@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

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 (1066) hide show
  1. package/dist/2dmaf-RRV3ORZR.js +1373 -0
  2. package/dist/AIProjectAdmin-DKLEFCGX.js +958 -0
  3. package/dist/AppHeader-WQ2F7HZY.js +835 -0
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  911. /package/dist/{chunk-HLUZOZXJ.js.map → chunk-M66VDGSH.js.map} +0 -0
  912. /package/dist/{chunk-5AZNP47R.js.map → chunk-MJN6RDXB.js.map} +0 -0
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  918. /package/dist/{chunk-E55LLYRX.js.map → chunk-OOWXMY7U.js.map} +0 -0
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  924. /package/dist/{chunk-GAPI4MML.js.map → chunk-RVKADD4L.js.map} +0 -0
  925. /package/dist/{chunk-33K5PA52.js.map → chunk-S5ZCK44Z.js.map} +0 -0
  926. /package/dist/{chunk-ZTHM2TKP.js.map → chunk-SNRIVNQ3.js.map} +0 -0
  927. /package/dist/{chunk-WFCSOTBO.js.map → chunk-TAM7UCAI.js.map} +0 -0
  928. /package/dist/{chunk-NSTL4MY2.js.map → chunk-UJELJXJG.js.map} +0 -0
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  930. /package/dist/{chunk-3RSKOPIY.js.map → chunk-W76X6W73.js.map} +0 -0
  931. /package/dist/{chunk-PFRWS4CR.js.map → chunk-W7OS7BNM.js.map} +0 -0
  932. /package/dist/{chunk-Q2L44HK3.js.map → chunk-WTTD6DUL.js.map} +0 -0
  933. /package/dist/{chunk-2GYWFQML.js.map → chunk-WXPFMVU6.js.map} +0 -0
  934. /package/dist/{chunk-BOZJHPJP.js.map → chunk-YBLTSYQV.js.map} +0 -0
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  937. /package/dist/{controls.config-P5PG2DHW.js.map → controls.config-3AJKR4ZZ.js.map} +0 -0
  938. /package/dist/{correlation-U3EDLNHR.js.map → correlation-DXTAWSLU.js.map} +0 -0
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  944. /package/dist/{dnaMethylation-OIZMHMLK.js.map → dnaMethylation-N3WNK6XA.js.map} +0 -0
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  951. /package/dist/{geneExpression-ZMERB64E.js.map → geneExpression-VWUMM2LU.js.map} +0 -0
  952. /package/dist/{geneORA-FXVUCXGX.js.map → geneORA-3VWFWDYI.js.map} +0 -0
  953. /package/dist/{geneRanking-SFK4UBKQ.js.map → geneRanking-PKDVD5OD.js.map} +0 -0
  954. /package/dist/{geneVariant-IYEHB4H7.js.map → geneVariant-IFIJQXH4.js.map} +0 -0
  955. /package/dist/{geneVariant-LIRRLUFR.js.map → geneVariant-WZSOG4GI.js.map} +0 -0
  956. /package/dist/{geneVariant.integration.spec-Y2NPNTYX.js.map → geneVariant.integration.spec-6KQMWVHR.js.map} +0 -0
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  960. /package/dist/{grin2-V36KLEBU.js.map → grin2-FT5BQJMB.js.map} +0 -0
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  962. /package/dist/{hierCluster-YWC3XYPV.js.map → hierCluster-HMJF3PBE.js.map} +0 -0
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  967. /package/dist/{importPlot-7QGANZGK.js.map → importPlot-VMYXDP66.js.map} +0 -0
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  969. /package/dist/{launch.adhoc-LWLBQJS5.js.map → junction-VO4IGMW2.js.map} +0 -0
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  1001. /package/dist/{plot.barplot-JEPRZSCU.js.map → plot.barplot-R333TMG2.js.map} +0 -0
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  1014. /package/dist/{render-N5FOF247.js.map → regression.inputs.term-XS54IQC2.js.map} +0 -0
  1015. /package/dist/{sampleView-ICOT2R6O.js.map → regression.inputs.values.table-LNPM3MX5.js.map} +0 -0
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  1019. /package/dist/{singleCellGeneExpression-YR2ZT34W.js.map → render-SEB6GFXQ.js.map} +0 -0
  1020. /package/dist/{report-DW3OHB67.js.map → report-U6L3KBYG.js.map} +0 -0
  1021. /package/dist/{singleCellPlot-3ICIOILE.js.map → sampleView-QAAJ26KT.js.map} +0 -0
  1022. /package/dist/{samplelst-TJEVASYG.js.map → samplelst-KYRXJSZN.js.map} +0 -0
  1023. /package/dist/{samplematrix-6DAWCXQ3.js.map → samplematrix-STLF2QA5.js.map} +0 -0
  1024. /package/dist/{sc-53LNOB7N.js.map → sc-HL6YSMDX.js.map} +0 -0
  1025. /package/dist/{scatter-DKYSS4DL.js.map → scatter-BSGDMOC2.js.map} +0 -0
  1026. /package/dist/{selectGenomeWithTklst-WTX66TV3.js.map → selectGenomeWithTklst-4NHQDTE6.js.map} +0 -0
  1027. /package/dist/{snp-VIURB7L3.js.map → singleCellCellType-3E2IU42J.js.map} +0 -0
  1028. /package/dist/{ssGSEA-THW4WFMI.js.map → singleCellGeneExpression-53UUGYTK.js.map} +0 -0
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  1030. /package/dist/{singlecell-KX7W4U57.js.map → singlecell-IJR7BJYT.js.map} +0 -0
  1031. /package/dist/{singlecell-6ZUFA3BQ.js.map → singlecell-OK6GJFWL.js.map} +0 -0
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  1033. /package/dist/{snp.unit.spec-ACZNZUNS.js.map → snp.unit.spec-2Y4A3XYI.js.map} +0 -0
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  1037. /package/dist/{spliceevent.noeventdiagram-YTXWWNTJ.js.map → spliceevent.noeventdiagram-II753XAK.js.map} +0 -0
  1038. /package/dist/{survival-QNEI6YVK.js.map → ssGSEA-JPJ3C4JI.js.map} +0 -0
  1039. /package/dist/{ssGSEA.unit.spec-HTRGQI2K.js.map → ssGSEA.unit.spec-45F5OCDK.js.map} +0 -0
  1040. /package/dist/{summarizeCnvGeneexp-RFYC3H2Z.js.map → summarizeCnvGeneexp-55DNXHXA.js.map} +0 -0
  1041. /package/dist/{summarizeMutationCnv-7AYEMHAI.js.map → summarizeMutationCnv-QX7BADYL.js.map} +0 -0
  1042. /package/dist/{termCollection-CDF5LYUG.js.map → summarizeMutationDiagnosis-MHFM7RX6.js.map} +0 -0
  1043. /package/dist/{summarizeMutationSurvival-QJHZRQBZ.js.map → summarizeMutationSurvival-G4KHSUBN.js.map} +0 -0
  1044. /package/dist/{tk-OEQFO73V.js.map → summary-PJYRCQNY.js.map} +0 -0
  1045. /package/dist/{summary.integration.spec-HQISXGNL.js.map → summary.integration.spec-KPKROD6L.js.map} +0 -0
  1046. /package/dist/{sunburst-65LSYRXX.js.map → sunburst-IGIV2RBE.js.map} +0 -0
  1047. /package/dist/{survival-UI74VXSM.js.map → survival-DINCIWW7.js.map} +0 -0
  1048. /package/dist/{svgraph-PSX2NER3.js.map → svgraph-EUEZWGVR.js.map} +0 -0
  1049. /package/dist/{svmr-QDQ33EFX.js.map → svmr-B24LODSC.js.map} +0 -0
  1050. /package/dist/{table-LWAI27UO.js.map → table-XSJJ3UZV.js.map} +0 -0
  1051. /package/dist/{toggleButtons-YK7TIFF2.js.map → termCollection-IAB3425K.js.map} +0 -0
  1052. /package/dist/{tvs.density-3XJ6DBGO.js.map → termCollectionFractionSelection-35YKAOUY.js.map} +0 -0
  1053. /package/dist/{tvs.dt-CZDC4TSR.js.map → tk-25EJJDRK.js.map} +0 -0
  1054. /package/dist/{tp.ui-SHNERDGC.js.map → tp.ui-VGA62NFM.js.map} +0 -0
  1055. /package/dist/{tvs.numeric-TOEPASWN.js.map → tvs.density-G56327WY.js.map} +0 -0
  1056. /package/dist/{violin-2YGXTBDS.js.map → tvs.dt-DFW36WKO.js.map} +0 -0
  1057. /package/dist/{tvs.dtcnv.categorical-OPBDHZGB.js.map → tvs.dtcnv.categorical-ZP33EO3A.js.map} +0 -0
  1058. /package/dist/{tvs.dtcnv.continuous-AR6P4EP3.js.map → tvs.dtcnv.continuous-FJTMQF4J.js.map} +0 -0
  1059. /package/dist/{tvs.dtfusion-2YQ7N6FQ.js.map → tvs.dtfusion-FTDQWNKM.js.map} +0 -0
  1060. /package/dist/{tvs.dtitd-ATCHW735.js.map → tvs.dtitd-W5VEECJ2.js.map} +0 -0
  1061. /package/dist/{tvs.dtsnvindel-WHHWAATJ.js.map → tvs.dtsnvindel-UOXSLCDZ.js.map} +0 -0
  1062. /package/dist/{tvs.dtsv-3UMCW65O.js.map → tvs.dtsv-HWCPRVBO.js.map} +0 -0
  1063. /package/dist/{violin.interactivity-J6BE2UQL.js.map → tvs.numeric-7TGKWQYU.js.map} +0 -0
  1064. /package/dist/{tvs.samplelst-M7XKXRTZ.js.map → tvs.samplelst-OWD22ITS.js.map} +0 -0
  1065. /package/dist/{violin.renderer-3GRUWP2U.js.map → violin-2IAVZGFF.js.map} +0 -0
  1066. /package/dist/{vocabulary-2INCVPYJ.js.map → violin.interactivity-STOCZMVN.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-5VOPABBA.js";
11
- import "./chunk-HJ6L54YS.js";
12
- import "./chunk-LSEFWW72.js";
13
- import "./chunk-Z5U6HOE4.js";
14
- import {
15
- Menu
16
- } from "./chunk-HYOEWQ5P.js";
17
- import "./chunk-HBW42TDT.js";
18
- import "./chunk-FN5XPUPH.js";
19
- import "./chunk-5ABGFJSP.js";
20
- import "./chunk-IIT367QZ.js";
21
- import "./chunk-RZGEKL77.js";
22
- import "./chunk-XPY6AWXO.js";
23
- import "./chunk-NELOT3NJ.js";
24
- import "./chunk-M6EF3WVV.js";
25
- import "./chunk-7IYJZZQI.js";
26
- import "./chunk-M3J4MINX.js";
27
- import "./chunk-PF4DSFDR.js";
28
- import "./chunk-LFCYMSVA.js";
29
- import "./chunk-I6WR4CG7.js";
30
- import "./chunk-2X6W4E3W.js";
31
- import "./chunk-NYRZNRG5.js";
32
- import "./chunk-JNITUVXP.js";
33
- import {
34
- category10_default
35
- } from "./chunk-3XVVN66M.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-NSTL4MY2.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-7MSVYKQU.js.map
@@ -1,58 +0,0 @@
1
- import {
2
- Matrix,
3
- componentInit,
4
- makeChartBtnMenu,
5
- matrixInit
6
- } from "./chunk-G5S4R77D.js";
7
- import "./chunk-G764NXQN.js";
8
- import "./chunk-ESGXULRH.js";
9
- import "./chunk-T25QNZHB.js";
10
- import "./chunk-W3WPPOXH.js";
11
- import "./chunk-OXVLWQ6M.js";
12
- import "./chunk-HUBO743S.js";
13
- import "./chunk-BHGISFCA.js";
14
- import "./chunk-ONPKE6DC.js";
15
- import "./chunk-DDKS3MV3.js";
16
- import "./chunk-UGRQXBL4.js";
17
- import "./chunk-CDD7LYJM.js";
18
- import "./chunk-YQBS2ZCK.js";
19
- import "./chunk-RKO6BL5N.js";
20
- import "./chunk-V2OJLJSK.js";
21
- import "./chunk-5VOPABBA.js";
22
- import "./chunk-HJ6L54YS.js";
23
- import "./chunk-LSEFWW72.js";
24
- import "./chunk-Z5U6HOE4.js";
25
- import "./chunk-HYOEWQ5P.js";
26
- import "./chunk-HBW42TDT.js";
27
- import "./chunk-FN5XPUPH.js";
28
- import "./chunk-5ABGFJSP.js";
29
- import "./chunk-IIT367QZ.js";
30
- import "./chunk-RZGEKL77.js";
31
- import "./chunk-XPY6AWXO.js";
32
- import "./chunk-NELOT3NJ.js";
33
- import "./chunk-M6EF3WVV.js";
34
- import "./chunk-7IYJZZQI.js";
35
- import "./chunk-M3J4MINX.js";
36
- import "./chunk-PF4DSFDR.js";
37
- import "./chunk-LFCYMSVA.js";
38
- import "./chunk-I6WR4CG7.js";
39
- import "./chunk-2X6W4E3W.js";
40
- import "./chunk-NYRZNRG5.js";
41
- import "./chunk-JNITUVXP.js";
42
- import "./chunk-3XVVN66M.js";
43
- import "./chunk-LOZEKOES.js";
44
- import "./chunk-VQZ2Z5YU.js";
45
- import "./chunk-NSTL4MY2.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-BGLWC25D.js.map