@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

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 (937) hide show
  1. package/dist/2dmaf-PBJ3POZQ.js +1371 -0
  2. package/dist/AIProjectAdmin-5IAXCACJ.js +830 -0
  3. package/dist/AppHeader-HLUE2IQT.js +833 -0
  4. package/dist/BoxPlot-NAQS5MHV.js +1217 -0
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  174. package/dist/dnaMethylation-4VDQBBGJ.js +36 -0
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  835. /package/dist/{matrix.integration.spec-PQH67KRM.js.map → matrix.integration.spec-XHGSEBYM.js.map} +0 -0
  836. /package/dist/{matrix.interactivity-JW4AXAWO.js.map → matrix.interactivity-OZS7R32Z.js.map} +0 -0
  837. /package/dist/{matrix.layout-I56KRVCO.js.map → matrix.layout-GBQJ7O3H.js.map} +0 -0
  838. /package/dist/{matrix.legend-42LQGAGX.js.map → matrix.legend-AGTC5JPS.js.map} +0 -0
  839. /package/dist/{matrix.renderers-IX3FCNBK.js.map → matrix.renderers-L5D5NLLR.js.map} +0 -0
  840. /package/dist/{matrix.serieses-4B2WB526.js.map → matrix.serieses-DDQOSCL4.js.map} +0 -0
  841. /package/dist/{matrix.sort-BJACNR7G.js.map → matrix.sort-6VF7VNFX.js.map} +0 -0
  842. /package/dist/{matrix.sort.unit.spec-3KKDKIPY.js.map → matrix.sort.unit.spec-QGJBVO3X.js.map} +0 -0
  843. /package/dist/{matrix.sorterUi-W6XFYZY2.js.map → matrix.sorterUi-UE7CBIUP.js.map} +0 -0
  844. /package/dist/{matrix.sorterUi.unit.spec-CMJ7EBIW.js.map → matrix.sorterUi.unit.spec-CTLTVJCO.js.map} +0 -0
  845. /package/dist/{mavb-ROAE6WYA.js.map → mavb-MU7H7YWY.js.map} +0 -0
  846. /package/dist/{mds.fimo-UGK5OWCF.js.map → mds.fimo-ELCNQMNR.js.map} +0 -0
  847. /package/dist/{mds.samplescatterplot-5KFUAYSB.js.map → mds.samplescatterplot-P7N4SXYT.js.map} +0 -0
  848. /package/dist/{mds.survivalplot-2EVNZUX5.js.map → mds.survivalplot-KJFW4IRT.js.map} +0 -0
  849. /package/dist/{oncomatrix-UGFXSXQJ.js.map → oncomatrix-Q5X3O65P.js.map} +0 -0
  850. /package/dist/{oncomatrix.spec-FEP7BR7L.js.map → oncomatrix.spec-CJGXXI3U.js.map} +0 -0
  851. /package/dist/{plot.2dvaf-WXGLWCOC.js.map → plot.2dvaf-CDPVMUPX.js.map} +0 -0
  852. /package/dist/{plot.app-IZAFRTBU.js.map → plot.app-BSPQMQCI.js.map} +0 -0
  853. /package/dist/{plot.barplot-Z4VWOPFJ.js.map → plot.barplot-C33LEV4Q.js.map} +0 -0
  854. /package/dist/{plot.boxplot-QU2KZSB7.js.map → plot.boxplot-XH7FN6PC.js.map} +0 -0
  855. /package/dist/{plot.brainImaging-U643YIK7.js.map → plot.brainImaging-5BB455FT.js.map} +0 -0
  856. /package/dist/{plot.disco-3BV6YEBC.js.map → plot.disco-3YUN6XAY.js.map} +0 -0
  857. /package/dist/{plot.dzi-DWXPOOQE.js.map → plot.dzi-RZWAL5UC.js.map} +0 -0
  858. /package/dist/{plot.ssgq-GXB2GZO3.js.map → plot.ssgq-M763HWMN.js.map} +0 -0
  859. /package/dist/{plot.vaf2cov-EKRIADPB.js.map → plot.vaf2cov-EAHQV6FD.js.map} +0 -0
  860. /package/dist/{plot.wsi-E2LLE6HI.js.map → plot.wsi-2BDC3RJS.js.map} +0 -0
  861. /package/dist/{polar-MZLIUXHO.js.map → polar-3SJ5SUNJ.js.map} +0 -0
  862. /package/dist/{polar2-IUVHNQM4.js.map → polar2-3GTEGZUL.js.map} +0 -0
  863. /package/dist/{profile.spec-JRW6KYUI.js.map → profile.spec-AR7JLQYT.js.map} +0 -0
  864. /package/dist/{profileBarchart-N7HJMYZ5.js.map → profileBarchart-GLTPPW2O.js.map} +0 -0
  865. /package/dist/{profileForms-Q5TPGPQP.js.map → profileForms-FE4GHA2T.js.map} +0 -0
  866. /package/dist/{profilePlot-TXTUYDVE.js.map → profilePlot-3JXEZUX5.js.map} +0 -0
  867. /package/dist/{profileRadar-ICEASI7W.js.map → profileRadar-NA2WUSHG.js.map} +0 -0
  868. /package/dist/{profileRadarFacility-NFMRNJYX.js.map → profileRadarFacility-6UNT4GPM.js.map} +0 -0
  869. /package/dist/{proteinView-K3JFNORQ.js.map → proteinView-ESTBC3K2.js.map} +0 -0
  870. /package/dist/{proteomeAbundance-LTB3QR3G.js.map → proteomeAbundance-GDK5EIE7.js.map} +0 -0
  871. /package/dist/{proteomeAbundance-DE4NVBCN.js.map → proteomeAbundance-NVLYQRKI.js.map} +0 -0
  872. /package/dist/{qualitative-DFGWQURY.js.map → qualitative-TUNIICQ4.js.map} +0 -0
  873. /package/dist/{regression-TTQTAEGD.js.map → regression-22IF77A7.js.map} +0 -0
  874. /package/dist/{regression.inputs-2LU2XRGC.js.map → regression.inputs-VCVMUBA7.js.map} +0 -0
  875. /package/dist/{regression.inputs.term-G57GL57T.js.map → regression.inputs.term-6FWVBNJT.js.map} +0 -0
  876. /package/dist/{regression.inputs.values.table-JSEM3PXL.js.map → regression.inputs.values.table-2FXOWLKN.js.map} +0 -0
  877. /package/dist/{regression.integration.spec-XJQJAIC3.js.map → regression.integration.spec-2UMB7EIG.js.map} +0 -0
  878. /package/dist/{regression.results-3YNM6LLQ.js.map → regression.results-27XHC5GE.js.map} +0 -0
  879. /package/dist/{regression.spec-S6WFCPSW.js.map → regression.spec-5Q4J7TJZ.js.map} +0 -0
  880. /package/dist/{report-YRAV4MY4.js.map → report-B4RRLC7Q.js.map} +0 -0
  881. /package/dist/{sampleScatter.spec-MBJ4XNTX.js.map → sampleScatter.spec-TXZYLGM7.js.map} +0 -0
  882. /package/dist/{sampleView-IUR3ZEN7.js.map → sampleView-2WKGJUSX.js.map} +0 -0
  883. /package/dist/{samplelst-C2NBFGH6.js.map → samplelst-NJZOPYYJ.js.map} +0 -0
  884. /package/dist/{samplematrix-AOK2HHSB.js.map → samplematrix-ZXOLANI5.js.map} +0 -0
  885. /package/dist/{sc-XT3Z5XJI.js.map → sc-4IYYVV2I.js.map} +0 -0
  886. /package/dist/{scatter-SAHKZRFL.js.map → scatter-UBF4N6ON.js.map} +0 -0
  887. /package/dist/{scatter.integration.spec-6KRDNHHH.js.map → scatter.integration.spec-JNGJ4BU5.js.map} +0 -0
  888. /package/dist/{selectGenomeWithTklst-2YVZ4JWV.js.map → selectGenomeWithTklst-7ICTRJNK.js.map} +0 -0
  889. /package/dist/{singleCellCellType-NFN5GQJM.js.map → singleCellCellType-Y5ETQYDC.js.map} +0 -0
  890. /package/dist/{singleCellCellType.unit.spec-CR4IJ4DA.js.map → singleCellCellType.unit.spec-TLLZRMD7.js.map} +0 -0
  891. /package/dist/{singleCellGeneExpression-7AQGLXTR.js.map → singleCellGeneExpression-HZRIE2XT.js.map} +0 -0
  892. /package/dist/{singleCellGeneExpression.unit.spec-QYNWSV2G.js.map → singleCellGeneExpression.unit.spec-K435LTFJ.js.map} +0 -0
  893. /package/dist/{singleCellPlot-IWFEG44C.js.map → singleCellPlot-T7MKCAAW.js.map} +0 -0
  894. /package/dist/{singlecell-EATPLH66.js.map → singlecell-K662WWCH.js.map} +0 -0
  895. /package/dist/{singlecell-3QNV4OMZ.js.map → singlecell-KVLDYQ36.js.map} +0 -0
  896. /package/dist/{snp-UP7WL7WG.js.map → snp-JNV3DX5W.js.map} +0 -0
  897. /package/dist/{snp.unit.spec-Y5NWQ442.js.map → snp.unit.spec-7KFVZUWR.js.map} +0 -0
  898. /package/dist/{snplocus-WAQK2AZG.js.map → snplocus-VJLA35TV.js.map} +0 -0
  899. /package/dist/{spliceevent.a53ss.diagram-FFK27UIB.js.map → spliceevent.a53ss.diagram-MZPU6IBF.js.map} +0 -0
  900. /package/dist/{spliceevent.exonskip.diagram-KWEF2OZJ.js.map → spliceevent.exonskip.diagram-OOYBJT4F.js.map} +0 -0
  901. /package/dist/{spliceevent.noeventdiagram-PU4TI7OM.js.map → spliceevent.noeventdiagram-KPEZVRFS.js.map} +0 -0
  902. /package/dist/{ssGSEA-N6QOAVLW.js.map → ssGSEA-GPPPUU2J.js.map} +0 -0
  903. /package/dist/{ssGSEA.unit.spec-KQBNZNNP.js.map → ssGSEA.unit.spec-4SRZ4NRN.js.map} +0 -0
  904. /package/dist/{summarizeCnvGeneexp-NWX4M6LZ.js.map → summarizeCnvGeneexp-NRLEM4X4.js.map} +0 -0
  905. /package/dist/{summarizeGeneexpSurvival-N5VTE2G6.js.map → summarizeGeneexpSurvival-BJLP43OZ.js.map} +0 -0
  906. /package/dist/{summarizeMutationCnv-VV7CVAA7.js.map → summarizeMutationCnv-7DCCBY5U.js.map} +0 -0
  907. /package/dist/{summarizeMutationDiagnosis-5RHSG7L6.js.map → summarizeMutationDiagnosis-HATSCOMG.js.map} +0 -0
  908. /package/dist/{summarizeMutationSurvival-22YYXGS5.js.map → summarizeMutationSurvival-XIRZFWDJ.js.map} +0 -0
  909. /package/dist/{summary-P3WIKJS7.js.map → summary-VOFTJ76P.js.map} +0 -0
  910. /package/dist/{summary.integration.spec-ULGRPICW.js.map → summary.integration.spec-2C5RCIY4.js.map} +0 -0
  911. /package/dist/{summaryInput-IH4EVNF5.js.map → summaryInput-DIIECI4W.js.map} +0 -0
  912. /package/dist/{sunburst-VJJ3UVYC.js.map → sunburst-CYROEYTG.js.map} +0 -0
  913. /package/dist/{survival-2ZE3N62A.js.map → survival-5Y3DFIES.js.map} +0 -0
  914. /package/dist/{survival-ASCLKIII.js.map → survival-WCPGEHW5.js.map} +0 -0
  915. /package/dist/{svgraph-AYR2UPNK.js.map → svgraph-3T6XL7TR.js.map} +0 -0
  916. /package/dist/{svmr-MOMW5DNY.js.map → svmr-GUBPSOID.js.map} +0 -0
  917. /package/dist/{table-PQB6KCEY.js.map → table-NTS6ROT7.js.map} +0 -0
  918. /package/dist/{termCollection-OQMUUTW6.js.map → termCollection-EE72SAHN.js.map} +0 -0
  919. /package/dist/{termCollection-5AY2AWT4.js.map → termCollection-ZZXLZ3UE.js.map} +0 -0
  920. /package/dist/{termCollection.unit.spec-BUAXYIJK.js.map → termCollection.unit.spec-3CTEJRTX.js.map} +0 -0
  921. /package/dist/{tk-EJLFFA5H.js.map → tk-6FIXPXTM.js.map} +0 -0
  922. /package/dist/{tp.ui-WUW6A7KP.js.map → tp.ui-4ESL6SCH.js.map} +0 -0
  923. /package/dist/{tvs.density-HSVPDDGA.js.map → tvs.density-AQ5GD437.js.map} +0 -0
  924. /package/dist/{tvs.dt-MVJXQMNU.js.map → tvs.dt-G5FMPWPL.js.map} +0 -0
  925. /package/dist/{tvs.dtcnv.categorical-FIIDWVK7.js.map → tvs.dtcnv.categorical-EYQ6RTHD.js.map} +0 -0
  926. /package/dist/{tvs.dtcnv.continuous-JPQU3JA2.js.map → tvs.dtcnv.continuous-PSQMFFNX.js.map} +0 -0
  927. /package/dist/{tvs.dtfusion-BW35GOQM.js.map → tvs.dtfusion-4F6627GK.js.map} +0 -0
  928. /package/dist/{tvs.dtsnvindel-AEMFZ4EH.js.map → tvs.dtsnvindel-YNYVLJEI.js.map} +0 -0
  929. /package/dist/{tvs.dtsv-JHTU7UFD.js.map → tvs.dtsv-X2K4K4RN.js.map} +0 -0
  930. /package/dist/{tvs.numeric-ICUGA4WY.js.map → tvs.numeric-ZN2R7BH3.js.map} +0 -0
  931. /package/dist/{tvs.samplelst-VD2NFFFS.js.map → tvs.samplelst-XZK4BE3H.js.map} +0 -0
  932. /package/dist/{tvs.termCollection-IKE5Q74D.js.map → tvs.termCollection-ZAX57TN4.js.map} +0 -0
  933. /package/dist/{violin-DPMJLHQG.js.map → violin-YEMSGTYF.js.map} +0 -0
  934. /package/dist/{violin.integration.spec-A4PNR4ES.js.map → violin.integration.spec-TULH2DWL.js.map} +0 -0
  935. /package/dist/{violin.interactivity-TS4DYUE5.js.map → violin.interactivity-RX2CDFVC.js.map} +0 -0
  936. /package/dist/{violin.renderer-53L4PXUT.js.map → violin.renderer-OJJDZFMZ.js.map} +0 -0
  937. /package/dist/{vocabulary-4MPFHKYC.js.map → vocabulary-726CSMNM.js.map} +0 -0
@@ -0,0 +1,591 @@
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-2LCTMDCS.js";
11
+ import "./chunk-HJ6L54YS.js";
12
+ import "./chunk-E5JQ3PN6.js";
13
+ import "./chunk-RCYTUKAJ.js";
14
+ import {
15
+ Menu
16
+ } from "./chunk-A6TQGNDQ.js";
17
+ import "./chunk-HYZG6OPC.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-JOT4WDJE.js";
28
+ import "./chunk-OTCYJP7G.js";
29
+ import "./chunk-GXINX3WK.js";
30
+ import "./chunk-SOED2SLH.js";
31
+ import "./chunk-XRVBHNCW.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-MCYB3EST.js.map
@@ -0,0 +1,57 @@
1
+ import {
2
+ Matrix,
3
+ componentInit,
4
+ makeChartBtnMenu,
5
+ matrixInit
6
+ } from "./chunk-3DN47Y2E.js";
7
+ import "./chunk-6CRWDKT7.js";
8
+ import "./chunk-7M45T6YS.js";
9
+ import "./chunk-M3EBH2WK.js";
10
+ import "./chunk-F5D4ADBB.js";
11
+ import "./chunk-OH7PDA2Z.js";
12
+ import "./chunk-2TMP56TB.js";
13
+ import "./chunk-KBDY6GE3.js";
14
+ import "./chunk-YA73ETIT.js";
15
+ import "./chunk-UFDQ2R2Q.js";
16
+ import "./chunk-VYIO7T6J.js";
17
+ import "./chunk-M5Z3GYRH.js";
18
+ import "./chunk-RH573XZP.js";
19
+ import "./chunk-A5TSPTYC.js";
20
+ import "./chunk-ZIAGMGMS.js";
21
+ import "./chunk-V2OJLJSK.js";
22
+ import "./chunk-2LCTMDCS.js";
23
+ import "./chunk-HJ6L54YS.js";
24
+ import "./chunk-E5JQ3PN6.js";
25
+ import "./chunk-RCYTUKAJ.js";
26
+ import "./chunk-A6TQGNDQ.js";
27
+ import "./chunk-HYZG6OPC.js";
28
+ import "./chunk-FN5XPUPH.js";
29
+ import "./chunk-LSEFWW72.js";
30
+ import "./chunk-5EF5U7MX.js";
31
+ import "./chunk-IQIXGTQV.js";
32
+ import "./chunk-UCLS2SVB.js";
33
+ import "./chunk-MVTCBVSX.js";
34
+ import "./chunk-F6V4AYWP.js";
35
+ import "./chunk-5OHXYXLD.js";
36
+ import "./chunk-DQC5FFGV.js";
37
+ import "./chunk-JOT4WDJE.js";
38
+ import "./chunk-OTCYJP7G.js";
39
+ import "./chunk-GXINX3WK.js";
40
+ import "./chunk-SOED2SLH.js";
41
+ import "./chunk-XRVBHNCW.js";
42
+ import "./chunk-BEWDIM6H.js";
43
+ import "./chunk-IH7ILDJS.js";
44
+ import "./chunk-LOZEKOES.js";
45
+ import "./chunk-TOU7EVFQ.js";
46
+ import "./chunk-OAWQ6LOO.js";
47
+ import "./chunk-SEEYV6P2.js";
48
+ import "./chunk-NDWTN4U5.js";
49
+ import "./chunk-OMR2DT66.js";
50
+ import "./chunk-HFNDKYVF.js";
51
+ export {
52
+ Matrix,
53
+ componentInit,
54
+ makeChartBtnMenu,
55
+ matrixInit
56
+ };
57
+ //# sourceMappingURL=matrix-ID662DZG.js.map