73T.js.map → tp.ui-HAKSWLFB.js.map} +0 -0
  966. /package/dist/{tvs.categorical-3X6CO5EA.js.map → tvs.categorical-G4DM4JY5.js.map} +0 -0
  967. /package/dist/{tvs.condition-YZQSSONN.js.map → tvs.condition-E5NUQONB.js.map} +0 -0
  968. /package/dist/{tvs.dt-GCMLLAJC.js.map → tvs.dt-T4BK24VZ.js.map} +0 -0
  969. /package/dist/{tvs.dtcnv.categorical-ZSYUQQXP.js.map → tvs.dtcnv.categorical-V57TZFRA.js.map} +0 -0
  970. /package/dist/{tvs.dtcnv.continuous-T67YFFAE.js.map → tvs.dtcnv.continuous-D4YIB4PN.js.map} +0 -0
  971. /package/dist/{tvs.dtfusion-VR2NAX3F.js.map → tvs.dtfusion-6DUFLUNH.js.map} +0 -0
  972. /package/dist/{tvs.dtitd-O3MIZPZO.js.map → tvs.dtitd-GOEPAQGR.js.map} +0 -0
  973. /package/dist/{tvs.dtsnvindel-6G7UNHSQ.js.map → tvs.dtsnvindel-ASTXGC4O.js.map} +0 -0
  974. /package/dist/{tvs.dtsv-VZ2I4AMH.js.map → tvs.dtsv-7TGDEWXK.js.map} +0 -0
  975. /package/dist/{tvs.multivalue-6KFI5ELB.js.map → tvs.multivalue-SEIGL2W6.js.map} +0 -0
  976. /package/dist/{tvs.numeric-SFSOLXVF.js.map → tvs.numeric-MLLX5L7Z.js.map} +0 -0
  977. /package/dist/{tvs.samplelst-WD5UMMTP.js.map → tvs.samplelst-HAV7C2EA.js.map} +0 -0
  978. /package/dist/{tvs.survival-A2RUXAXJ.js.map → tvs.survival-3B522MT2.js.map} +0 -0
  979. /package/dist/{tvs.termCollection-NVW4LO44.js.map → tvs.termCollection-R5NG4VXP.js.map} +0 -0
  980. /package/dist/{vocabulary-FASF5IUM.js.map → vocabulary-LBNHNSEN.js.map} +0 -0
@@ -1,583 +0,0 @@
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-3YQYWX4M.js";
11
- import "./chunk-HJ6L54YS.js";
12
- import "./chunk-R3RD3VEX.js";
13
- import {
14
- Menu
15
- } from "./chunk-CNFTQSNE.js";
16
- import "./chunk-RIHO7ZD5.js";
17
- import "./chunk-TVJOSRCH.js";
18
- import "./chunk-3CIL7KH7.js";
19
- import "./chunk-T4XPCSLP.js";
20
- import "./chunk-KBTFT76L.js";
21
- import "./chunk-W5J3LTYS.js";
22
- import "./chunk-MHWYRNGA.js";
23
- import "./chunk-JHLF2ZC2.js";
24
- import {
25
- axisBottom,
26
- axisLeft,
27
- category10_default
28
- } from "./chunk-WJLRU5OF.js";
29
- import "./chunk-HBNB5TRH.js";
30
- import "./chunk-PF4DSFDR.js";
31
- import {
32
- format,
33
- linear,
34
- log,
35
- ordinal,
36
- time,
37
- timeParse
38
- } from "./chunk-4OLM3KSB.js";
39
- import "./chunk-PWYMHUXY.js";
40
- import "./chunk-TLT4YIG3.js";
41
- import "./chunk-5R63Q5KH.js";
42
- import {
43
- select_default
44
- } from "./chunk-I6Y4O3RR.js";
45
- import "./chunk-Q5RDQNIT.js";
46
- import "./chunk-HS5PO5ZQ.js";
47
-
48
- // src/maftimeline.js
49
- var zerovalue = 1e-5;
50
- var showcircle = true;
51
- var maflogscale = true;
52
- var tip = new Menu();
53
- function maftimelineui(genomes, holder, sandbox_header) {
54
- let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
55
- if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
56
- else {
57
- ;
58
- [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
59
- pane.header.text("MAF timeline plot");
60
- }
61
- inputdiv.append("p").html(
62
- "<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
63
- );
64
- inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
65
- {
66
- const id = Math.random().toString();
67
- const p = inputdiv.append("p");
68
- p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
69
- maflogscale = !maflogscale;
70
- });
71
- p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
72
- }
73
- const fileui = () => {
74
- filediv.selectAll("*").remove();
75
- const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
76
- saydiv.text("");
77
- const file = event.target.files[0];
78
- if (!file) {
79
- fileui();
80
- return;
81
- }
82
- if (file.size == 0) {
83
- saydiv.text("Wrong file: " + file.name);
84
- fileui();
85
- return;
86
- }
87
- const reader = new FileReader();
88
- reader.onload = (event2) => {
89
- const lines = event2.target.result.trim().split(/\r?\n/);
90
- const [err, header] = parseheader(lines[0].trim());
91
- if (err) {
92
- saydiv.text("File header error: " + err);
93
- fileui();
94
- return;
95
- }
96
- const badlines = [];
97
- const data = {};
98
- let good = 0;
99
- for (let i = 1; i < lines.length; i++) {
100
- if (lines[i] == "") continue;
101
- if (lines[i][0] == "#") continue;
102
- const m = parseline(i, lines[i], header, badlines, data);
103
- if (m) {
104
- good++;
105
- }
106
- }
107
- if (badlines.length) {
108
- bulk_badline(header, badlines);
109
- }
110
- if (good == 0) {
111
- fileui();
112
- return;
113
- }
114
- let visual_holder;
115
- if (pane) {
116
- disappear(pane.pane);
117
- const pane2 = newpane({ x: 100, y: 100, toshrink: true });
118
- pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
119
- visual_holder = pane2.body;
120
- }
121
- if (holder !== void 0) {
122
- visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
123
- inputdiv.selectAll("*").remove();
124
- saydiv.text("");
125
- }
126
- render(data, header, visual_holder);
127
- };
128
- reader.onerror = function() {
129
- saydiv.text("Error reading file " + file.name);
130
- fileui();
131
- return;
132
- };
133
- saydiv.text("Parsing file " + file.name + " ...");
134
- reader.readAsText(file, "utf8");
135
- });
136
- setTimeout(() => butt.node().focus(), 1100);
137
- };
138
- fileui();
139
- }
140
- function parseheader(line) {
141
- const header = line.toLowerCase().split(" ");
142
- if (header.length <= 1) return ["columns must be separated by tab"];
143
- const htry = (...lst) => {
144
- for (const i2 of lst) {
145
- const j = header.indexOf(i2);
146
- if (j != -1) return j;
147
- }
148
- return -1;
149
- };
150
- let i = htry("person", "patient", "caseid");
151
- if (i == -1) return ["person missing"];
152
- header[i] = "patient";
153
- i = htry("sample", "sampleid");
154
- if (i == -1) return ["sample missing"];
155
- header[i] = "sample";
156
- i = htry("snv4");
157
- if (i == -1) return ["snv4 missing"];
158
- header[i] = "snv4";
159
- i = htry("date", "dateofsample");
160
- if (i == -1) return ["date missing"];
161
- header[i] = "date";
162
- i = htry("mutant_readcount", "mutantcount");
163
- if (i != -1) header[i] = "mutant_readcount";
164
- i = htry("ref_readcount", "refcount");
165
- if (i != -1) header[i] = "ref_readcount";
166
- i = htry("total_readcount", "coveragecount");
167
- if (i == -1) return ["total_readcount missing"];
168
- header[i] = "coverage";
169
- i = htry("maf");
170
- if (i == -1) return ["maf missing"];
171
- header[i] = "maf";
172
- i = htry("call_manual");
173
- if (i != -1) header[i] = "call_manual";
174
- return [null, header];
175
- }
176
- function parseline(i, line, header, badlines, data) {
177
- const lst = line.split(" ");
178
- const m = {};
179
- for (let j = 0; j < header.length; j++) {
180
- m[header[j]] = lst[j];
181
- }
182
- if (!m.patient) {
183
- badlines.push([i, "missing patient", lst]);
184
- return;
185
- }
186
- if (!data[m.patient]) {
187
- data[m.patient] = {
188
- snv4: {},
189
- show: false
190
- };
191
- }
192
- if (!m.snv4) {
193
- badlines.push([i, "missing snv4", lst]);
194
- return;
195
- }
196
- if (!data[m.patient].snv4[m.snv4]) {
197
- data[m.patient].snv4[m.snv4] = {
198
- mutationname: m.snv4,
199
- samples: [],
200
- subidx: void 0
201
- };
202
- }
203
- if (m.gene) {
204
- data[m.patient].snv4[m.snv4].gene = m.gene;
205
- }
206
- if (!m.maf) {
207
- badlines.push([i, "missing maf", lst]);
208
- return;
209
- }
210
- let v = Number.parseFloat(m.maf);
211
- if (Number.isNaN(v)) {
212
- badlines.push([i, "invalid maf", lst]);
213
- return;
214
- }
215
- if (v < zerovalue) {
216
- v = zerovalue;
217
- }
218
- m.maf = v;
219
- if (!m.coverage) {
220
- badlines.push([i, "missing total_readcount", lst]);
221
- return;
222
- }
223
- if (m.call_manual && m.call_manual == "wildtype") {
224
- m.maf = zerovalue;
225
- }
226
- v = Number.parseInt(m.coverage);
227
- if (Number.isNaN(v)) {
228
- badlines.push([i, "invalid total_readcount", lst]);
229
- return;
230
- }
231
- m.coverage = v;
232
- let date;
233
- if (m.date) {
234
- const f = timeParse("%m/%d/%Y");
235
- date = f(m.date);
236
- m.Date = m.date;
237
- } else {
238
- badlines.push([i, "missing date", lst]);
239
- return;
240
- }
241
- if (date == null) {
242
- badlines.push([i, "cannot parse date", lst]);
243
- return;
244
- }
245
- m.date = date;
246
- if (!m.sample) {
247
- badlines.push([i, "missing sample", lst]);
248
- return;
249
- }
250
- data[m.patient].snv4[m.snv4].samples.push(m);
251
- return true;
252
- }
253
- function render(data, header, holder) {
254
- const table = holder.append("table").style("margin", "20px");
255
- const tr1 = table.append("tr");
256
- let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
257
- td.append("button").text("Toggle circle visibility").on("click", () => {
258
- showcircle = !showcircle;
259
- for (const n in data) {
260
- if (data[n].show) {
261
- data[n].handle.node().click();
262
- break;
263
- }
264
- }
265
- });
266
- const patientholder = td.append("div").style("margin-top", "10px");
267
- const td1 = tr1.append("td").style("vertical-align", "top");
268
- const graphholder = td1.append("div").style("display", "inline-block");
269
- const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
270
- const tr2 = table.append("tr");
271
- const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
272
- const gtr1 = tiantable.append("tr");
273
- td = gtr1.append("td").style("vertical-align", "top");
274
- td.append("div").text("Shared").style("font-size", "2em");
275
- const graph1holder = td.append("div").style("border", "solid 1px black");
276
- td = gtr1.append("td").style("vertical-align", "top");
277
- td.append("div").text("Rising").style("font-size", "2em");
278
- const graph2holder = td.append("div").style("border", "solid 1px black");
279
- const gtr2 = tiantable.append("tr");
280
- td = gtr2.append("td").style("vertical-align", "top");
281
- td.append("div").text("Falling").style("font-size", "2em");
282
- const graph3holder = td.append("div").style("border", "solid 1px black");
283
- td = gtr2.append("td").style("vertical-align", "top");
284
- td.append("div").text("R-only").style("font-size", "2em");
285
- const graph4holder = td.append("div").style("border", "solid 1px black");
286
- for (const patient in data) {
287
- const snvlst = [];
288
- const colors = ordinal(category10_default);
289
- for (const x in data[patient].snv4) {
290
- const snv = data[patient].snv4[x];
291
- snv.show = true;
292
- snv.color = colors(snv.mutationname);
293
- snv.samples.sort((a, b) => a.date - b.date);
294
- for (const s of snv.samples) {
295
- s.color = snv.color;
296
- }
297
- snvlst.push(snv);
298
- }
299
- const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
300
- for (const pn in data) {
301
- data[pn].handle.style("color", "black");
302
- data[pn].show = false;
303
- }
304
- data[patient].handle.style("color", "red");
305
- data[patient].show = true;
306
- makegraph(snvlst, header, graphholder);
307
- makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
308
- makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
309
- });
310
- data[patient].handle = div;
311
- }
312
- for (const n in data) {
313
- data[n].handle.node().click();
314
- break;
315
- }
316
- }
317
- function makesubgraph(snvlst, g1, g2, g3, g4) {
318
- g1.selectAll("*").remove();
319
- g2.selectAll("*").remove();
320
- g3.selectAll("*").remove();
321
- g4.selectAll("*").remove();
322
- const l1 = [];
323
- const l2 = [];
324
- const l3 = [];
325
- const l4 = [];
326
- for (const snv of snvlst) {
327
- switch (snv.subidx) {
328
- case 1:
329
- l1.push(snv);
330
- break;
331
- case 2:
332
- l2.push(snv);
333
- break;
334
- case 3:
335
- l3.push(snv);
336
- break;
337
- case 4:
338
- l4.push(snv);
339
- break;
340
- }
341
- }
342
- if (l1.length) {
343
- makegraph(l1, null, g1, true);
344
- } else {
345
- g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
346
- }
347
- if (l2.length) {
348
- makegraph(l2, null, g2, true);
349
- } else {
350
- g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
351
- }
352
- if (l3.length) {
353
- makegraph(l3, null, g3, true);
354
- } else {
355
- g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
356
- }
357
- if (l4.length) {
358
- makegraph(l4, null, g4, true);
359
- } else {
360
- g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
361
- }
362
- }
363
- function makegraph(snvlst0, header, holder, issub) {
364
- holder.selectAll("*").remove();
365
- const samples = [];
366
- const snvlst = [];
367
- for (const snv of snvlst0) {
368
- if (!issub && !snv.show) continue;
369
- snvlst.push(snv);
370
- for (const s of snv.samples) {
371
- samples.push(s);
372
- }
373
- }
374
- if (snvlst.length == 0) return;
375
- let mindate = snvlst[0].samples[0].date;
376
- let maxdate = snvlst[0].samples[0].date;
377
- let maxmaf = snvlst[0].samples[0].maf;
378
- let maxcoverage = snvlst[0].samples[0].coverage;
379
- for (const snv of snvlst) {
380
- for (const s of snv.samples) {
381
- mindate = Math.min(mindate, s.date);
382
- maxdate = Math.max(maxdate, s.date);
383
- maxmaf = Math.max(maxmaf, s.maf);
384
- maxcoverage = Math.max(maxcoverage, s.coverage);
385
- }
386
- }
387
- const svg = holder.append("svg");
388
- const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
389
- let width = 600;
390
- let height = 400;
391
- let xpad, ypad, minradius;
392
- const xaxisg = svg.append("g");
393
- const yaxisg = svg.append("g");
394
- const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
395
- event.preventDefault();
396
- const x = event.clientX;
397
- const y = event.clientY;
398
- const w0 = width;
399
- const h0 = height;
400
- const body = select_default(document.body);
401
- body.on("mousemove", (event2) => {
402
- setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
403
- }).on("mouseup", () => {
404
- body.on("mousemove", null).on("mouseup", null);
405
- });
406
- });
407
- const xscale = time().domain([mindate, maxdate]);
408
- const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
409
- const rscale = linear().domain([1, maxcoverage]);
410
- const g = svg.append("g");
411
- const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
412
- let circles;
413
- if (showcircle) {
414
- circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
415
- event.target.setAttribute("fill-opacity", 0.4);
416
- tip.clear();
417
- tip.show(event.clientX, event.clientY);
418
- const lst = [];
419
- for (const k in d) {
420
- if (k == "color") continue;
421
- if (k == "gene") {
422
- lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
423
- continue;
424
- }
425
- if (k == "date") continue;
426
- if (k == "url") {
427
- lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
428
- continue;
429
- }
430
- lst.push({ k, v: d[k] });
431
- }
432
- make_table_2col(tip.d, lst);
433
- }).on("mouseout", (event) => {
434
- event.target.setAttribute("fill-opacity", 0.1);
435
- });
436
- }
437
- const legend = svg.append("g");
438
- const setsize = (w, h) => {
439
- width = w;
440
- height = h;
441
- minradius = 2;
442
- const maxradius = Math.max(width, height) / 30;
443
- xpad = maxradius;
444
- ypad = maxradius;
445
- rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
446
- xscale.range([0, width]);
447
- yscale.range([height, 0]);
448
- svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
449
- xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
450
- yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
451
- drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
452
- axisstyle({
453
- axis: xaxisg.call(axisBottom().scale(xscale)),
454
- showline: true,
455
- color: "black",
456
- fontsize: Math.max(12, Math.min(20, width / 100))
457
- });
458
- axisstyle({
459
- axis: yaxisg.call(
460
- axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
461
- ),
462
- showline: true,
463
- color: "black",
464
- fontsize: Math.max(12, Math.min(20, height / 100))
465
- });
466
- g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
467
- lines.attr("d", (d) => {
468
- const lst = [];
469
- for (let i = 0; i < d.samples.length; i++) {
470
- const s = d.samples[i];
471
- lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
472
- }
473
- return lst.join(" ");
474
- });
475
- if (showcircle) {
476
- circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
477
- }
478
- legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
479
- legend.selectAll("*").remove();
480
- let y = minradius;
481
- if (showcircle) {
482
- legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
483
- legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
484
- y += 5 + minradius + maxradius;
485
- legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
486
- legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
487
- y += 15 + maxradius;
488
- }
489
- const fontsize = 12;
490
- for (const snv of snvlst) {
491
- legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
492
- if (showcircle) {
493
- legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
494
- }
495
- 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) => {
496
- event.target.setAttribute("font-weight", "bold");
497
- lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
498
- }).on("mouseout", (event) => {
499
- event.target.setAttribute("font-weight", "normal");
500
- lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
501
- });
502
- y += fontsize + 10;
503
- }
504
- };
505
- setsize(width, height);
506
- holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
507
- to_svg(svg.node(), "maf-timeline");
508
- });
509
- }
510
- function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
511
- holder.selectAll("*").remove();
512
- const table = holder.append("table");
513
- for (const snv of snvlst) {
514
- const tr = table.append("tr");
515
- const td1 = tr.append("td");
516
- td1.text(snv.gene).style("color", snv.color);
517
- const td2 = tr.append("td");
518
- const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
519
- snv.checkbox = checkbox;
520
- checkbox.on("change", (event) => {
521
- snv.show = event.target.checked;
522
- makegraph(snvlst, header, graphholder);
523
- });
524
- const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
525
- for (const s2 of snvlst) {
526
- s2.show = false;
527
- s2.checkbox.property("checked", false);
528
- }
529
- snv.show = true;
530
- snv.checkbox.property("checked", true);
531
- makegraph(snvlst, header, graphholder);
532
- });
533
- let cname = Math.random();
534
- const td11 = tr.append("td");
535
- const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
536
- td11.append("label").html("&nbsp;shared").attr("for", cname);
537
- cname = Math.random();
538
- const td22 = tr.append("td");
539
- const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
540
- td22.append("label").html("&nbsp;rising").attr("for", cname);
541
- cname = Math.random();
542
- const td33 = tr.append("td");
543
- const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
544
- td33.append("label").html("&nbsp;falling").attr("for", cname);
545
- cname = Math.random();
546
- const td44 = tr.append("td");
547
- const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
548
- td44.append("label").html("&nbsp;R-only").attr("for", cname);
549
- if (snv.subidx == 1) c1.property("checked", true);
550
- if (snv.subidx == 2) c2.property("checked", true);
551
- if (snv.subidx == 3) c3.property("checked", true);
552
- if (snv.subidx == 4) c4.property("checked", true);
553
- const cchange = (which, check) => {
554
- if (!check.checked) {
555
- snv.subidx = -1;
556
- } else {
557
- snv.subidx = which;
558
- if (which == 1) {
559
- c2.property("checked", false);
560
- c3.property("checked", false);
561
- c4.property("checked", false);
562
- } else if (which == 2) {
563
- c1.property("checked", false);
564
- c3.property("checked", false);
565
- c4.property("checked", false);
566
- } else if (which == 3) {
567
- c1.property("checked", false);
568
- c2.property("checked", false);
569
- c4.property("checked", false);
570
- } else {
571
- c1.property("checked", false);
572
- c2.property("checked", false);
573
- c3.property("checked", false);
574
- }
575
- }
576
- makesubgraph(snvlst, g1, g2, g3, g4);
577
- };
578
- }
579
- }
580
- export {
581
- maftimelineui as default
582
- };
583
- //# sourceMappingURL=maftimeline-Y2LETT7W.js.map
@@ -1,50 +0,0 @@
1
- import {
2
- Matrix,
3
- componentInit,
4
- makeChartBtnMenu,
5
- matrixInit
6
- } from "./chunk-3TO7TWHS.js";
7
- import "./chunk-MEUSRAOE.js";
8
- import "./chunk-6T4MN7LV.js";
9
- import "./chunk-Z5ECCUNG.js";
10
- import "./chunk-GUW7VTUL.js";
11
- import "./chunk-QQH32U6O.js";
12
- import "./chunk-5DI4UNH5.js";
13
- import "./chunk-W5SPLFIG.js";
14
- import "./chunk-4MGXKCPS.js";
15
- import "./chunk-N4ULQIGJ.js";
16
- import "./chunk-C2MCQZWH.js";
17
- import "./chunk-DDKS3MV3.js";
18
- import "./chunk-EYKJQJ7R.js";
19
- import "./chunk-2OMX5AYB.js";
20
- import "./chunk-II5ZAY52.js";
21
- import "./chunk-V2OJLJSK.js";
22
- import "./chunk-3YQYWX4M.js";
23
- import "./chunk-HJ6L54YS.js";
24
- import "./chunk-R3RD3VEX.js";
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- import "./chunk-CNFTQSNE.js";
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- import "./chunk-RIHO7ZD5.js";
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- import "./chunk-TVJOSRCH.js";
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- import "./chunk-3CIL7KH7.js";
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- import "./chunk-T4XPCSLP.js";
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- import "./chunk-KBTFT76L.js";
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- import "./chunk-W5J3LTYS.js";
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- import "./chunk-MHWYRNGA.js";
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- import "./chunk-JHLF2ZC2.js";
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- import "./chunk-WJLRU5OF.js";
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- import "./chunk-HBNB5TRH.js";
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- import "./chunk-PF4DSFDR.js";
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- import "./chunk-4OLM3KSB.js";
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- import "./chunk-PWYMHUXY.js";
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- import "./chunk-TLT4YIG3.js";
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- import "./chunk-5R63Q5KH.js";
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- import "./chunk-I6Y4O3RR.js";
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- import "./chunk-Q5RDQNIT.js";
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- import "./chunk-HS5PO5ZQ.js";
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- export {
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- Matrix,
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- componentInit,
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- makeChartBtnMenu,
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- matrixInit
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- };
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- //# sourceMappingURL=matrix-LADX4K5W.js.map
@@ -1,55 +0,0 @@
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- import {
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- Matrix,
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- componentInit,
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- makeChartBtnMenu,
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- matrixInit
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- } from "./chunk-3TO7TWHS.js";
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- import "./chunk-MEUSRAOE.js";
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- import "./chunk-6T4MN7LV.js";
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- import "./chunk-Z5ECCUNG.js";
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- import "./chunk-GUW7VTUL.js";
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- import {
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- getPlotConfig,
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- setComputedConfig
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- } from "./chunk-QQH32U6O.js";
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- import "./chunk-5DI4UNH5.js";
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- import "./chunk-W5SPLFIG.js";
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- import "./chunk-4MGXKCPS.js";
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- import "./chunk-N4ULQIGJ.js";
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- import "./chunk-C2MCQZWH.js";
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- import "./chunk-DDKS3MV3.js";
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- import "./chunk-EYKJQJ7R.js";
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- import "./chunk-2OMX5AYB.js";
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- import "./chunk-II5ZAY52.js";
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- import "./chunk-V2OJLJSK.js";
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- import "./chunk-3YQYWX4M.js";
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- import "./chunk-HJ6L54YS.js";
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- import "./chunk-R3RD3VEX.js";
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- import "./chunk-CNFTQSNE.js";
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- import "./chunk-RIHO7ZD5.js";
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- import "./chunk-TVJOSRCH.js";
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- import "./chunk-3CIL7KH7.js";
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- import "./chunk-T4XPCSLP.js";
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- import "./chunk-KBTFT76L.js";
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- import "./chunk-W5J3LTYS.js";
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- import "./chunk-MHWYRNGA.js";
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- import "./chunk-JHLF2ZC2.js";
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- import "./chunk-WJLRU5OF.js";
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- import "./chunk-HBNB5TRH.js";
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- import "./chunk-PF4DSFDR.js";
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- import "./chunk-4OLM3KSB.js";
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- import "./chunk-PWYMHUXY.js";
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- import "./chunk-TLT4YIG3.js";
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- import "./chunk-5R63Q5KH.js";
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- import "./chunk-I6Y4O3RR.js";
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- import "./chunk-Q5RDQNIT.js";
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- import "./chunk-HS5PO5ZQ.js";
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- export {
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- Matrix,
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- componentInit,
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- getPlotConfig,
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- makeChartBtnMenu,
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- matrixInit,
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- setComputedConfig
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- };
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- //# sourceMappingURL=matrix-M63KP6IL.js.map