@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

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 (957) hide show
  1. package/dist/2dmaf-R3PFZNRN.js +1373 -0
  2. package/dist/AIProjectAdmin-DM3KG6SR.js +958 -0
  3. package/dist/AppHeader-6DZQ6YZX.js +835 -0
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  5. package/dist/CorrelationVolcano-U5UMJNH5.js +619 -0
  6. package/dist/DE-AXNYWIQK.js +95 -0
  7. package/dist/DEinput-JH6YY6LS.js +301 -0
  8. package/dist/DifferentialAnalysis-25P4CGIY.js +242 -0
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  10. package/dist/Disco-NVMLF3BK.js +3392 -0
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  848. /package/dist/{importPlot-A3PFUP6K.js.map → isoformExpression-4SLLCVFD.js.map} +0 -0
  849. /package/dist/{isoformExpression.unit.spec-SLB6XIX4.js.map → isoformExpression.unit.spec-GEL4JJ64.js.map} +0 -0
  850. /package/dist/{isoformExpression-5L4O3WKL.js.map → launch.adhoc-LWLBQJS5.js.map} +0 -0
  851. /package/dist/{leftlabel.sample-OSIRTJFW.js.map → leftlabel.sample-RTEZOIH2.js.map} +0 -0
  852. /package/dist/{legacyDataset-TNIIJABK.js.map → legacyDataset-VLD7ZYWI.js.map} +0 -0
  853. /package/dist/{lollipop-LAELXNQY.js.map → lollipop-XKQK5QZU.js.map} +0 -0
  854. /package/dist/{maf-HZAYVZFO.js.map → maf-AZQPPWDO.js.map} +0 -0
  855. /package/dist/{maftimeline-BLBNUGAL.js.map → maftimeline-7MSVYKQU.js.map} +0 -0
  856. /package/dist/{launch.adhoc-QI7TPYSC.js.map → matrix-BGLWC25D.js.map} +0 -0
  857. /package/dist/{matrix-LVJSHXDM.js.map → matrix-IQR5SRMK.js.map} +0 -0
  858. /package/dist/{matrix-S5QQV4JU.js.map → matrix.cells-5C57NWOY.js.map} +0 -0
  859. /package/dist/{matrix.cells-JUTRYPG4.js.map → matrix.config-2DQXAN2E.js.map} +0 -0
  860. /package/dist/{matrix.config-ZTWWYNIZ.js.map → matrix.data-ADCGF5H6.js.map} +0 -0
  861. /package/dist/{matrix.data-BREYB54F.js.map → matrix.groups-V4ITQ5F7.js.map} +0 -0
  862. /package/dist/{matrix.groups-WMHTLOXC.js.map → matrix.interactivity-JNELJFOV.js.map} +0 -0
  863. /package/dist/{matrix.interactivity-TMBVAM5M.js.map → matrix.layout-WBVIV6GR.js.map} +0 -0
  864. /package/dist/{matrix.layout-POK5NOUV.js.map → matrix.legend-YHOWPK77.js.map} +0 -0
  865. /package/dist/{matrix.legend-6XVQ67AC.js.map → matrix.renderers-5BGVRR3M.js.map} +0 -0
  866. /package/dist/{matrix.renderers-G5FQZZ73.js.map → matrix.serieses-2GZJOASZ.js.map} +0 -0
  867. /package/dist/{matrix.serieses-XNLQSQS6.js.map → matrix.sort-WKIWPJKP.js.map} +0 -0
  868. /package/dist/{matrix.sort.unit.spec-65BDBQUV.js.map → matrix.sort.unit.spec-L2E4D4AS.js.map} +0 -0
  869. /package/dist/{matrix.sort-XNES23OQ.js.map → matrix.sorterUi-TEJWWJ64.js.map} +0 -0
  870. /package/dist/{matrix.sorterUi.unit.spec-GZQBW7F7.js.map → matrix.sorterUi.unit.spec-SHP7C4P7.js.map} +0 -0
  871. /package/dist/{mavb-T2UCRWWM.js.map → mavb-4MXNYUEO.js.map} +0 -0
  872. /package/dist/{mds.fimo-65UUK7ER.js.map → mds.fimo-WHIJIBOI.js.map} +0 -0
  873. /package/dist/{mds.samplescatterplot-4NHGQBJF.js.map → mds.samplescatterplot-BRJ6NG2D.js.map} +0 -0
  874. /package/dist/{mds.survivalplot-WVAHDM3Z.js.map → mds.survivalplot-OPCMB5PB.js.map} +0 -0
  875. /package/dist/{numericDictTermCluster-CXASCSQ6.js.map → numericDictTermCluster-7MIFOP2K.js.map} +0 -0
  876. /package/dist/{oncomatrix-5WMOICWR.js.map → oncomatrix-BGG6BEUI.js.map} +0 -0
  877. /package/dist/{oncomatrix.spec-POVBNFJR.js.map → oncomatrix.spec-LYQ4L4F3.js.map} +0 -0
  878. /package/dist/{plot.2dvaf-63K5RSIU.js.map → plot.2dvaf-6WVCP2ZI.js.map} +0 -0
  879. /package/dist/{matrix.sorterUi-WC2YX7S7.js.map → plot.app-MLBP6WFP.js.map} +0 -0
  880. /package/dist/{plot.barplot-IQTYHNFE.js.map → plot.barplot-JEPRZSCU.js.map} +0 -0
  881. /package/dist/{plot.boxplot-2RMTO7AS.js.map → plot.boxplot-GNFW42VM.js.map} +0 -0
  882. /package/dist/{plot.brainImaging-DLUHAHHG.js.map → plot.brainImaging-5ACNSD45.js.map} +0 -0
  883. /package/dist/{plot.disco-WK6GDLNF.js.map → plot.disco-Q2V2KKIH.js.map} +0 -0
  884. /package/dist/{plot.dzi-3V3FWE7U.js.map → plot.dzi-KVT6S7K7.js.map} +0 -0
  885. /package/dist/{plot.ssgq-TENK2RP4.js.map → plot.ssgq-4N3KFJQ2.js.map} +0 -0
  886. /package/dist/{plot.vaf2cov-P2QOOZGZ.js.map → plot.vaf2cov-ITRG5U43.js.map} +0 -0
  887. /package/dist/{plot.wsi-BVRGJF4E.js.map → plot.wsi-26YZNU4V.js.map} +0 -0
  888. /package/dist/{polar2-NNOZOQQJ.js.map → polar2-J7GVUK4X.js.map} +0 -0
  889. /package/dist/{profileForms-RS4GEZZV.js.map → profileForms-VXV2JLXU.js.map} +0 -0
  890. /package/dist/{plot.app-V5IY25QS.js.map → profilePlot-ZZYZK4SY.js.map} +0 -0
  891. /package/dist/{proteinView-NPKJAQAI.js.map → proteinView-7KN532D3.js.map} +0 -0
  892. /package/dist/{profilePlot-3DLME3NH.js.map → qualitative-MLRVLIAU.js.map} +0 -0
  893. /package/dist/{radar2-EX7YBNMT.js.map → radar2-WM2ZBOH3.js.map} +0 -0
  894. /package/dist/{radarFacility2-WU5O6O77.js.map → radarFacility2-3SBR2JJ3.js.map} +0 -0
  895. /package/dist/{qualitative-S45RXXRJ.js.map → regression-WMRPQJW2.js.map} +0 -0
  896. /package/dist/{regression-7MCOYJVD.js.map → regression.inputs-VWZKSYNY.js.map} +0 -0
  897. /package/dist/{regression.inputs-QHSWJ23R.js.map → regression.inputs.term-OWE6GWHM.js.map} +0 -0
  898. /package/dist/{regression.inputs.term-EJ4Z5Q5O.js.map → regression.inputs.values.table-4INNZQI2.js.map} +0 -0
  899. /package/dist/{regression.integration.spec-XOX7OXXA.js.map → regression.integration.spec-XKQ2JOOT.js.map} +0 -0
  900. /package/dist/{regression.inputs.values.table-YKMAWNXN.js.map → regression.results-VZBYMBYC.js.map} +0 -0
  901. /package/dist/{regression.spec-YIIY2AZA.js.map → regression.spec-DU3UTDCJ.js.map} +0 -0
  902. /package/dist/{regression.results-YKPOTPCC.js.map → render-N5FOF247.js.map} +0 -0
  903. /package/dist/{report-JEJFCWUU.js.map → report-DW3OHB67.js.map} +0 -0
  904. /package/dist/{sampleScatter.spec-LBAZBDYA.js.map → sampleScatter.spec-REFSK2V4.js.map} +0 -0
  905. /package/dist/{sampleView-WKZT5ZFE.js.map → sampleView-ICOT2R6O.js.map} +0 -0
  906. /package/dist/{samplelst-HXM3H6M4.js.map → samplelst-TJEVASYG.js.map} +0 -0
  907. /package/dist/{samplematrix-LCGHK2EK.js.map → samplematrix-6DAWCXQ3.js.map} +0 -0
  908. /package/dist/{sc-3OE2G4BU.js.map → sc-53LNOB7N.js.map} +0 -0
  909. /package/dist/{scatter-AGVUDTTU.js.map → scatter-DKYSS4DL.js.map} +0 -0
  910. /package/dist/{selectGenomeWithTklst-WF2XZ6GH.js.map → selectGenomeWithTklst-WTX66TV3.js.map} +0 -0
  911. /package/dist/{singleCellCellType-2SRGROMS.js.map → singleCellCellType-D2CN2BHQ.js.map} +0 -0
  912. /package/dist/{singleCellCellType.unit.spec-DCGHNRJI.js.map → singleCellCellType.unit.spec-LADUCI4R.js.map} +0 -0
  913. /package/dist/{singleCellGeneExpression-RASZA4NO.js.map → singleCellGeneExpression-YR2ZT34W.js.map} +0 -0
  914. /package/dist/{singleCellGeneExpression.unit.spec-5MRGH2OO.js.map → singleCellGeneExpression.unit.spec-BM63M432.js.map} +0 -0
  915. /package/dist/{singleCellPlot-TIYA3GNM.js.map → singleCellPlot-3ICIOILE.js.map} +0 -0
  916. /package/dist/{singlecell-JS5SIZHY.js.map → singlecell-6ZUFA3BQ.js.map} +0 -0
  917. /package/dist/{singlecell-CFA43TTU.js.map → singlecell-KX7W4U57.js.map} +0 -0
  918. /package/dist/{snp-VXZXPMKS.js.map → snp-VIURB7L3.js.map} +0 -0
  919. /package/dist/{snp.unit.spec-TR5TCO7X.js.map → snp.unit.spec-ACZNZUNS.js.map} +0 -0
  920. /package/dist/{snplocus-VLPH5Y65.js.map → snplocus-3LW4ZUZR.js.map} +0 -0
  921. /package/dist/{spliceevent.a53ss.diagram-PATK67SH.js.map → spliceevent.a53ss.diagram-AKTZGWNM.js.map} +0 -0
  922. /package/dist/{spliceevent.noeventdiagram-4NPNZUEN.js.map → spliceevent.noeventdiagram-YTXWWNTJ.js.map} +0 -0
  923. /package/dist/{ssGSEA-XMW5BLAU.js.map → ssGSEA-THW4WFMI.js.map} +0 -0
  924. /package/dist/{ssGSEA.unit.spec-ASUWKVUT.js.map → ssGSEA.unit.spec-HTRGQI2K.js.map} +0 -0
  925. /package/dist/{summarizeCnvGeneexp-KWRFGX32.js.map → summarizeCnvGeneexp-RFYC3H2Z.js.map} +0 -0
  926. /package/dist/{summarizeGeneexpSurvival-FIPIMEJR.js.map → summarizeGeneexpSurvival-DQBZUTQ6.js.map} +0 -0
  927. /package/dist/{summarizeMutationCnv-IUYRVLZG.js.map → summarizeMutationCnv-7AYEMHAI.js.map} +0 -0
  928. /package/dist/{summarizeMutationDiagnosis-ZFJPCABL.js.map → summarizeMutationDiagnosis-AKFJDSAF.js.map} +0 -0
  929. /package/dist/{summarizeMutationSurvival-HFHYB7DT.js.map → summarizeMutationSurvival-QJHZRQBZ.js.map} +0 -0
  930. /package/dist/{summary-AZUNEZ5I.js.map → summary-A5P7AYK4.js.map} +0 -0
  931. /package/dist/{summary.integration.spec-WLBAJL44.js.map → summary.integration.spec-HQISXGNL.js.map} +0 -0
  932. /package/dist/{summaryInput-NJWVXDXW.js.map → summaryInput-HP675QOQ.js.map} +0 -0
  933. /package/dist/{sunburst-PXGF4WM6.js.map → sunburst-65LSYRXX.js.map} +0 -0
  934. /package/dist/{survival-ZZ4QLZHK.js.map → survival-QNEI6YVK.js.map} +0 -0
  935. /package/dist/{survival-RAU4XCKG.js.map → survival-UI74VXSM.js.map} +0 -0
  936. /package/dist/{svgraph-7UCFRL6A.js.map → svgraph-PSX2NER3.js.map} +0 -0
  937. /package/dist/{svmr-DB3RY2ID.js.map → svmr-QDQ33EFX.js.map} +0 -0
  938. /package/dist/{table-HJRWWXGM.js.map → table-LWAI27UO.js.map} +0 -0
  939. /package/dist/{termCollection-WPON7RG3.js.map → termCollection-3JHR74FG.js.map} +0 -0
  940. /package/dist/{termCollection-AW7M6DTP.js.map → termCollection-CDF5LYUG.js.map} +0 -0
  941. /package/dist/{termCollection.unit.spec-254ESHOE.js.map → termCollection.unit.spec-HOJKYWHF.js.map} +0 -0
  942. /package/dist/{tk-SUAFM5YA.js.map → tk-OEQFO73V.js.map} +0 -0
  943. /package/dist/{tp.ui-ELEQGSK2.js.map → tp.ui-SHNERDGC.js.map} +0 -0
  944. /package/dist/{tvs.dt-DCXY66YY.js.map → tvs.dt-CZDC4TSR.js.map} +0 -0
  945. /package/dist/{tvs.dtcnv.categorical-SFQZMYX7.js.map → tvs.dtcnv.categorical-OPBDHZGB.js.map} +0 -0
  946. /package/dist/{tvs.dtcnv.continuous-AUZNJMC3.js.map → tvs.dtcnv.continuous-AR6P4EP3.js.map} +0 -0
  947. /package/dist/{tvs.dtfusion-5F7MYFHZ.js.map → tvs.dtfusion-2YQ7N6FQ.js.map} +0 -0
  948. /package/dist/{tvs.dtsnvindel-JJSPL4PH.js.map → tvs.dtsnvindel-WHHWAATJ.js.map} +0 -0
  949. /package/dist/{tvs.dtsv-DARTSV5H.js.map → tvs.dtsv-3UMCW65O.js.map} +0 -0
  950. /package/dist/{tvs.numeric-KYAU5OV3.js.map → tvs.numeric-TOEPASWN.js.map} +0 -0
  951. /package/dist/{tvs.samplelst-HHBIO26C.js.map → tvs.samplelst-M7XKXRTZ.js.map} +0 -0
  952. /package/dist/{tvs.termCollection-KCMALH6B.js.map → tvs.termCollection-WT4WZMYR.js.map} +0 -0
  953. /package/dist/{violin-C26FW5WK.js.map → violin-2YGXTBDS.js.map} +0 -0
  954. /package/dist/{violin.integration.spec-QQ43XWHQ.js.map → violin.integration.spec-YWNHVAGS.js.map} +0 -0
  955. /package/dist/{violin.interactivity-H2BHC6M4.js.map → violin.interactivity-J6BE2UQL.js.map} +0 -0
  956. /package/dist/{violin.renderer-GSG2I7AV.js.map → violin.renderer-3GRUWP2U.js.map} +0 -0
  957. /package/dist/{vocabulary-3G525O5V.js.map → vocabulary-2INCVPYJ.js.map} +0 -0
@@ -1,593 +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-WY2PGUVX.js";
11
- import "./chunk-HJ6L54YS.js";
12
- import "./chunk-LSEFWW72.js";
13
- import "./chunk-MBUQ34CF.js";
14
- import {
15
- Menu
16
- } from "./chunk-HYOEWQ5P.js";
17
- import "./chunk-HBW42TDT.js";
18
- import "./chunk-LQJMCE7G.js";
19
- import "./chunk-FN5XPUPH.js";
20
- import "./chunk-IIT367QZ.js";
21
- import "./chunk-RZGEKL77.js";
22
- import "./chunk-OVSKJROY.js";
23
- import "./chunk-A3URBFXN.js";
24
- import "./chunk-LYVLF6HO.js";
25
- import "./chunk-7IYJZZQI.js";
26
- import "./chunk-M3J4MINX.js";
27
- import "./chunk-PF4DSFDR.js";
28
- import "./chunk-I73KUUYG.js";
29
- import "./chunk-NNFAUP2I.js";
30
- import "./chunk-7KRS7L4U.js";
31
- import "./chunk-BKPDYW5T.js";
32
- import "./chunk-JNITUVXP.js";
33
- import {
34
- category10_default
35
- } from "./chunk-TJYRBEBK.js";
36
- import {
37
- axisBottom,
38
- axisLeft
39
- } from "./chunk-LOZEKOES.js";
40
- import "./chunk-VQZ2Z5YU.js";
41
- import {
42
- format,
43
- linear,
44
- log,
45
- ordinal,
46
- time,
47
- timeParse
48
- } from "./chunk-SOTB4FRE.js";
49
- import "./chunk-TLT4YIG3.js";
50
- import "./chunk-KYBIQBXE.js";
51
- import {
52
- select_default
53
- } from "./chunk-I6Y4O3RR.js";
54
- import "./chunk-OMR2DT66.js";
55
- import "./chunk-DQC5FFGV.js";
56
- import "./chunk-HFNDKYVF.js";
57
-
58
- // src/maftimeline.js
59
- var zerovalue = 1e-5;
60
- var showcircle = true;
61
- var maflogscale = true;
62
- var tip = new Menu();
63
- function maftimelineui(genomes, holder, sandbox_header) {
64
- let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
65
- if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
66
- else {
67
- ;
68
- [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
69
- pane.header.text("MAF timeline plot");
70
- }
71
- inputdiv.append("p").html(
72
- "<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
73
- );
74
- inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
75
- {
76
- const id = Math.random().toString();
77
- const p = inputdiv.append("p");
78
- p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
79
- maflogscale = !maflogscale;
80
- });
81
- p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
82
- }
83
- const fileui = () => {
84
- filediv.selectAll("*").remove();
85
- const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
86
- saydiv.text("");
87
- const file = event.target.files[0];
88
- if (!file) {
89
- fileui();
90
- return;
91
- }
92
- if (file.size == 0) {
93
- saydiv.text("Wrong file: " + file.name);
94
- fileui();
95
- return;
96
- }
97
- const reader = new FileReader();
98
- reader.onload = (event2) => {
99
- const lines = event2.target.result.trim().split(/\r?\n/);
100
- const [err, header] = parseheader(lines[0].trim());
101
- if (err) {
102
- saydiv.text("File header error: " + err);
103
- fileui();
104
- return;
105
- }
106
- const badlines = [];
107
- const data = {};
108
- let good = 0;
109
- for (let i = 1; i < lines.length; i++) {
110
- if (lines[i] == "") continue;
111
- if (lines[i][0] == "#") continue;
112
- const m = parseline(i, lines[i], header, badlines, data);
113
- if (m) {
114
- good++;
115
- }
116
- }
117
- if (badlines.length) {
118
- bulk_badline(header, badlines);
119
- }
120
- if (good == 0) {
121
- fileui();
122
- return;
123
- }
124
- let visual_holder;
125
- if (pane) {
126
- disappear(pane.pane);
127
- const pane2 = newpane({ x: 100, y: 100, toshrink: true });
128
- pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
129
- visual_holder = pane2.body;
130
- }
131
- if (holder !== void 0) {
132
- visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
133
- inputdiv.selectAll("*").remove();
134
- saydiv.text("");
135
- }
136
- render(data, header, visual_holder);
137
- };
138
- reader.onerror = function() {
139
- saydiv.text("Error reading file " + file.name);
140
- fileui();
141
- return;
142
- };
143
- saydiv.text("Parsing file " + file.name + " ...");
144
- reader.readAsText(file, "utf8");
145
- });
146
- setTimeout(() => butt.node().focus(), 1100);
147
- };
148
- fileui();
149
- }
150
- function parseheader(line) {
151
- const header = line.toLowerCase().split(" ");
152
- if (header.length <= 1) return ["columns must be separated by tab"];
153
- const htry = (...lst) => {
154
- for (const i2 of lst) {
155
- const j = header.indexOf(i2);
156
- if (j != -1) return j;
157
- }
158
- return -1;
159
- };
160
- let i = htry("person", "patient", "caseid");
161
- if (i == -1) return ["person missing"];
162
- header[i] = "patient";
163
- i = htry("sample", "sampleid");
164
- if (i == -1) return ["sample missing"];
165
- header[i] = "sample";
166
- i = htry("snv4");
167
- if (i == -1) return ["snv4 missing"];
168
- header[i] = "snv4";
169
- i = htry("date", "dateofsample");
170
- if (i == -1) return ["date missing"];
171
- header[i] = "date";
172
- i = htry("mutant_readcount", "mutantcount");
173
- if (i != -1) header[i] = "mutant_readcount";
174
- i = htry("ref_readcount", "refcount");
175
- if (i != -1) header[i] = "ref_readcount";
176
- i = htry("total_readcount", "coveragecount");
177
- if (i == -1) return ["total_readcount missing"];
178
- header[i] = "coverage";
179
- i = htry("maf");
180
- if (i == -1) return ["maf missing"];
181
- header[i] = "maf";
182
- i = htry("call_manual");
183
- if (i != -1) header[i] = "call_manual";
184
- return [null, header];
185
- }
186
- function parseline(i, line, header, badlines, data) {
187
- const lst = line.split(" ");
188
- const m = {};
189
- for (let j = 0; j < header.length; j++) {
190
- m[header[j]] = lst[j];
191
- }
192
- if (!m.patient) {
193
- badlines.push([i, "missing patient", lst]);
194
- return;
195
- }
196
- if (!data[m.patient]) {
197
- data[m.patient] = {
198
- snv4: {},
199
- show: false
200
- };
201
- }
202
- if (!m.snv4) {
203
- badlines.push([i, "missing snv4", lst]);
204
- return;
205
- }
206
- if (!data[m.patient].snv4[m.snv4]) {
207
- data[m.patient].snv4[m.snv4] = {
208
- mutationname: m.snv4,
209
- samples: [],
210
- subidx: void 0
211
- };
212
- }
213
- if (m.gene) {
214
- data[m.patient].snv4[m.snv4].gene = m.gene;
215
- }
216
- if (!m.maf) {
217
- badlines.push([i, "missing maf", lst]);
218
- return;
219
- }
220
- let v = Number.parseFloat(m.maf);
221
- if (Number.isNaN(v)) {
222
- badlines.push([i, "invalid maf", lst]);
223
- return;
224
- }
225
- if (v < zerovalue) {
226
- v = zerovalue;
227
- }
228
- m.maf = v;
229
- if (!m.coverage) {
230
- badlines.push([i, "missing total_readcount", lst]);
231
- return;
232
- }
233
- if (m.call_manual && m.call_manual == "wildtype") {
234
- m.maf = zerovalue;
235
- }
236
- v = Number.parseInt(m.coverage);
237
- if (Number.isNaN(v)) {
238
- badlines.push([i, "invalid total_readcount", lst]);
239
- return;
240
- }
241
- m.coverage = v;
242
- let date;
243
- if (m.date) {
244
- const f = timeParse("%m/%d/%Y");
245
- date = f(m.date);
246
- m.Date = m.date;
247
- } else {
248
- badlines.push([i, "missing date", lst]);
249
- return;
250
- }
251
- if (date == null) {
252
- badlines.push([i, "cannot parse date", lst]);
253
- return;
254
- }
255
- m.date = date;
256
- if (!m.sample) {
257
- badlines.push([i, "missing sample", lst]);
258
- return;
259
- }
260
- data[m.patient].snv4[m.snv4].samples.push(m);
261
- return true;
262
- }
263
- function render(data, header, holder) {
264
- const table = holder.append("table").style("margin", "20px");
265
- const tr1 = table.append("tr");
266
- let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
267
- td.append("button").text("Toggle circle visibility").on("click", () => {
268
- showcircle = !showcircle;
269
- for (const n in data) {
270
- if (data[n].show) {
271
- data[n].handle.node().click();
272
- break;
273
- }
274
- }
275
- });
276
- const patientholder = td.append("div").style("margin-top", "10px");
277
- const td1 = tr1.append("td").style("vertical-align", "top");
278
- const graphholder = td1.append("div").style("display", "inline-block");
279
- const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
280
- const tr2 = table.append("tr");
281
- const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
282
- const gtr1 = tiantable.append("tr");
283
- td = gtr1.append("td").style("vertical-align", "top");
284
- td.append("div").text("Shared").style("font-size", "2em");
285
- const graph1holder = td.append("div").style("border", "solid 1px black");
286
- td = gtr1.append("td").style("vertical-align", "top");
287
- td.append("div").text("Rising").style("font-size", "2em");
288
- const graph2holder = td.append("div").style("border", "solid 1px black");
289
- const gtr2 = tiantable.append("tr");
290
- td = gtr2.append("td").style("vertical-align", "top");
291
- td.append("div").text("Falling").style("font-size", "2em");
292
- const graph3holder = td.append("div").style("border", "solid 1px black");
293
- td = gtr2.append("td").style("vertical-align", "top");
294
- td.append("div").text("R-only").style("font-size", "2em");
295
- const graph4holder = td.append("div").style("border", "solid 1px black");
296
- for (const patient in data) {
297
- const snvlst = [];
298
- const colors = ordinal(category10_default);
299
- for (const x in data[patient].snv4) {
300
- const snv = data[patient].snv4[x];
301
- snv.show = true;
302
- snv.color = colors(snv.mutationname);
303
- snv.samples.sort((a, b) => a.date - b.date);
304
- for (const s of snv.samples) {
305
- s.color = snv.color;
306
- }
307
- snvlst.push(snv);
308
- }
309
- const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
310
- for (const pn in data) {
311
- data[pn].handle.style("color", "black");
312
- data[pn].show = false;
313
- }
314
- data[patient].handle.style("color", "red");
315
- data[patient].show = true;
316
- makegraph(snvlst, header, graphholder);
317
- makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
318
- makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
319
- });
320
- data[patient].handle = div;
321
- }
322
- for (const n in data) {
323
- data[n].handle.node().click();
324
- break;
325
- }
326
- }
327
- function makesubgraph(snvlst, g1, g2, g3, g4) {
328
- g1.selectAll("*").remove();
329
- g2.selectAll("*").remove();
330
- g3.selectAll("*").remove();
331
- g4.selectAll("*").remove();
332
- const l1 = [];
333
- const l2 = [];
334
- const l3 = [];
335
- const l4 = [];
336
- for (const snv of snvlst) {
337
- switch (snv.subidx) {
338
- case 1:
339
- l1.push(snv);
340
- break;
341
- case 2:
342
- l2.push(snv);
343
- break;
344
- case 3:
345
- l3.push(snv);
346
- break;
347
- case 4:
348
- l4.push(snv);
349
- break;
350
- }
351
- }
352
- if (l1.length) {
353
- makegraph(l1, null, g1, true);
354
- } else {
355
- g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
356
- }
357
- if (l2.length) {
358
- makegraph(l2, null, g2, true);
359
- } else {
360
- g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
361
- }
362
- if (l3.length) {
363
- makegraph(l3, null, g3, true);
364
- } else {
365
- g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
366
- }
367
- if (l4.length) {
368
- makegraph(l4, null, g4, true);
369
- } else {
370
- g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
371
- }
372
- }
373
- function makegraph(snvlst0, header, holder, issub) {
374
- holder.selectAll("*").remove();
375
- const samples = [];
376
- const snvlst = [];
377
- for (const snv of snvlst0) {
378
- if (!issub && !snv.show) continue;
379
- snvlst.push(snv);
380
- for (const s of snv.samples) {
381
- samples.push(s);
382
- }
383
- }
384
- if (snvlst.length == 0) return;
385
- let mindate = snvlst[0].samples[0].date;
386
- let maxdate = snvlst[0].samples[0].date;
387
- let maxmaf = snvlst[0].samples[0].maf;
388
- let maxcoverage = snvlst[0].samples[0].coverage;
389
- for (const snv of snvlst) {
390
- for (const s of snv.samples) {
391
- mindate = Math.min(mindate, s.date);
392
- maxdate = Math.max(maxdate, s.date);
393
- maxmaf = Math.max(maxmaf, s.maf);
394
- maxcoverage = Math.max(maxcoverage, s.coverage);
395
- }
396
- }
397
- const svg = holder.append("svg");
398
- const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
399
- let width = 600;
400
- let height = 400;
401
- let xpad, ypad, minradius;
402
- const xaxisg = svg.append("g");
403
- const yaxisg = svg.append("g");
404
- const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
405
- event.preventDefault();
406
- const x = event.clientX;
407
- const y = event.clientY;
408
- const w0 = width;
409
- const h0 = height;
410
- const body = select_default(document.body);
411
- body.on("mousemove", (event2) => {
412
- setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
413
- }).on("mouseup", () => {
414
- body.on("mousemove", null).on("mouseup", null);
415
- });
416
- });
417
- const xscale = time().domain([mindate, maxdate]);
418
- const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
419
- const rscale = linear().domain([1, maxcoverage]);
420
- const g = svg.append("g");
421
- const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
422
- let circles;
423
- if (showcircle) {
424
- circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
425
- event.target.setAttribute("fill-opacity", 0.4);
426
- tip.clear();
427
- tip.show(event.clientX, event.clientY);
428
- const lst = [];
429
- for (const k in d) {
430
- if (k == "color") continue;
431
- if (k == "gene") {
432
- lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
433
- continue;
434
- }
435
- if (k == "date") continue;
436
- if (k == "url") {
437
- lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
438
- continue;
439
- }
440
- lst.push({ k, v: d[k] });
441
- }
442
- make_table_2col(tip.d, lst);
443
- }).on("mouseout", (event) => {
444
- event.target.setAttribute("fill-opacity", 0.1);
445
- });
446
- }
447
- const legend = svg.append("g");
448
- const setsize = (w, h) => {
449
- width = w;
450
- height = h;
451
- minradius = 2;
452
- const maxradius = Math.max(width, height) / 30;
453
- xpad = maxradius;
454
- ypad = maxradius;
455
- rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
456
- xscale.range([0, width]);
457
- yscale.range([height, 0]);
458
- svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
459
- xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
460
- yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
461
- drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
462
- axisstyle({
463
- axis: xaxisg.call(axisBottom().scale(xscale)),
464
- showline: true,
465
- color: "black",
466
- fontsize: Math.max(12, Math.min(20, width / 100))
467
- });
468
- axisstyle({
469
- axis: yaxisg.call(
470
- axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
471
- ),
472
- showline: true,
473
- color: "black",
474
- fontsize: Math.max(12, Math.min(20, height / 100))
475
- });
476
- g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
477
- lines.attr("d", (d) => {
478
- const lst = [];
479
- for (let i = 0; i < d.samples.length; i++) {
480
- const s = d.samples[i];
481
- lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
482
- }
483
- return lst.join(" ");
484
- });
485
- if (showcircle) {
486
- circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
487
- }
488
- legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
489
- legend.selectAll("*").remove();
490
- let y = minradius;
491
- if (showcircle) {
492
- legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
493
- legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
494
- y += 5 + minradius + maxradius;
495
- legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
496
- legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
497
- y += 15 + maxradius;
498
- }
499
- const fontsize = 12;
500
- for (const snv of snvlst) {
501
- legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
502
- if (showcircle) {
503
- legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
504
- }
505
- 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) => {
506
- event.target.setAttribute("font-weight", "bold");
507
- lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
508
- }).on("mouseout", (event) => {
509
- event.target.setAttribute("font-weight", "normal");
510
- lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
511
- });
512
- y += fontsize + 10;
513
- }
514
- };
515
- setsize(width, height);
516
- holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
517
- to_svg(svg.node(), "maf-timeline");
518
- });
519
- }
520
- function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
521
- holder.selectAll("*").remove();
522
- const table = holder.append("table");
523
- for (const snv of snvlst) {
524
- const tr = table.append("tr");
525
- const td1 = tr.append("td");
526
- td1.text(snv.gene).style("color", snv.color);
527
- const td2 = tr.append("td");
528
- const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
529
- snv.checkbox = checkbox;
530
- checkbox.on("change", (event) => {
531
- snv.show = event.target.checked;
532
- makegraph(snvlst, header, graphholder);
533
- });
534
- const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
535
- for (const s2 of snvlst) {
536
- s2.show = false;
537
- s2.checkbox.property("checked", false);
538
- }
539
- snv.show = true;
540
- snv.checkbox.property("checked", true);
541
- makegraph(snvlst, header, graphholder);
542
- });
543
- let cname = Math.random();
544
- const td11 = tr.append("td");
545
- const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
546
- td11.append("label").html("&nbsp;shared").attr("for", cname);
547
- cname = Math.random();
548
- const td22 = tr.append("td");
549
- const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
550
- td22.append("label").html("&nbsp;rising").attr("for", cname);
551
- cname = Math.random();
552
- const td33 = tr.append("td");
553
- const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
554
- td33.append("label").html("&nbsp;falling").attr("for", cname);
555
- cname = Math.random();
556
- const td44 = tr.append("td");
557
- const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
558
- td44.append("label").html("&nbsp;R-only").attr("for", cname);
559
- if (snv.subidx == 1) c1.property("checked", true);
560
- if (snv.subidx == 2) c2.property("checked", true);
561
- if (snv.subidx == 3) c3.property("checked", true);
562
- if (snv.subidx == 4) c4.property("checked", true);
563
- const cchange = (which, check) => {
564
- if (!check.checked) {
565
- snv.subidx = -1;
566
- } else {
567
- snv.subidx = which;
568
- if (which == 1) {
569
- c2.property("checked", false);
570
- c3.property("checked", false);
571
- c4.property("checked", false);
572
- } else if (which == 2) {
573
- c1.property("checked", false);
574
- c3.property("checked", false);
575
- c4.property("checked", false);
576
- } else if (which == 3) {
577
- c1.property("checked", false);
578
- c2.property("checked", false);
579
- c4.property("checked", false);
580
- } else {
581
- c1.property("checked", false);
582
- c2.property("checked", false);
583
- c3.property("checked", false);
584
- }
585
- }
586
- makesubgraph(snvlst, g1, g2, g3, g4);
587
- };
588
- }
589
- }
590
- export {
591
- maftimelineui as default
592
- };
593
- //# sourceMappingURL=maftimeline-BLBNUGAL.js.map
@@ -1,58 +0,0 @@
1
- import {
2
- Matrix,
3
- componentInit,
4
- makeChartBtnMenu,
5
- matrixInit
6
- } from "./chunk-SLHWUFAW.js";
7
- import "./chunk-A45KH7LP.js";
8
- import "./chunk-FISP5YN2.js";
9
- import "./chunk-DDKS3MV3.js";
10
- import "./chunk-5CR24RTX.js";
11
- import "./chunk-IFK24IXL.js";
12
- import "./chunk-4O6H4ZHL.js";
13
- import "./chunk-J6ZOUCWN.js";
14
- import "./chunk-YYFQPGIE.js";
15
- import "./chunk-VDZ5QOF6.js";
16
- import "./chunk-N7O7NPUO.js";
17
- import "./chunk-HUBO743S.js";
18
- import "./chunk-L6A2BEXB.js";
19
- import "./chunk-WKT46ZJ6.js";
20
- import "./chunk-V2OJLJSK.js";
21
- import "./chunk-WY2PGUVX.js";
22
- import "./chunk-HJ6L54YS.js";
23
- import "./chunk-LSEFWW72.js";
24
- import "./chunk-MBUQ34CF.js";
25
- import "./chunk-HYOEWQ5P.js";
26
- import "./chunk-HBW42TDT.js";
27
- import "./chunk-LQJMCE7G.js";
28
- import "./chunk-FN5XPUPH.js";
29
- import "./chunk-IIT367QZ.js";
30
- import "./chunk-RZGEKL77.js";
31
- import "./chunk-OVSKJROY.js";
32
- import "./chunk-A3URBFXN.js";
33
- import "./chunk-LYVLF6HO.js";
34
- import "./chunk-7IYJZZQI.js";
35
- import "./chunk-M3J4MINX.js";
36
- import "./chunk-PF4DSFDR.js";
37
- import "./chunk-I73KUUYG.js";
38
- import "./chunk-NNFAUP2I.js";
39
- import "./chunk-7KRS7L4U.js";
40
- import "./chunk-BKPDYW5T.js";
41
- import "./chunk-JNITUVXP.js";
42
- import "./chunk-TJYRBEBK.js";
43
- import "./chunk-LOZEKOES.js";
44
- import "./chunk-VQZ2Z5YU.js";
45
- import "./chunk-SOTB4FRE.js";
46
- import "./chunk-TLT4YIG3.js";
47
- import "./chunk-KYBIQBXE.js";
48
- import "./chunk-I6Y4O3RR.js";
49
- import "./chunk-OMR2DT66.js";
50
- import "./chunk-DQC5FFGV.js";
51
- import "./chunk-HFNDKYVF.js";
52
- export {
53
- Matrix,
54
- componentInit,
55
- makeChartBtnMenu,
56
- matrixInit
57
- };
58
- //# sourceMappingURL=matrix-LVJSHXDM.js.map