@sjcrh/proteinpaint-client 2.182.0 → 2.182.1

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 (1007) hide show
  1. package/dist/2dmaf-YHYYSSKR.js +1371 -0
  2. package/dist/AIProjectAdmin-D4AASQBM.js +830 -0
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  876. /package/dist/{expclust.gdc.spec-SP7VOL64.js.map → expclust.gdc.spec-VWIQFY67.js.map} +0 -0
  877. /package/dist/{facet-HDB4VDGU.js.map → facet-CHP3VUWS.js.map} +0 -0
  878. /package/dist/{geneExpClustering-6ZPOLTDJ.js.map → geneExpClustering-YDIDEH2O.js.map} +0 -0
  879. /package/dist/{geneExpression-T7QUHV5S.js.map → geneExpression-FA5RJRHZ.js.map} +0 -0
  880. /package/dist/{geneExpression-T6YIG4XQ.js.map → geneExpression-X2KXJPND.js.map} +0 -0
  881. /package/dist/{geneExpression.unit.spec-DO52L5IB.js.map → geneExpression.unit.spec-3LVHYZGG.js.map} +0 -0
  882. /package/dist/{geneORA-KOUDUWUO.js.map → geneORA-4CAYRKSN.js.map} +0 -0
  883. /package/dist/{geneVariant-FVR76F6I.js.map → geneVariant-OCOTNUH4.js.map} +0 -0
  884. /package/dist/{geneVariant-I5QUITKG.js.map → geneVariant-Y4L5W5HF.js.map} +0 -0
  885. /package/dist/{geneVariant.integration.spec-D4IRM7B5.js.map → geneVariant.integration.spec-BOJ5MM5K.js.map} +0 -0
  886. /package/dist/{genefusion.ui-35IYSZD7.js.map → genefusion.ui-I6HZOBIV.js.map} +0 -0
  887. /package/dist/{geneset-7ZHJ5KWK.js.map → geneset-GEWKDAAT.js.map} +0 -0
  888. /package/dist/{genomeBrowser.spec-VXASVLNH.js.map → genomeBrowser.spec-FDEGH4DY.js.map} +0 -0
  889. /package/dist/{grin2-IY26UUQI.js.map → grin2-K56B6XBZ.js.map} +0 -0
  890. /package/dist/{grin2-7NM56COO.js.map → grin2-V6FMM44N.js.map} +0 -0
  891. /package/dist/{gsea-TORO46C6.js.map → gsea-UNPPRU2U.js.map} +0 -0
  892. /package/dist/{hierCluster-3BKEGW6P.js.map → hierCluster-DXAWRQNI.js.map} +0 -0
  893. /package/dist/{hierCluster-HM3LOM6V.js.map → hierCluster-SPIQA2M2.js.map} +0 -0
  894. /package/dist/{hierCluster.config-LDO5IGQ5.js.map → hierCluster.config-JW6D3T3Q.js.map} +0 -0
  895. /package/dist/{hierCluster.integration.spec-XO5R6CQT.js.map → hierCluster.integration.spec-5NXZY4LG.js.map} +0 -0
  896. /package/dist/{hierCluster.interactivity-NVQ6262K.js.map → hierCluster.interactivity-CPPBXHM7.js.map} +0 -0
  897. /package/dist/{hierCluster.renderers-SWPPNBLU.js.map → hierCluster.renderers-A6MEGO2B.js.map} +0 -0
  898. /package/dist/{imagePlot-V4WLAPV6.js.map → imagePlot-QLAHCULW.js.map} +0 -0
  899. /package/dist/{importPlot-NZKQEOX4.js.map → importPlot-6ITZ6U7G.js.map} +0 -0
  900. /package/dist/{isoformExpression-TIZBIGNL.js.map → isoformExpression-7GAUF2QV.js.map} +0 -0
  901. /package/dist/{jspdf.es.min-DO4YWL2R.js.map → jspdf.es.min-FC3BCETM.js.map} +0 -0
  902. /package/dist/{launch.adhoc-JYEN42NM.js.map → launch.adhoc-HFHBAUR6.js.map} +0 -0
  903. /package/dist/{leftlabel.sample-43DL3J3H.js.map → leftlabel.sample-CWPJUCHR.js.map} +0 -0
  904. /package/dist/{legacyDataset-QRSNRVUA.js.map → legacyDataset-PBCPC5I7.js.map} +0 -0
  905. /package/dist/{lollipop-NMWZ4FVF.js.map → lollipop-QFRQLEER.js.map} +0 -0
  906. /package/dist/{maf-DS3EOVGV.js.map → maf-OEODBT3Y.js.map} +0 -0
  907. /package/dist/{maftimeline-ZB2753S7.js.map → maftimeline-2DFIF4C4.js.map} +0 -0
  908. /package/dist/{matrix-RCGQWQ3C.js.map → matrix-3HFB5TUU.js.map} +0 -0
  909. /package/dist/{matrix-WTTEK4FT.js.map → matrix-MIXK27AD.js.map} +0 -0
  910. /package/dist/{matrix.cells-UO5ASQ35.js.map → matrix.cells-U7AQNEBP.js.map} +0 -0
  911. /package/dist/{matrix.config-3UQAT3QR.js.map → matrix.config-FX5MHX6O.js.map} +0 -0
  912. /package/dist/{matrix.controls-PRZ77K5L.js.map → matrix.controls-5K7BB5Z4.js.map} +0 -0
  913. /package/dist/{matrix.data-4W73RQ3H.js.map → matrix.data-EEIY6AO4.js.map} +0 -0
  914. /package/dist/{matrix.dom-IZFFS4RQ.js.map → matrix.dom-6QL3AJMW.js.map} +0 -0
  915. /package/dist/{matrix.groups-5VMPI7SA.js.map → matrix.groups-CUB6UWC5.js.map} +0 -0
  916. /package/dist/{matrix.integration.spec-2F5LDLC2.js.map → matrix.integration.spec-ML4T7FRG.js.map} +0 -0
  917. /package/dist/{matrix.interactivity-MIPZ6ELV.js.map → matrix.interactivity-QMPWX63Q.js.map} +0 -0
  918. /package/dist/{matrix.layout-EO5LVYRO.js.map → matrix.layout-7SEF6MYI.js.map} +0 -0
  919. /package/dist/{matrix.legend-QBFBFEUG.js.map → matrix.legend-42LQGAGX.js.map} +0 -0
  920. /package/dist/{matrix.renderers-ERJXVCQL.js.map → matrix.renderers-ZF7LLER3.js.map} +0 -0
  921. /package/dist/{matrix.serieses-E23EPXHA.js.map → matrix.serieses-4B2WB526.js.map} +0 -0
  922. /package/dist/{matrix.sort-I4UGMEXR.js.map → matrix.sort-BJACNR7G.js.map} +0 -0
  923. /package/dist/{matrix.sort.unit.spec-CRGF6CSE.js.map → matrix.sort.unit.spec-ZGSM7HDJ.js.map} +0 -0
  924. /package/dist/{matrix.sorterUi-YLSYTYLE.js.map → matrix.sorterUi-W6XFYZY2.js.map} +0 -0
  925. /package/dist/{matrix.sorterUi.unit.spec-ENG3ICOO.js.map → matrix.sorterUi.unit.spec-V34ZZD7A.js.map} +0 -0
  926. /package/dist/{mavb-5WR7OJHI.js.map → mavb-NVQVFU6E.js.map} +0 -0
  927. /package/dist/{mds.fimo-3ZRH7BBJ.js.map → mds.fimo-HOCF6U6K.js.map} +0 -0
  928. /package/dist/{mds.samplescatterplot-RPXR2FVK.js.map → mds.samplescatterplot-ULD5BK5R.js.map} +0 -0
  929. /package/dist/{mds.survivalplot-WSSMYUZD.js.map → mds.survivalplot-5US32RQD.js.map} +0 -0
  930. /package/dist/{oncomatrix-JKYPUJQR.js.map → oncomatrix-Y3G3MUJJ.js.map} +0 -0
  931. /package/dist/{oncomatrix.spec-OEGU4DYK.js.map → oncomatrix.spec-MFUJLWEP.js.map} +0 -0
  932. /package/dist/{plot.2dvaf-ZGARLQNK.js.map → plot.2dvaf-F4WZ4YPU.js.map} +0 -0
  933. /package/dist/{plot.app-TKUJH3LK.js.map → plot.app-YFFLLBU5.js.map} +0 -0
  934. /package/dist/{plot.barplot-FEIPGDZ2.js.map → plot.barplot-2EJ2MWQD.js.map} +0 -0
  935. /package/dist/{plot.boxplot-6RASUMZB.js.map → plot.boxplot-AKZM443E.js.map} +0 -0
  936. /package/dist/{plot.brainImaging-ZJPFWX2W.js.map → plot.brainImaging-DR6WJNFZ.js.map} +0 -0
  937. /package/dist/{plot.dzi-PC34YI6Y.js.map → plot.dzi-R2MR7HAT.js.map} +0 -0
  938. /package/dist/{plot.ssgq-Z4UNJKWO.js.map → plot.ssgq-C52YIUFY.js.map} +0 -0
  939. /package/dist/{plot.vaf2cov-NZ4WULKT.js.map → plot.vaf2cov-FOD3K7BC.js.map} +0 -0
  940. /package/dist/{plot.wsi-YYXFAZWY.js.map → plot.wsi-D2TXYERK.js.map} +0 -0
  941. /package/dist/{polar-X2GPIBLB.js.map → polar-2LC35O6K.js.map} +0 -0
  942. /package/dist/{polar2-TZ553QQH.js.map → polar2-QPUOEUJZ.js.map} +0 -0
  943. /package/dist/{profile.spec-VB6VMFLY.js.map → profile.spec-3NCDGHLX.js.map} +0 -0
  944. /package/dist/{profileBarchart-SKJSTC7B.js.map → profileBarchart-PPQ3NL4D.js.map} +0 -0
  945. /package/dist/{profileForms-RLOGSMAQ.js.map → profileForms-GS3VVW65.js.map} +0 -0
  946. /package/dist/{profilePlot-267ZS3RG.js.map → profilePlot-DQWFH5NC.js.map} +0 -0
  947. /package/dist/{profileRadar-KGOBHCSF.js.map → profileRadar-KAKRDC4R.js.map} +0 -0
  948. /package/dist/{proteomeAbundance-PGHZSVAF.js.map → proteomeAbundance-DE4NVBCN.js.map} +0 -0
  949. /package/dist/{proteomeAbundance-JUYAYO5I.js.map → proteomeAbundance-LTB3QR3G.js.map} +0 -0
  950. /package/dist/{qualitative-3IECKKJM.js.map → qualitative-YOFAROVR.js.map} +0 -0
  951. /package/dist/{regression-J6FFRPXN.js.map → regression-PF6IAHJK.js.map} +0 -0
  952. /package/dist/{regression.inputs-T7LWBSYZ.js.map → regression.inputs-77IUYED3.js.map} +0 -0
  953. /package/dist/{regression.inputs.term-TT7PNX6G.js.map → regression.inputs.term-WWCHU6KF.js.map} +0 -0
  954. /package/dist/{regression.inputs.values.table-SHFUNKCS.js.map → regression.inputs.values.table-I6GM6MU7.js.map} +0 -0
  955. /package/dist/{regression.results-D4WX6VIV.js.map → regression.results-6GXNKYUS.js.map} +0 -0
  956. /package/dist/{regression.spec-7SW55L7X.js.map → regression.spec-MEFQNY34.js.map} +0 -0
  957. /package/dist/{report-QYOZ4BRF.js.map → report-LG3UKZHL.js.map} +0 -0
  958. /package/dist/{sampleScatter.spec-JCHFMGNF.js.map → sampleScatter.spec-D3IK7MSA.js.map} +0 -0
  959. /package/dist/{sampleView-7RPKNAZC.js.map → sampleView-XUI2J5EC.js.map} +0 -0
  960. /package/dist/{samplelst-4WNPHZVG.js.map → samplelst-A7IHCBAX.js.map} +0 -0
  961. /package/dist/{samplematrix-CG52DSXJ.js.map → samplematrix-VGUU7Q75.js.map} +0 -0
  962. /package/dist/{sc-OJSWILSA.js.map → sc-UVKVT2RY.js.map} +0 -0
  963. /package/dist/{scatter-LG2RMMEC.js.map → scatter-UILUYOGO.js.map} +0 -0
  964. /package/dist/{selectGenomeWithTklst-QXRVE6N4.js.map → selectGenomeWithTklst-LWKIMZEJ.js.map} +0 -0
  965. /package/dist/{singleCellCellType-XBSRL33U.js.map → singleCellCellType-TI52WQQ4.js.map} +0 -0
  966. /package/dist/{singleCellGeneExpression-64ECP62X.js.map → singleCellGeneExpression-I5SAHMGI.js.map} +0 -0
  967. /package/dist/{singleCellPlot-E5F62JY6.js.map → singleCellPlot-HRWCHYCI.js.map} +0 -0
  968. /package/dist/{singlecell-S7B5V7NK.js.map → singlecell-BHPP7KCO.js.map} +0 -0
  969. /package/dist/{singlecell-FCY5EOUV.js.map → singlecell-PQNKBKR7.js.map} +0 -0
  970. /package/dist/{snp-ACKX4GRX.js.map → snp-V4YGI7B3.js.map} +0 -0
  971. /package/dist/{snp.unit.spec-QBGHKKUD.js.map → snp.unit.spec-JSUCMGNP.js.map} +0 -0
  972. /package/dist/{snplocus-7EUOW7J7.js.map → snplocus-3YT5NNCH.js.map} +0 -0
  973. /package/dist/{spliceevent.a53ss.diagram-ALQZA35Z.js.map → spliceevent.a53ss.diagram-QEQJ44YH.js.map} +0 -0
  974. /package/dist/{spliceevent.exonskip.diagram-UF7WJA5R.js.map → spliceevent.exonskip.diagram-HMWVSOJG.js.map} +0 -0
  975. /package/dist/{spliceevent.noeventdiagram-4HPGRNRR.js.map → spliceevent.noeventdiagram-L5HUCT5A.js.map} +0 -0
  976. /package/dist/{ssGSEA-FDRBBBLJ.js.map → ssGSEA-Z3XRCBYW.js.map} +0 -0
  977. /package/dist/{ssGSEA.unit.spec-EZEOWJVV.js.map → ssGSEA.unit.spec-EUCTV2XJ.js.map} +0 -0
  978. /package/dist/{summarizeMutationDiagnosis-LALOJTHV.js.map → summarizeMutationDiagnosis-HFFYLQOF.js.map} +0 -0
  979. /package/dist/{summarizeMutationSurvival-TSNTSOBZ.js.map → summarizeMutationSurvival-OBK6YILP.js.map} +0 -0
  980. /package/dist/{summary-YRHVS64T.js.map → summary-W55WWIU2.js.map} +0 -0
  981. /package/dist/{summary.integration.spec-766YQLQA.js.map → summary.integration.spec-X2PNAUKW.js.map} +0 -0
  982. /package/dist/{summaryInput-VQ2X6GSX.js.map → summaryInput-X547Q6C7.js.map} +0 -0
  983. /package/dist/{survival-TVA3ZWVP.js.map → survival-PAJZHZPD.js.map} +0 -0
  984. /package/dist/{survival-FQXZH2MM.js.map → survival-TQPWMOD5.js.map} +0 -0
  985. /package/dist/{svg2pdf.es.min-EZ4UYRSH.js.map → svg2pdf.es.min-CYTPRWNB.js.map} +0 -0
  986. /package/dist/{svgraph-4BFBO7EL.js.map → svgraph-Y35C2M3D.js.map} +0 -0
  987. /package/dist/{svmr-ML7GAIIA.js.map → svmr-WGCIR7PE.js.map} +0 -0
  988. /package/dist/{table-SMLMUWPP.js.map → table-Q3B2YXEN.js.map} +0 -0
  989. /package/dist/{termCollection-EE6AOIVA.js.map → termCollection-A6YTSM5I.js.map} +0 -0
  990. /package/dist/{termCollection-22CPTISZ.js.map → termCollection-NTFNVQ7D.js.map} +0 -0
  991. /package/dist/{termCollection.unit.spec-4DIW3CJ3.js.map → termCollection.unit.spec-BX54PHKT.js.map} +0 -0
  992. /package/dist/{tk-ITZCKOQ5.js.map → tk-OCBZ7YR6.js.map} +0 -0
  993. /package/dist/{tp.ui-R6HVKCBC.js.map → tp.ui-ZT47N2CO.js.map} +0 -0
  994. /package/dist/{tvs.density-AQ5GD437.js.map → tvs.density-HSVPDDGA.js.map} +0 -0
  995. /package/dist/{tvs.dt-2263TBEJ.js.map → tvs.dt-BFB253O3.js.map} +0 -0
  996. /package/dist/{tvs.dtcnv.categorical-TRRHL33N.js.map → tvs.dtcnv.categorical-ARGAYIDO.js.map} +0 -0
  997. /package/dist/{tvs.dtcnv.continuous-GREYNF52.js.map → tvs.dtcnv.continuous-JCU23ERV.js.map} +0 -0
  998. /package/dist/{tvs.dtfusion-XOX46L3M.js.map → tvs.dtfusion-FV64XLZI.js.map} +0 -0
  999. /package/dist/{tvs.dtsnvindel-IDMXT53F.js.map → tvs.dtsnvindel-DMOXMEVL.js.map} +0 -0
  1000. /package/dist/{tvs.dtsv-ZDWFYH2C.js.map → tvs.dtsv-53FSZEPV.js.map} +0 -0
  1001. /package/dist/{tvs.numeric-ZN2R7BH3.js.map → tvs.numeric-ICUGA4WY.js.map} +0 -0
  1002. /package/dist/{tvs.samplelst-GAP76HRH.js.map → tvs.samplelst-MVPL6VXX.js.map} +0 -0
  1003. /package/dist/{tvs.termCollection-GQ65UKSI.js.map → tvs.termCollection-UGJXTHTG.js.map} +0 -0
  1004. /package/dist/{violin-JGDL62YA.js.map → violin-ZLUDGSQG.js.map} +0 -0
  1005. /package/dist/{violin.interactivity-H4RP4K5U.js.map → violin.interactivity-ULDOCZWW.js.map} +0 -0
  1006. /package/dist/{violin.renderer-QPHLACDC.js.map → violin.renderer-KJAXPMIK.js.map} +0 -0
  1007. /package/dist/{vocabulary-7JACY4J2.js.map → vocabulary-34YUQ4ZQ.js.map} +0 -0
@@ -1,591 +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-7FEHI46K.js";
11
- import "./chunk-HJ6L54YS.js";
12
- import "./chunk-XD6BFNMR.js";
13
- import {
14
- Menu
15
- } from "./chunk-2SRMRC6L.js";
16
- import "./chunk-TCPU43TU.js";
17
- import "./chunk-XDI4UFCZ.js";
18
- import "./chunk-FN5XPUPH.js";
19
- import "./chunk-LSEFWW72.js";
20
- import "./chunk-5EF5U7MX.js";
21
- import "./chunk-IQIXGTQV.js";
22
- import "./chunk-UCLS2SVB.js";
23
- import "./chunk-MVTCBVSX.js";
24
- import "./chunk-F6V4AYWP.js";
25
- import "./chunk-5OHXYXLD.js";
26
- import "./chunk-DQC5FFGV.js";
27
- import "./chunk-DVDDXOWT.js";
28
- import "./chunk-6MSCYO7K.js";
29
- import "./chunk-22NJUYET.js";
30
- import "./chunk-MDL2HG3N.js";
31
- import "./chunk-IGEQI6MR.js";
32
- import "./chunk-BEWDIM6H.js";
33
- import {
34
- category10_default
35
- } from "./chunk-IH7ILDJS.js";
36
- import {
37
- axisBottom,
38
- axisLeft
39
- } from "./chunk-LOZEKOES.js";
40
- import "./chunk-TOU7EVFQ.js";
41
- import {
42
- format,
43
- linear,
44
- log,
45
- ordinal,
46
- time,
47
- timeParse
48
- } from "./chunk-OAWQ6LOO.js";
49
- import "./chunk-SEEYV6P2.js";
50
- import {
51
- select_default
52
- } from "./chunk-NDWTN4U5.js";
53
- import "./chunk-OMR2DT66.js";
54
- import "./chunk-HFNDKYVF.js";
55
-
56
- // src/maftimeline.js
57
- var zerovalue = 1e-5;
58
- var showcircle = true;
59
- var maflogscale = true;
60
- var tip = new Menu();
61
- function maftimelineui(genomes, holder, sandbox_header) {
62
- let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
63
- if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
64
- else {
65
- ;
66
- [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
67
- pane.header.text("MAF timeline plot");
68
- }
69
- inputdiv.append("p").html(
70
- "<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
71
- );
72
- inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
73
- {
74
- const id = Math.random().toString();
75
- const p = inputdiv.append("p");
76
- p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
77
- maflogscale = !maflogscale;
78
- });
79
- p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
80
- }
81
- const fileui = () => {
82
- filediv.selectAll("*").remove();
83
- const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
84
- saydiv.text("");
85
- const file = event.target.files[0];
86
- if (!file) {
87
- fileui();
88
- return;
89
- }
90
- if (file.size == 0) {
91
- saydiv.text("Wrong file: " + file.name);
92
- fileui();
93
- return;
94
- }
95
- const reader = new FileReader();
96
- reader.onload = (event2) => {
97
- const lines = event2.target.result.trim().split(/\r?\n/);
98
- const [err, header] = parseheader(lines[0].trim());
99
- if (err) {
100
- saydiv.text("File header error: " + err);
101
- fileui();
102
- return;
103
- }
104
- const badlines = [];
105
- const data = {};
106
- let good = 0;
107
- for (let i = 1; i < lines.length; i++) {
108
- if (lines[i] == "") continue;
109
- if (lines[i][0] == "#") continue;
110
- const m = parseline(i, lines[i], header, badlines, data);
111
- if (m) {
112
- good++;
113
- }
114
- }
115
- if (badlines.length) {
116
- bulk_badline(header, badlines);
117
- }
118
- if (good == 0) {
119
- fileui();
120
- return;
121
- }
122
- let visual_holder;
123
- if (pane) {
124
- disappear(pane.pane);
125
- const pane2 = newpane({ x: 100, y: 100, toshrink: true });
126
- pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
127
- visual_holder = pane2.body;
128
- }
129
- if (holder !== void 0) {
130
- visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
131
- inputdiv.selectAll("*").remove();
132
- saydiv.text("");
133
- }
134
- render(data, header, visual_holder);
135
- };
136
- reader.onerror = function() {
137
- saydiv.text("Error reading file " + file.name);
138
- fileui();
139
- return;
140
- };
141
- saydiv.text("Parsing file " + file.name + " ...");
142
- reader.readAsText(file, "utf8");
143
- });
144
- setTimeout(() => butt.node().focus(), 1100);
145
- };
146
- fileui();
147
- }
148
- function parseheader(line) {
149
- const header = line.toLowerCase().split(" ");
150
- if (header.length <= 1) return ["columns must be separated by tab"];
151
- const htry = (...lst) => {
152
- for (const i2 of lst) {
153
- const j = header.indexOf(i2);
154
- if (j != -1) return j;
155
- }
156
- return -1;
157
- };
158
- let i = htry("person", "patient", "caseid");
159
- if (i == -1) return ["person missing"];
160
- header[i] = "patient";
161
- i = htry("sample", "sampleid");
162
- if (i == -1) return ["sample missing"];
163
- header[i] = "sample";
164
- i = htry("snv4");
165
- if (i == -1) return ["snv4 missing"];
166
- header[i] = "snv4";
167
- i = htry("date", "dateofsample");
168
- if (i == -1) return ["date missing"];
169
- header[i] = "date";
170
- i = htry("mutant_readcount", "mutantcount");
171
- if (i != -1) header[i] = "mutant_readcount";
172
- i = htry("ref_readcount", "refcount");
173
- if (i != -1) header[i] = "ref_readcount";
174
- i = htry("total_readcount", "coveragecount");
175
- if (i == -1) return ["total_readcount missing"];
176
- header[i] = "coverage";
177
- i = htry("maf");
178
- if (i == -1) return ["maf missing"];
179
- header[i] = "maf";
180
- i = htry("call_manual");
181
- if (i != -1) header[i] = "call_manual";
182
- return [null, header];
183
- }
184
- function parseline(i, line, header, badlines, data) {
185
- const lst = line.split(" ");
186
- const m = {};
187
- for (let j = 0; j < header.length; j++) {
188
- m[header[j]] = lst[j];
189
- }
190
- if (!m.patient) {
191
- badlines.push([i, "missing patient", lst]);
192
- return;
193
- }
194
- if (!data[m.patient]) {
195
- data[m.patient] = {
196
- snv4: {},
197
- show: false
198
- };
199
- }
200
- if (!m.snv4) {
201
- badlines.push([i, "missing snv4", lst]);
202
- return;
203
- }
204
- if (!data[m.patient].snv4[m.snv4]) {
205
- data[m.patient].snv4[m.snv4] = {
206
- mutationname: m.snv4,
207
- samples: [],
208
- subidx: void 0
209
- };
210
- }
211
- if (m.gene) {
212
- data[m.patient].snv4[m.snv4].gene = m.gene;
213
- }
214
- if (!m.maf) {
215
- badlines.push([i, "missing maf", lst]);
216
- return;
217
- }
218
- let v = Number.parseFloat(m.maf);
219
- if (Number.isNaN(v)) {
220
- badlines.push([i, "invalid maf", lst]);
221
- return;
222
- }
223
- if (v < zerovalue) {
224
- v = zerovalue;
225
- }
226
- m.maf = v;
227
- if (!m.coverage) {
228
- badlines.push([i, "missing total_readcount", lst]);
229
- return;
230
- }
231
- if (m.call_manual && m.call_manual == "wildtype") {
232
- m.maf = zerovalue;
233
- }
234
- v = Number.parseInt(m.coverage);
235
- if (Number.isNaN(v)) {
236
- badlines.push([i, "invalid total_readcount", lst]);
237
- return;
238
- }
239
- m.coverage = v;
240
- let date;
241
- if (m.date) {
242
- const f = timeParse("%m/%d/%Y");
243
- date = f(m.date);
244
- m.Date = m.date;
245
- } else {
246
- badlines.push([i, "missing date", lst]);
247
- return;
248
- }
249
- if (date == null) {
250
- badlines.push([i, "cannot parse date", lst]);
251
- return;
252
- }
253
- m.date = date;
254
- if (!m.sample) {
255
- badlines.push([i, "missing sample", lst]);
256
- return;
257
- }
258
- data[m.patient].snv4[m.snv4].samples.push(m);
259
- return true;
260
- }
261
- function render(data, header, holder) {
262
- const table = holder.append("table").style("margin", "20px");
263
- const tr1 = table.append("tr");
264
- let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
265
- td.append("button").text("Toggle circle visibility").on("click", () => {
266
- showcircle = !showcircle;
267
- for (const n in data) {
268
- if (data[n].show) {
269
- data[n].handle.node().click();
270
- break;
271
- }
272
- }
273
- });
274
- const patientholder = td.append("div").style("margin-top", "10px");
275
- const td1 = tr1.append("td").style("vertical-align", "top");
276
- const graphholder = td1.append("div").style("display", "inline-block");
277
- const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
278
- const tr2 = table.append("tr");
279
- const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
280
- const gtr1 = tiantable.append("tr");
281
- td = gtr1.append("td").style("vertical-align", "top");
282
- td.append("div").text("Shared").style("font-size", "2em");
283
- const graph1holder = td.append("div").style("border", "solid 1px black");
284
- td = gtr1.append("td").style("vertical-align", "top");
285
- td.append("div").text("Rising").style("font-size", "2em");
286
- const graph2holder = td.append("div").style("border", "solid 1px black");
287
- const gtr2 = tiantable.append("tr");
288
- td = gtr2.append("td").style("vertical-align", "top");
289
- td.append("div").text("Falling").style("font-size", "2em");
290
- const graph3holder = td.append("div").style("border", "solid 1px black");
291
- td = gtr2.append("td").style("vertical-align", "top");
292
- td.append("div").text("R-only").style("font-size", "2em");
293
- const graph4holder = td.append("div").style("border", "solid 1px black");
294
- for (const patient in data) {
295
- const snvlst = [];
296
- const colors = ordinal(category10_default);
297
- for (const x in data[patient].snv4) {
298
- const snv = data[patient].snv4[x];
299
- snv.show = true;
300
- snv.color = colors(snv.mutationname);
301
- snv.samples.sort((a, b) => a.date - b.date);
302
- for (const s of snv.samples) {
303
- s.color = snv.color;
304
- }
305
- snvlst.push(snv);
306
- }
307
- const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
308
- for (const pn in data) {
309
- data[pn].handle.style("color", "black");
310
- data[pn].show = false;
311
- }
312
- data[patient].handle.style("color", "red");
313
- data[patient].show = true;
314
- makegraph(snvlst, header, graphholder);
315
- makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
316
- makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
317
- });
318
- data[patient].handle = div;
319
- }
320
- for (const n in data) {
321
- data[n].handle.node().click();
322
- break;
323
- }
324
- }
325
- function makesubgraph(snvlst, g1, g2, g3, g4) {
326
- g1.selectAll("*").remove();
327
- g2.selectAll("*").remove();
328
- g3.selectAll("*").remove();
329
- g4.selectAll("*").remove();
330
- const l1 = [];
331
- const l2 = [];
332
- const l3 = [];
333
- const l4 = [];
334
- for (const snv of snvlst) {
335
- switch (snv.subidx) {
336
- case 1:
337
- l1.push(snv);
338
- break;
339
- case 2:
340
- l2.push(snv);
341
- break;
342
- case 3:
343
- l3.push(snv);
344
- break;
345
- case 4:
346
- l4.push(snv);
347
- break;
348
- }
349
- }
350
- if (l1.length) {
351
- makegraph(l1, null, g1, true);
352
- } else {
353
- g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
354
- }
355
- if (l2.length) {
356
- makegraph(l2, null, g2, true);
357
- } else {
358
- g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
359
- }
360
- if (l3.length) {
361
- makegraph(l3, null, g3, true);
362
- } else {
363
- g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
364
- }
365
- if (l4.length) {
366
- makegraph(l4, null, g4, true);
367
- } else {
368
- g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
369
- }
370
- }
371
- function makegraph(snvlst0, header, holder, issub) {
372
- holder.selectAll("*").remove();
373
- const samples = [];
374
- const snvlst = [];
375
- for (const snv of snvlst0) {
376
- if (!issub && !snv.show) continue;
377
- snvlst.push(snv);
378
- for (const s of snv.samples) {
379
- samples.push(s);
380
- }
381
- }
382
- if (snvlst.length == 0) return;
383
- let mindate = snvlst[0].samples[0].date;
384
- let maxdate = snvlst[0].samples[0].date;
385
- let maxmaf = snvlst[0].samples[0].maf;
386
- let maxcoverage = snvlst[0].samples[0].coverage;
387
- for (const snv of snvlst) {
388
- for (const s of snv.samples) {
389
- mindate = Math.min(mindate, s.date);
390
- maxdate = Math.max(maxdate, s.date);
391
- maxmaf = Math.max(maxmaf, s.maf);
392
- maxcoverage = Math.max(maxcoverage, s.coverage);
393
- }
394
- }
395
- const svg = holder.append("svg");
396
- const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
397
- let width = 600;
398
- let height = 400;
399
- let xpad, ypad, minradius;
400
- const xaxisg = svg.append("g");
401
- const yaxisg = svg.append("g");
402
- const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
403
- event.preventDefault();
404
- const x = event.clientX;
405
- const y = event.clientY;
406
- const w0 = width;
407
- const h0 = height;
408
- const body = select_default(document.body);
409
- body.on("mousemove", (event2) => {
410
- setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
411
- }).on("mouseup", () => {
412
- body.on("mousemove", null).on("mouseup", null);
413
- });
414
- });
415
- const xscale = time().domain([mindate, maxdate]);
416
- const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
417
- const rscale = linear().domain([1, maxcoverage]);
418
- const g = svg.append("g");
419
- const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
420
- let circles;
421
- if (showcircle) {
422
- circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
423
- event.target.setAttribute("fill-opacity", 0.4);
424
- tip.clear();
425
- tip.show(event.clientX, event.clientY);
426
- const lst = [];
427
- for (const k in d) {
428
- if (k == "color") continue;
429
- if (k == "gene") {
430
- lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
431
- continue;
432
- }
433
- if (k == "date") continue;
434
- if (k == "url") {
435
- lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
436
- continue;
437
- }
438
- lst.push({ k, v: d[k] });
439
- }
440
- make_table_2col(tip.d, lst);
441
- }).on("mouseout", (event) => {
442
- event.target.setAttribute("fill-opacity", 0.1);
443
- });
444
- }
445
- const legend = svg.append("g");
446
- const setsize = (w, h) => {
447
- width = w;
448
- height = h;
449
- minradius = 2;
450
- const maxradius = Math.max(width, height) / 30;
451
- xpad = maxradius;
452
- ypad = maxradius;
453
- rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
454
- xscale.range([0, width]);
455
- yscale.range([height, 0]);
456
- svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
457
- xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
458
- yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
459
- drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
460
- axisstyle({
461
- axis: xaxisg.call(axisBottom().scale(xscale)),
462
- showline: true,
463
- color: "black",
464
- fontsize: Math.max(12, Math.min(20, width / 100))
465
- });
466
- axisstyle({
467
- axis: yaxisg.call(
468
- axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
469
- ),
470
- showline: true,
471
- color: "black",
472
- fontsize: Math.max(12, Math.min(20, height / 100))
473
- });
474
- g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
475
- lines.attr("d", (d) => {
476
- const lst = [];
477
- for (let i = 0; i < d.samples.length; i++) {
478
- const s = d.samples[i];
479
- lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
480
- }
481
- return lst.join(" ");
482
- });
483
- if (showcircle) {
484
- circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
485
- }
486
- legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
487
- legend.selectAll("*").remove();
488
- let y = minradius;
489
- if (showcircle) {
490
- legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
491
- legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
492
- y += 5 + minradius + maxradius;
493
- legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
494
- legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
495
- y += 15 + maxradius;
496
- }
497
- const fontsize = 12;
498
- for (const snv of snvlst) {
499
- legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
500
- if (showcircle) {
501
- legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
502
- }
503
- 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) => {
504
- event.target.setAttribute("font-weight", "bold");
505
- lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
506
- }).on("mouseout", (event) => {
507
- event.target.setAttribute("font-weight", "normal");
508
- lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
509
- });
510
- y += fontsize + 10;
511
- }
512
- };
513
- setsize(width, height);
514
- holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
515
- to_svg(svg.node(), "maf-timeline");
516
- });
517
- }
518
- function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
519
- holder.selectAll("*").remove();
520
- const table = holder.append("table");
521
- for (const snv of snvlst) {
522
- const tr = table.append("tr");
523
- const td1 = tr.append("td");
524
- td1.text(snv.gene).style("color", snv.color);
525
- const td2 = tr.append("td");
526
- const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
527
- snv.checkbox = checkbox;
528
- checkbox.on("change", (event) => {
529
- snv.show = event.target.checked;
530
- makegraph(snvlst, header, graphholder);
531
- });
532
- const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
533
- for (const s2 of snvlst) {
534
- s2.show = false;
535
- s2.checkbox.property("checked", false);
536
- }
537
- snv.show = true;
538
- snv.checkbox.property("checked", true);
539
- makegraph(snvlst, header, graphholder);
540
- });
541
- let cname = Math.random();
542
- const td11 = tr.append("td");
543
- const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
544
- td11.append("label").html("&nbsp;shared").attr("for", cname);
545
- cname = Math.random();
546
- const td22 = tr.append("td");
547
- const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
548
- td22.append("label").html("&nbsp;rising").attr("for", cname);
549
- cname = Math.random();
550
- const td33 = tr.append("td");
551
- const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
552
- td33.append("label").html("&nbsp;falling").attr("for", cname);
553
- cname = Math.random();
554
- const td44 = tr.append("td");
555
- const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
556
- td44.append("label").html("&nbsp;R-only").attr("for", cname);
557
- if (snv.subidx == 1) c1.property("checked", true);
558
- if (snv.subidx == 2) c2.property("checked", true);
559
- if (snv.subidx == 3) c3.property("checked", true);
560
- if (snv.subidx == 4) c4.property("checked", true);
561
- const cchange = (which, check) => {
562
- if (!check.checked) {
563
- snv.subidx = -1;
564
- } else {
565
- snv.subidx = which;
566
- if (which == 1) {
567
- c2.property("checked", false);
568
- c3.property("checked", false);
569
- c4.property("checked", false);
570
- } else if (which == 2) {
571
- c1.property("checked", false);
572
- c3.property("checked", false);
573
- c4.property("checked", false);
574
- } else if (which == 3) {
575
- c1.property("checked", false);
576
- c2.property("checked", false);
577
- c4.property("checked", false);
578
- } else {
579
- c1.property("checked", false);
580
- c2.property("checked", false);
581
- c3.property("checked", false);
582
- }
583
- }
584
- makesubgraph(snvlst, g1, g2, g3, g4);
585
- };
586
- }
587
- }
588
- export {
589
- maftimelineui as default
590
- };
591
- //# sourceMappingURL=maftimeline-ZB2753S7.js.map
@@ -1,57 +0,0 @@
1
- import {
2
- Matrix,
3
- componentInit,
4
- makeChartBtnMenu,
5
- matrixInit
6
- } from "./chunk-IBTPGSYI.js";
7
- import "./chunk-GO5SIPFE.js";
8
- import "./chunk-FOEZG4VX.js";
9
- import "./chunk-Y3TDC7NU.js";
10
- import "./chunk-GPOECA3V.js";
11
- import "./chunk-UR3C4SCH.js";
12
- import "./chunk-AETE4F7R.js";
13
- import "./chunk-GTOY3JJO.js";
14
- import "./chunk-7A7NMCQ3.js";
15
- import "./chunk-IC7SUXJD.js";
16
- import "./chunk-IIRU6VK2.js";
17
- import "./chunk-VJ37HKM6.js";
18
- import "./chunk-A5TSPTYC.js";
19
- import "./chunk-XOBD3EAM.js";
20
- import "./chunk-JOXUBWN3.js";
21
- import "./chunk-V2OJLJSK.js";
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- import "./chunk-7FEHI46K.js";
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- import "./chunk-HJ6L54YS.js";
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- import "./chunk-XD6BFNMR.js";
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- import "./chunk-2SRMRC6L.js";
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- import "./chunk-TCPU43TU.js";
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- import "./chunk-XDI4UFCZ.js";
28
- import "./chunk-FN5XPUPH.js";
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- import "./chunk-LSEFWW72.js";
30
- import "./chunk-5EF5U7MX.js";
31
- import "./chunk-IQIXGTQV.js";
32
- import "./chunk-UCLS2SVB.js";
33
- import "./chunk-MVTCBVSX.js";
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- import "./chunk-F6V4AYWP.js";
35
- import "./chunk-5OHXYXLD.js";
36
- import "./chunk-DQC5FFGV.js";
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- import "./chunk-DVDDXOWT.js";
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- import "./chunk-6MSCYO7K.js";
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- import "./chunk-22NJUYET.js";
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- import "./chunk-MDL2HG3N.js";
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- import "./chunk-IGEQI6MR.js";
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- import "./chunk-BEWDIM6H.js";
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- import "./chunk-IH7ILDJS.js";
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- import "./chunk-LOZEKOES.js";
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- import "./chunk-TOU7EVFQ.js";
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- import "./chunk-OAWQ6LOO.js";
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- import "./chunk-SEEYV6P2.js";
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- import "./chunk-NDWTN4U5.js";
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- import "./chunk-OMR2DT66.js";
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- import "./chunk-HFNDKYVF.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-RCGQWQ3C.js.map