@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

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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  32. package/dist/ProteomeInput-PK4ZM3SZ.js +395 -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
@@ -1,592 +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-LN3QYBGI.js";
11
- import "./chunk-HJ6L54YS.js";
12
- import "./chunk-LSEFWW72.js";
13
- import "./chunk-BTJFVY3R.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-UWYCEYML.js";
23
- import "./chunk-7UHUOC6F.js";
24
- import "./chunk-YC6ZJ7RP.js";
25
- import "./chunk-MVTCBVSX.js";
26
- import "./chunk-2K5DSRBJ.js";
27
- import "./chunk-ZYY54HBU.js";
28
- import "./chunk-EGWVYY7K.js";
29
- import "./chunk-AMYSEKPF.js";
30
- import "./chunk-AQVOYTLS.js";
31
- import "./chunk-TV74I3Y5.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-L4QG7XZE.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-7URL27MC.js.map
@@ -1,57 +0,0 @@
1
- import {
2
- Matrix,
3
- componentInit,
4
- makeChartBtnMenu,
5
- matrixInit
6
- } from "./chunk-KMQ6GQ3I.js";
7
- import "./chunk-ROLVOPVR.js";
8
- import "./chunk-NYX4B5CO.js";
9
- import "./chunk-DDKS3MV3.js";
10
- import "./chunk-LY7GD74F.js";
11
- import "./chunk-4KSU6NBP.js";
12
- import "./chunk-LTSR7SLO.js";
13
- import "./chunk-ANGDY7VC.js";
14
- import "./chunk-5SMOOFRW.js";
15
- import "./chunk-6NMH6WPB.js";
16
- import "./chunk-IABWKPRK.js";
17
- import "./chunk-HUBO743S.js";
18
- import "./chunk-ENWVV6EU.js";
19
- import "./chunk-2QULGYVE.js";
20
- import "./chunk-V2OJLJSK.js";
21
- import "./chunk-LN3QYBGI.js";
22
- import "./chunk-HJ6L54YS.js";
23
- import "./chunk-LSEFWW72.js";
24
- import "./chunk-BTJFVY3R.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-UWYCEYML.js";
32
- import "./chunk-7UHUOC6F.js";
33
- import "./chunk-YC6ZJ7RP.js";
34
- import "./chunk-MVTCBVSX.js";
35
- import "./chunk-2K5DSRBJ.js";
36
- import "./chunk-ZYY54HBU.js";
37
- import "./chunk-EGWVYY7K.js";
38
- import "./chunk-AMYSEKPF.js";
39
- import "./chunk-AQVOYTLS.js";
40
- import "./chunk-TV74I3Y5.js";
41
- import "./chunk-KSGA62R2.js";
42
- import "./chunk-LOZEKOES.js";
43
- import "./chunk-TOU7EVFQ.js";
44
- import "./chunk-OAWQ6LOO.js";
45
- import "./chunk-L4QG7XZE.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-6EK5WGIG.js.map