@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

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 (930) hide show
  1. package/dist/2dmaf-VTMPVZGT.js +1367 -0
  2. package/dist/AggMatrixInput-CH3RQ2QC.js +406 -0
  3. package/dist/AggregateMatrix-DPCHUOMF.js +41 -0
  4. package/dist/AppHeader-RA7T467G.js +830 -0
  5. package/dist/BoxPlot-7Q7SMT26.js +1211 -0
  6. package/dist/CorrelationVolcano-YV4UHOAX.js +617 -0
  7. package/dist/Cuminc-ZN53C3MD.js +1219 -0
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  23. package/dist/HicApp-VKET4QHD.js +2245 -0
  24. package/dist/IDCViewer-RLLTXGD7.js +10812 -0
  25. package/dist/NumBinaryEditor-GYHOYPQL.js +279 -0
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  177. package/dist/dnaMethylation-CX22TSRO.js +33 -0
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  837. /package/dist/{matrix.sort-EDXHT6NZ.js.map → matrix.sort-XSGPH44J.js.map} +0 -0
  838. /package/dist/{matrix.sort.unit.spec-LSNY7PHU.js.map → matrix.sort.unit.spec-JF75F4I4.js.map} +0 -0
  839. /package/dist/{matrix.sorterUi-3DRNHG5Z.js.map → matrix.sorterUi-WL5I6S3K.js.map} +0 -0
  840. /package/dist/{matrix.sorterUi.unit.spec-GNIIWGRJ.js.map → matrix.sorterUi.unit.spec-66JMV5BK.js.map} +0 -0
  841. /package/dist/{matrix.unit.spec-7A6ZFRXI.js.map → matrix.unit.spec-36AR4I43.js.map} +0 -0
  842. /package/dist/{mavb-M5AXPLYX.js.map → mavb-ZH4RO77H.js.map} +0 -0
  843. /package/dist/{mds.fimo-QE5OFA22.js.map → mds.fimo-MVP2G5PS.js.map} +0 -0
  844. /package/dist/{mds.samplescatterplot-664EOHX2.js.map → mds.samplescatterplot-GYJ3OI4N.js.map} +0 -0
  845. /package/dist/{mds.survivalplot-H4TJD44D.js.map → mds.survivalplot-Q6MYQGTB.js.map} +0 -0
  846. /package/dist/{multivalue-JD3CNQJR.js.map → multivalue-BGFMPH4X.js.map} +0 -0
  847. /package/dist/{numericDictTermCluster-XPKEYXD7.js.map → numericDictTermCluster-FNNVLIWB.js.map} +0 -0
  848. /package/dist/{oncomatrix-TX5PZQ76.js.map → oncomatrix-LIIALWWN.js.map} +0 -0
  849. /package/dist/{oncomatrix.spec-6X2WAHL7.js.map → oncomatrix.spec-NEMLM2ZN.js.map} +0 -0
  850. /package/dist/{plot.2dvaf-5OHUFTMK.js.map → plot.2dvaf-HJO3SKNK.js.map} +0 -0
  851. /package/dist/{plot.app-XIVVJHWG.js.map → plot.app-WSLFOFSR.js.map} +0 -0
  852. /package/dist/{plot.barplot-PSODLAXD.js.map → plot.barplot-SPI5JA37.js.map} +0 -0
  853. /package/dist/{plot.boxplot-W3ASYFOG.js.map → plot.boxplot-4W3XEY5I.js.map} +0 -0
  854. /package/dist/{plot.brainImaging-JGDLKLR7.js.map → plot.brainImaging-KEOUTYIB.js.map} +0 -0
  855. /package/dist/{plot.disco-TPMXTTZK.js.map → plot.disco-7IDMKNAQ.js.map} +0 -0
  856. /package/dist/{plot.ssgq-KIZIOZIF.js.map → plot.ssgq-IOKUGDC4.js.map} +0 -0
  857. /package/dist/{plot.vaf2cov-MSMW72IY.js.map → plot.vaf2cov-SFSZ6M43.js.map} +0 -0
  858. /package/dist/{polar2-LA4MSRRN.js.map → polar2-PLPE5TX5.js.map} +0 -0
  859. /package/dist/{profileForms-BJRNB2ZF.js.map → profileForms-ZDHG67GM.js.map} +0 -0
  860. /package/dist/{profilePlot-DDO53C4T.js.map → profilePlot-UUZA2YG6.js.map} +0 -0
  861. /package/dist/{proteinView-NFUR42XQ.js.map → proteinView-GHS3XARL.js.map} +0 -0
  862. /package/dist/{proteomeCohortCompare-OZVF3X66.js.map → proteomeCohortCompare-TQ3BGIPS.js.map} +0 -0
  863. /package/dist/{pseudbulk.unit.spec-RY72JF7A.js.map → pseudbulk.unit.spec-HFESRN7A.js.map} +0 -0
  864. /package/dist/{pseudobulk-UVT5G2VL.js.map → pseudobulk-ODXYIUD5.js.map} +0 -0
  865. /package/dist/{qualitative-X3VXNC7X.js.map → qualitative-WOSYAIGQ.js.map} +0 -0
  866. /package/dist/{radar2-RTVUJ3AN.js.map → radar2-2KXBS3Y3.js.map} +0 -0
  867. /package/dist/{radarFacility2-ZGLZ5AKM.js.map → radarFacility2-JCOKJQQF.js.map} +0 -0
  868. /package/dist/{rememberedGvQ.unit.spec-RLLLWU5M.js.map → rememberedGvQ.unit.spec-DYRO2LO5.js.map} +0 -0
  869. /package/dist/{render-LR5BOYW6.js.map → render-IJ6GE3NE.js.map} +0 -0
  870. /package/dist/{report-37W5OXUM.js.map → report-WLLFUA7L.js.map} +0 -0
  871. /package/dist/{sampleView-BDC2WPH7.js.map → sampleView-LPKSYUNF.js.map} +0 -0
  872. /package/dist/{samplelst-V2EIVZC5.js.map → samplelst-MNI2MGMT.js.map} +0 -0
  873. /package/dist/{samplematrix-XOSKILUL.js.map → samplematrix-KEKJP2B4.js.map} +0 -0
  874. /package/dist/{sc-ZVZPWQY7.js.map → sc-ZYKFRJU4.js.map} +0 -0
  875. /package/dist/{scatter-2ZE5MCYH.js.map → scatter-BAEZOFWA.js.map} +0 -0
  876. /package/dist/{scatter-ZOWFPGIS.js.map → scatter-IGFBIZ3B.js.map} +0 -0
  877. /package/dist/{selectGenomeWithTklst-EF7WYEAJ.js.map → selectGenomeWithTklst-HBHRXEDY.js.map} +0 -0
  878. /package/dist/{singleCellCellType-TKCGC3G3.js.map → singleCellCellType-PMFDV24B.js.map} +0 -0
  879. /package/dist/{singleCellCellType.unit.spec-JZ6UHC5F.js.map → singleCellCellType.unit.spec-ZLYDUDIY.js.map} +0 -0
  880. /package/dist/{singleCellGeneExpression-I2INGXGI.js.map → singleCellGeneExpression-SUYO3HR3.js.map} +0 -0
  881. /package/dist/{singleCellGeneExpression.unit.spec-KL77FSHZ.js.map → singleCellGeneExpression.unit.spec-3N3HRXFN.js.map} +0 -0
  882. /package/dist/{singleCellNumericValue-2X5NCEHL.js.map → singleCellNumericValue-BV7C6Y34.js.map} +0 -0
  883. /package/dist/{singleCellNumericValue.unit.spec-OUDBX5MY.js.map → singleCellNumericValue.unit.spec-7VJOMYQ6.js.map} +0 -0
  884. /package/dist/{singleCellPlot-Q6INE54V.js.map → singleCellPlot-BG7UJOHA.js.map} +0 -0
  885. /package/dist/{singlecell-5N2P5ZAT.js.map → singlecell-BANNFGBS.js.map} +0 -0
  886. /package/dist/{singlecell-NPSWMNI3.js.map → singlecell-ZUTL5ZWE.js.map} +0 -0
  887. /package/dist/{snp-2WPJYPDE.js.map → snp-BHG4NVK4.js.map} +0 -0
  888. /package/dist/{snp.unit.spec-PPWIIOX6.js.map → snp.unit.spec-Q3AZHQRC.js.map} +0 -0
  889. /package/dist/{snplocus-T3HZFZWA.js.map → snplocus-HTJL63M3.js.map} +0 -0
  890. /package/dist/{spliceevent.a53ss.diagram-APCF4LV5.js.map → spliceevent.a53ss.diagram-UKRIP7EP.js.map} +0 -0
  891. /package/dist/{spliceevent.exonskip.diagram-TT5JGBSC.js.map → spliceevent.exonskip.diagram-CU777CXQ.js.map} +0 -0
  892. /package/dist/{spliceevent.noeventdiagram-CPXQSX3Z.js.map → spliceevent.noeventdiagram-LGLXCF25.js.map} +0 -0
  893. /package/dist/{ssGSEA-FSX6P7HA.js.map → ssGSEA-BIEEKAKX.js.map} +0 -0
  894. /package/dist/{ssGSEA.unit.spec-TXYT665R.js.map → ssGSEA.unit.spec-YD4UDIRH.js.map} +0 -0
  895. /package/dist/{stattable-BD64SFYV.js.map → stattable-LFR3RSD6.js.map} +0 -0
  896. /package/dist/{studyCatalog-6BOWO4PO.js.map → studyCatalog-RINIZ277.js.map} +0 -0
  897. /package/dist/{summarizeCnvGeneexp-AMLYJIPU.js.map → summarizeCnvGeneexp-ZQFNPR65.js.map} +0 -0
  898. /package/dist/{summarizeGeneexpSurvival-IDM7T333.js.map → summarizeGeneexpSurvival-GIS7XMMH.js.map} +0 -0
  899. /package/dist/{summarizeMutationCnv-R6SYSJQC.js.map → summarizeMutationCnv-FWF7YIGR.js.map} +0 -0
  900. /package/dist/{summarizeMutationDiagnosis-XZJ4JLW2.js.map → summarizeMutationDiagnosis-V5L2OKTK.js.map} +0 -0
  901. /package/dist/{summarizeMutationSurvival-ABJ5RL4L.js.map → summarizeMutationSurvival-LAUUF6XN.js.map} +0 -0
  902. /package/dist/{summary-NVYCTE6P.js.map → summary-OMU3ACNE.js.map} +0 -0
  903. /package/dist/{summary.integration.spec-SSLTLVNW.js.map → summary.integration.spec-6JZAT73L.js.map} +0 -0
  904. /package/dist/{summaryInput-SJOZETRP.js.map → summaryInput-QIKL3HDD.js.map} +0 -0
  905. /package/dist/{sunburst-RU5ZPJKW.js.map → sunburst-32IW2R57.js.map} +0 -0
  906. /package/dist/{survival-BHJQMXKI.js.map → survival-BMOPVAN2.js.map} +0 -0
  907. /package/dist/{survival-DVG6Y2FV.js.map → survival-H5AWMQ36.js.map} +0 -0
  908. /package/dist/{survival.integration.spec-OJUPTY5N.js.map → survival.integration.spec-66UOWSZG.js.map} +0 -0
  909. /package/dist/{svgraph-ETFA4GRX.js.map → svgraph-B75FS3BB.js.map} +0 -0
  910. /package/dist/{svmr-AI3RU4JK.js.map → svmr-IUEUOHVO.js.map} +0 -0
  911. /package/dist/{table-YCTSMLQL.js.map → table-YAAH7WR6.js.map} +0 -0
  912. /package/dist/{termCollection-GMKEZR6D.js.map → termCollection-7F5ZG2DB.js.map} +0 -0
  913. /package/dist/{termCollection-VEVKKJZD.js.map → termCollection-KNFUELYY.js.map} +0 -0
  914. /package/dist/{termCollection.unit.spec-EU6YCEPX.js.map → termCollection.unit.spec-S6M6QC4C.js.map} +0 -0
  915. /package/dist/{termCollectionFractionSelection-UBS74X36.js.map → termCollectionFractionSelection-X22VMJWY.js.map} +0 -0
  916. /package/dist/{termCollectionFractionSelection.unit.spec-Y5OJFGDD.js.map → termCollectionFractionSelection.unit.spec-ELU6SD7P.js.map} +0 -0
  917. /package/dist/{tk-W6Z4FJMW.js.map → tk-TT666UVE.js.map} +0 -0
  918. /package/dist/{tk-HMF4HCNV.js.map → tk-UOPNJ323.js.map} +0 -0
  919. /package/dist/{tp.ui-NECRDJCS.js.map → tp.ui-HGAHRKO5.js.map} +0 -0
  920. /package/dist/{tvs.dt-2JEH3F35.js.map → tvs.dt-H7YYR4EB.js.map} +0 -0
  921. /package/dist/{tvs.dtcnv.categorical-YBXKEBR2.js.map → tvs.dtcnv.categorical-IPJTKGMF.js.map} +0 -0
  922. /package/dist/{tvs.dtcnv.continuous-AD3SJ6BY.js.map → tvs.dtcnv.continuous-XY5XZ4GH.js.map} +0 -0
  923. /package/dist/{tvs.dtfusion-ODI3CLQS.js.map → tvs.dtfusion-VFCBMXRM.js.map} +0 -0
  924. /package/dist/{tvs.dtitd-V3LYLPJY.js.map → tvs.dtitd-RZVW6FTR.js.map} +0 -0
  925. /package/dist/{tvs.dtsnvindel-R3V5LTNL.js.map → tvs.dtsnvindel-IDPJWSGC.js.map} +0 -0
  926. /package/dist/{tvs.dtsv-ZQLKEDLJ.js.map → tvs.dtsv-QERP756F.js.map} +0 -0
  927. /package/dist/{tvs.samplelst-G25A7HM6.js.map → tvs.samplelst-6KNDHBIU.js.map} +0 -0
  928. /package/dist/{tvs.termCollection-WLVCWDEJ.js.map → tvs.termCollection-GWPJK3NE.js.map} +0 -0
  929. /package/dist/{vocabulary-6K537FJM.js.map → vocabulary-C5FIZMPQ.js.map} +0 -0
  930. /package/dist/{wsi.direct-SNPPQPVO.js.map → wsi.direct-2RBCBXDA.js.map} +0 -0
@@ -0,0 +1,587 @@
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-C3HEDQPT.js";
11
+ import "./chunk-HJ6L54YS.js";
12
+ import "./chunk-KV4W2ACA.js";
13
+ import "./chunk-B6UXFX73.js";
14
+ import {
15
+ Menu
16
+ } from "./chunk-ELJX3QIQ.js";
17
+ import "./chunk-3FEP6B5T.js";
18
+ import "./chunk-EEB5VE2A.js";
19
+ import "./chunk-6RRZRISL.js";
20
+ import "./chunk-2KM4PRQM.js";
21
+ import "./chunk-OBDIJ4QS.js";
22
+ import "./chunk-6FG6JFZP.js";
23
+ import "./chunk-3XBG5HIV.js";
24
+ import "./chunk-SB36AUG7.js";
25
+ import "./chunk-WINIL2KN.js";
26
+ import "./chunk-PF4DSFDR.js";
27
+ import "./chunk-7X6NF7NI.js";
28
+ import "./chunk-W5J3LTYS.js";
29
+ import {
30
+ axisBottom,
31
+ axisLeft,
32
+ category10_default
33
+ } from "./chunk-Z2ZITHT4.js";
34
+ import {
35
+ format,
36
+ linear,
37
+ log,
38
+ ordinal,
39
+ time,
40
+ timeParse
41
+ } from "./chunk-4OLM3KSB.js";
42
+ import "./chunk-FXQXCOII.js";
43
+ import "./chunk-TLT4YIG3.js";
44
+ import "./chunk-5R63Q5KH.js";
45
+ import {
46
+ select_default
47
+ } from "./chunk-I6Y4O3RR.js";
48
+ import "./chunk-Q5RDQNIT.js";
49
+ import "./chunk-DQC5FFGV.js";
50
+ import "./chunk-HS5PO5ZQ.js";
51
+
52
+ // src/maftimeline.js
53
+ var zerovalue = 1e-5;
54
+ var showcircle = true;
55
+ var maflogscale = true;
56
+ var tip = new Menu();
57
+ function maftimelineui(genomes, holder, sandbox_header) {
58
+ let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
59
+ if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
60
+ else {
61
+ ;
62
+ [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
63
+ pane.header.text("MAF timeline plot");
64
+ }
65
+ inputdiv.append("p").html(
66
+ "<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
67
+ );
68
+ inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
69
+ {
70
+ const id = Math.random().toString();
71
+ const p = inputdiv.append("p");
72
+ p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
73
+ maflogscale = !maflogscale;
74
+ });
75
+ p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
76
+ }
77
+ const fileui = () => {
78
+ filediv.selectAll("*").remove();
79
+ const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
80
+ saydiv.text("");
81
+ const file = event.target.files[0];
82
+ if (!file) {
83
+ fileui();
84
+ return;
85
+ }
86
+ if (file.size == 0) {
87
+ saydiv.text("Wrong file: " + file.name);
88
+ fileui();
89
+ return;
90
+ }
91
+ const reader = new FileReader();
92
+ reader.onload = (event2) => {
93
+ const lines = event2.target.result.trim().split(/\r?\n/);
94
+ const [err, header] = parseheader(lines[0].trim());
95
+ if (err) {
96
+ saydiv.text("File header error: " + err);
97
+ fileui();
98
+ return;
99
+ }
100
+ const badlines = [];
101
+ const data = {};
102
+ let good = 0;
103
+ for (let i = 1; i < lines.length; i++) {
104
+ if (lines[i] == "") continue;
105
+ if (lines[i][0] == "#") continue;
106
+ const m = parseline(i, lines[i], header, badlines, data);
107
+ if (m) {
108
+ good++;
109
+ }
110
+ }
111
+ if (badlines.length) {
112
+ bulk_badline(header, badlines);
113
+ }
114
+ if (good == 0) {
115
+ fileui();
116
+ return;
117
+ }
118
+ let visual_holder;
119
+ if (pane) {
120
+ disappear(pane.pane);
121
+ const pane2 = newpane({ x: 100, y: 100, toshrink: true });
122
+ pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
123
+ visual_holder = pane2.body;
124
+ }
125
+ if (holder !== void 0) {
126
+ visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
127
+ inputdiv.selectAll("*").remove();
128
+ saydiv.text("");
129
+ }
130
+ render(data, header, visual_holder);
131
+ };
132
+ reader.onerror = function() {
133
+ saydiv.text("Error reading file " + file.name);
134
+ fileui();
135
+ return;
136
+ };
137
+ saydiv.text("Parsing file " + file.name + " ...");
138
+ reader.readAsText(file, "utf8");
139
+ });
140
+ setTimeout(() => butt.node().focus(), 1100);
141
+ };
142
+ fileui();
143
+ }
144
+ function parseheader(line) {
145
+ const header = line.toLowerCase().split(" ");
146
+ if (header.length <= 1) return ["columns must be separated by tab"];
147
+ const htry = (...lst) => {
148
+ for (const i2 of lst) {
149
+ const j = header.indexOf(i2);
150
+ if (j != -1) return j;
151
+ }
152
+ return -1;
153
+ };
154
+ let i = htry("person", "patient", "caseid");
155
+ if (i == -1) return ["person missing"];
156
+ header[i] = "patient";
157
+ i = htry("sample", "sampleid");
158
+ if (i == -1) return ["sample missing"];
159
+ header[i] = "sample";
160
+ i = htry("snv4");
161
+ if (i == -1) return ["snv4 missing"];
162
+ header[i] = "snv4";
163
+ i = htry("date", "dateofsample");
164
+ if (i == -1) return ["date missing"];
165
+ header[i] = "date";
166
+ i = htry("mutant_readcount", "mutantcount");
167
+ if (i != -1) header[i] = "mutant_readcount";
168
+ i = htry("ref_readcount", "refcount");
169
+ if (i != -1) header[i] = "ref_readcount";
170
+ i = htry("total_readcount", "coveragecount");
171
+ if (i == -1) return ["total_readcount missing"];
172
+ header[i] = "coverage";
173
+ i = htry("maf");
174
+ if (i == -1) return ["maf missing"];
175
+ header[i] = "maf";
176
+ i = htry("call_manual");
177
+ if (i != -1) header[i] = "call_manual";
178
+ return [null, header];
179
+ }
180
+ function parseline(i, line, header, badlines, data) {
181
+ const lst = line.split(" ");
182
+ const m = {};
183
+ for (let j = 0; j < header.length; j++) {
184
+ m[header[j]] = lst[j];
185
+ }
186
+ if (!m.patient) {
187
+ badlines.push([i, "missing patient", lst]);
188
+ return;
189
+ }
190
+ if (!data[m.patient]) {
191
+ data[m.patient] = {
192
+ snv4: {},
193
+ show: false
194
+ };
195
+ }
196
+ if (!m.snv4) {
197
+ badlines.push([i, "missing snv4", lst]);
198
+ return;
199
+ }
200
+ if (!data[m.patient].snv4[m.snv4]) {
201
+ data[m.patient].snv4[m.snv4] = {
202
+ mutationname: m.snv4,
203
+ samples: [],
204
+ subidx: void 0
205
+ };
206
+ }
207
+ if (m.gene) {
208
+ data[m.patient].snv4[m.snv4].gene = m.gene;
209
+ }
210
+ if (!m.maf) {
211
+ badlines.push([i, "missing maf", lst]);
212
+ return;
213
+ }
214
+ let v = Number.parseFloat(m.maf);
215
+ if (Number.isNaN(v)) {
216
+ badlines.push([i, "invalid maf", lst]);
217
+ return;
218
+ }
219
+ if (v < zerovalue) {
220
+ v = zerovalue;
221
+ }
222
+ m.maf = v;
223
+ if (!m.coverage) {
224
+ badlines.push([i, "missing total_readcount", lst]);
225
+ return;
226
+ }
227
+ if (m.call_manual && m.call_manual == "wildtype") {
228
+ m.maf = zerovalue;
229
+ }
230
+ v = Number.parseInt(m.coverage);
231
+ if (Number.isNaN(v)) {
232
+ badlines.push([i, "invalid total_readcount", lst]);
233
+ return;
234
+ }
235
+ m.coverage = v;
236
+ let date;
237
+ if (m.date) {
238
+ const f = timeParse("%m/%d/%Y");
239
+ date = f(m.date);
240
+ m.Date = m.date;
241
+ } else {
242
+ badlines.push([i, "missing date", lst]);
243
+ return;
244
+ }
245
+ if (date == null) {
246
+ badlines.push([i, "cannot parse date", lst]);
247
+ return;
248
+ }
249
+ m.date = date;
250
+ if (!m.sample) {
251
+ badlines.push([i, "missing sample", lst]);
252
+ return;
253
+ }
254
+ data[m.patient].snv4[m.snv4].samples.push(m);
255
+ return true;
256
+ }
257
+ function render(data, header, holder) {
258
+ const table = holder.append("table").style("margin", "20px");
259
+ const tr1 = table.append("tr");
260
+ let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
261
+ td.append("button").text("Toggle circle visibility").on("click", () => {
262
+ showcircle = !showcircle;
263
+ for (const n in data) {
264
+ if (data[n].show) {
265
+ data[n].handle.node().click();
266
+ break;
267
+ }
268
+ }
269
+ });
270
+ const patientholder = td.append("div").style("margin-top", "10px");
271
+ const td1 = tr1.append("td").style("vertical-align", "top");
272
+ const graphholder = td1.append("div").style("display", "inline-block");
273
+ const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
274
+ const tr2 = table.append("tr");
275
+ const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
276
+ const gtr1 = tiantable.append("tr");
277
+ td = gtr1.append("td").style("vertical-align", "top");
278
+ td.append("div").text("Shared").style("font-size", "2em");
279
+ const graph1holder = td.append("div").style("border", "solid 1px black");
280
+ td = gtr1.append("td").style("vertical-align", "top");
281
+ td.append("div").text("Rising").style("font-size", "2em");
282
+ const graph2holder = td.append("div").style("border", "solid 1px black");
283
+ const gtr2 = tiantable.append("tr");
284
+ td = gtr2.append("td").style("vertical-align", "top");
285
+ td.append("div").text("Falling").style("font-size", "2em");
286
+ const graph3holder = td.append("div").style("border", "solid 1px black");
287
+ td = gtr2.append("td").style("vertical-align", "top");
288
+ td.append("div").text("R-only").style("font-size", "2em");
289
+ const graph4holder = td.append("div").style("border", "solid 1px black");
290
+ for (const patient in data) {
291
+ const snvlst = [];
292
+ const colors = ordinal(category10_default);
293
+ for (const x in data[patient].snv4) {
294
+ const snv = data[patient].snv4[x];
295
+ snv.show = true;
296
+ snv.color = colors(snv.mutationname);
297
+ snv.samples.sort((a, b) => a.date - b.date);
298
+ for (const s of snv.samples) {
299
+ s.color = snv.color;
300
+ }
301
+ snvlst.push(snv);
302
+ }
303
+ const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
304
+ for (const pn in data) {
305
+ data[pn].handle.style("color", "black");
306
+ data[pn].show = false;
307
+ }
308
+ data[patient].handle.style("color", "red");
309
+ data[patient].show = true;
310
+ makegraph(snvlst, header, graphholder);
311
+ makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
312
+ makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
313
+ });
314
+ data[patient].handle = div;
315
+ }
316
+ for (const n in data) {
317
+ data[n].handle.node().click();
318
+ break;
319
+ }
320
+ }
321
+ function makesubgraph(snvlst, g1, g2, g3, g4) {
322
+ g1.selectAll("*").remove();
323
+ g2.selectAll("*").remove();
324
+ g3.selectAll("*").remove();
325
+ g4.selectAll("*").remove();
326
+ const l1 = [];
327
+ const l2 = [];
328
+ const l3 = [];
329
+ const l4 = [];
330
+ for (const snv of snvlst) {
331
+ switch (snv.subidx) {
332
+ case 1:
333
+ l1.push(snv);
334
+ break;
335
+ case 2:
336
+ l2.push(snv);
337
+ break;
338
+ case 3:
339
+ l3.push(snv);
340
+ break;
341
+ case 4:
342
+ l4.push(snv);
343
+ break;
344
+ }
345
+ }
346
+ if (l1.length) {
347
+ makegraph(l1, null, g1, true);
348
+ } else {
349
+ g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
350
+ }
351
+ if (l2.length) {
352
+ makegraph(l2, null, g2, true);
353
+ } else {
354
+ g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
355
+ }
356
+ if (l3.length) {
357
+ makegraph(l3, null, g3, true);
358
+ } else {
359
+ g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
360
+ }
361
+ if (l4.length) {
362
+ makegraph(l4, null, g4, true);
363
+ } else {
364
+ g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
365
+ }
366
+ }
367
+ function makegraph(snvlst0, header, holder, issub) {
368
+ holder.selectAll("*").remove();
369
+ const samples = [];
370
+ const snvlst = [];
371
+ for (const snv of snvlst0) {
372
+ if (!issub && !snv.show) continue;
373
+ snvlst.push(snv);
374
+ for (const s of snv.samples) {
375
+ samples.push(s);
376
+ }
377
+ }
378
+ if (snvlst.length == 0) return;
379
+ let mindate = snvlst[0].samples[0].date;
380
+ let maxdate = snvlst[0].samples[0].date;
381
+ let maxmaf = snvlst[0].samples[0].maf;
382
+ let maxcoverage = snvlst[0].samples[0].coverage;
383
+ for (const snv of snvlst) {
384
+ for (const s of snv.samples) {
385
+ mindate = Math.min(mindate, s.date);
386
+ maxdate = Math.max(maxdate, s.date);
387
+ maxmaf = Math.max(maxmaf, s.maf);
388
+ maxcoverage = Math.max(maxcoverage, s.coverage);
389
+ }
390
+ }
391
+ const svg = holder.append("svg");
392
+ const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
393
+ let width = 600;
394
+ let height = 400;
395
+ let xpad, ypad, minradius;
396
+ const xaxisg = svg.append("g");
397
+ const yaxisg = svg.append("g");
398
+ const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
399
+ event.preventDefault();
400
+ const x = event.clientX;
401
+ const y = event.clientY;
402
+ const w0 = width;
403
+ const h0 = height;
404
+ const body = select_default(document.body);
405
+ body.on("mousemove", (event2) => {
406
+ setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
407
+ }).on("mouseup", () => {
408
+ body.on("mousemove", null).on("mouseup", null);
409
+ });
410
+ });
411
+ const xscale = time().domain([mindate, maxdate]);
412
+ const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
413
+ const rscale = linear().domain([1, maxcoverage]);
414
+ const g = svg.append("g");
415
+ const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
416
+ let circles;
417
+ if (showcircle) {
418
+ circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
419
+ event.target.setAttribute("fill-opacity", 0.4);
420
+ tip.clear();
421
+ tip.show(event.clientX, event.clientY);
422
+ const lst = [];
423
+ for (const k in d) {
424
+ if (k == "color") continue;
425
+ if (k == "gene") {
426
+ lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
427
+ continue;
428
+ }
429
+ if (k == "date") continue;
430
+ if (k == "url") {
431
+ lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
432
+ continue;
433
+ }
434
+ lst.push({ k, v: d[k] });
435
+ }
436
+ make_table_2col(tip.d, lst);
437
+ }).on("mouseout", (event) => {
438
+ event.target.setAttribute("fill-opacity", 0.1);
439
+ });
440
+ }
441
+ const legend = svg.append("g");
442
+ const setsize = (w, h) => {
443
+ width = w;
444
+ height = h;
445
+ minradius = 2;
446
+ const maxradius = Math.max(width, height) / 30;
447
+ xpad = maxradius;
448
+ ypad = maxradius;
449
+ rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
450
+ xscale.range([0, width]);
451
+ yscale.range([height, 0]);
452
+ svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
453
+ xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
454
+ yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
455
+ drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
456
+ axisstyle({
457
+ axis: xaxisg.call(axisBottom().scale(xscale)),
458
+ showline: true,
459
+ color: "black",
460
+ fontsize: Math.max(12, Math.min(20, width / 100))
461
+ });
462
+ axisstyle({
463
+ axis: yaxisg.call(
464
+ axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
465
+ ),
466
+ showline: true,
467
+ color: "black",
468
+ fontsize: Math.max(12, Math.min(20, height / 100))
469
+ });
470
+ g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
471
+ lines.attr("d", (d) => {
472
+ const lst = [];
473
+ for (let i = 0; i < d.samples.length; i++) {
474
+ const s = d.samples[i];
475
+ lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
476
+ }
477
+ return lst.join(" ");
478
+ });
479
+ if (showcircle) {
480
+ circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
481
+ }
482
+ legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
483
+ legend.selectAll("*").remove();
484
+ let y = minradius;
485
+ if (showcircle) {
486
+ legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
487
+ legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
488
+ y += 5 + minradius + maxradius;
489
+ legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
490
+ legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
491
+ y += 15 + maxradius;
492
+ }
493
+ const fontsize = 12;
494
+ for (const snv of snvlst) {
495
+ legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
496
+ if (showcircle) {
497
+ legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
498
+ }
499
+ 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) => {
500
+ event.target.setAttribute("font-weight", "bold");
501
+ lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
502
+ }).on("mouseout", (event) => {
503
+ event.target.setAttribute("font-weight", "normal");
504
+ lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
505
+ });
506
+ y += fontsize + 10;
507
+ }
508
+ };
509
+ setsize(width, height);
510
+ holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
511
+ to_svg(svg.node(), "maf-timeline");
512
+ });
513
+ }
514
+ function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
515
+ holder.selectAll("*").remove();
516
+ const table = holder.append("table");
517
+ for (const snv of snvlst) {
518
+ const tr = table.append("tr");
519
+ const td1 = tr.append("td");
520
+ td1.text(snv.gene).style("color", snv.color);
521
+ const td2 = tr.append("td");
522
+ const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
523
+ snv.checkbox = checkbox;
524
+ checkbox.on("change", (event) => {
525
+ snv.show = event.target.checked;
526
+ makegraph(snvlst, header, graphholder);
527
+ });
528
+ const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
529
+ for (const s2 of snvlst) {
530
+ s2.show = false;
531
+ s2.checkbox.property("checked", false);
532
+ }
533
+ snv.show = true;
534
+ snv.checkbox.property("checked", true);
535
+ makegraph(snvlst, header, graphholder);
536
+ });
537
+ let cname = Math.random();
538
+ const td11 = tr.append("td");
539
+ const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
540
+ td11.append("label").html("&nbsp;shared").attr("for", cname);
541
+ cname = Math.random();
542
+ const td22 = tr.append("td");
543
+ const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
544
+ td22.append("label").html("&nbsp;rising").attr("for", cname);
545
+ cname = Math.random();
546
+ const td33 = tr.append("td");
547
+ const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
548
+ td33.append("label").html("&nbsp;falling").attr("for", cname);
549
+ cname = Math.random();
550
+ const td44 = tr.append("td");
551
+ const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
552
+ td44.append("label").html("&nbsp;R-only").attr("for", cname);
553
+ if (snv.subidx == 1) c1.property("checked", true);
554
+ if (snv.subidx == 2) c2.property("checked", true);
555
+ if (snv.subidx == 3) c3.property("checked", true);
556
+ if (snv.subidx == 4) c4.property("checked", true);
557
+ const cchange = (which, check) => {
558
+ if (!check.checked) {
559
+ snv.subidx = -1;
560
+ } else {
561
+ snv.subidx = which;
562
+ if (which == 1) {
563
+ c2.property("checked", false);
564
+ c3.property("checked", false);
565
+ c4.property("checked", false);
566
+ } else if (which == 2) {
567
+ c1.property("checked", false);
568
+ c3.property("checked", false);
569
+ c4.property("checked", false);
570
+ } else if (which == 3) {
571
+ c1.property("checked", false);
572
+ c2.property("checked", false);
573
+ c4.property("checked", false);
574
+ } else {
575
+ c1.property("checked", false);
576
+ c2.property("checked", false);
577
+ c3.property("checked", false);
578
+ }
579
+ }
580
+ makesubgraph(snvlst, g1, g2, g3, g4);
581
+ };
582
+ }
583
+ }
584
+ export {
585
+ maftimelineui as default
586
+ };
587
+ //# sourceMappingURL=maftimeline-75N6ZXEM.js.map
@@ -0,0 +1,54 @@
1
+ import {
2
+ Matrix,
3
+ componentInit,
4
+ makeChartBtnMenu,
5
+ matrixInit
6
+ } from "./chunk-A2UUXYH6.js";
7
+ import "./chunk-5LYVIIYR.js";
8
+ import "./chunk-CN6KJORZ.js";
9
+ import "./chunk-5FRETII3.js";
10
+ import "./chunk-WIQVSCD5.js";
11
+ import "./chunk-AR3HXZIW.js";
12
+ import "./chunk-67URJYN7.js";
13
+ import "./chunk-OEBGQKQR.js";
14
+ import "./chunk-JTQPPUDG.js";
15
+ import "./chunk-C2MCQZWH.js";
16
+ import "./chunk-DDKS3MV3.js";
17
+ import "./chunk-CFZ2ZW3E.js";
18
+ import "./chunk-Z6MCBFDM.js";
19
+ import "./chunk-NGMM2MNC.js";
20
+ import "./chunk-AVCEHJG7.js";
21
+ import "./chunk-V2OJLJSK.js";
22
+ import "./chunk-C3HEDQPT.js";
23
+ import "./chunk-HJ6L54YS.js";
24
+ import "./chunk-KV4W2ACA.js";
25
+ import "./chunk-B6UXFX73.js";
26
+ import "./chunk-ELJX3QIQ.js";
27
+ import "./chunk-3FEP6B5T.js";
28
+ import "./chunk-EEB5VE2A.js";
29
+ import "./chunk-6RRZRISL.js";
30
+ import "./chunk-2KM4PRQM.js";
31
+ import "./chunk-OBDIJ4QS.js";
32
+ import "./chunk-6FG6JFZP.js";
33
+ import "./chunk-3XBG5HIV.js";
34
+ import "./chunk-SB36AUG7.js";
35
+ import "./chunk-WINIL2KN.js";
36
+ import "./chunk-PF4DSFDR.js";
37
+ import "./chunk-7X6NF7NI.js";
38
+ import "./chunk-W5J3LTYS.js";
39
+ import "./chunk-Z2ZITHT4.js";
40
+ import "./chunk-4OLM3KSB.js";
41
+ import "./chunk-FXQXCOII.js";
42
+ import "./chunk-TLT4YIG3.js";
43
+ import "./chunk-5R63Q5KH.js";
44
+ import "./chunk-I6Y4O3RR.js";
45
+ import "./chunk-Q5RDQNIT.js";
46
+ import "./chunk-DQC5FFGV.js";
47
+ import "./chunk-HS5PO5ZQ.js";
48
+ export {
49
+ Matrix,
50
+ componentInit,
51
+ makeChartBtnMenu,
52
+ matrixInit
53
+ };
54
+ //# sourceMappingURL=matrix-QFKGEW5A.js.map
@@ -0,0 +1,59 @@
1
+ import {
2
+ Matrix,
3
+ componentInit,
4
+ makeChartBtnMenu,
5
+ matrixInit
6
+ } from "./chunk-A2UUXYH6.js";
7
+ import "./chunk-5LYVIIYR.js";
8
+ import "./chunk-CN6KJORZ.js";
9
+ import "./chunk-5FRETII3.js";
10
+ import {
11
+ getPlotConfig,
12
+ setComputedConfig
13
+ } from "./chunk-WIQVSCD5.js";
14
+ import "./chunk-AR3HXZIW.js";
15
+ import "./chunk-67URJYN7.js";
16
+ import "./chunk-OEBGQKQR.js";
17
+ import "./chunk-JTQPPUDG.js";
18
+ import "./chunk-C2MCQZWH.js";
19
+ import "./chunk-DDKS3MV3.js";
20
+ import "./chunk-CFZ2ZW3E.js";
21
+ import "./chunk-Z6MCBFDM.js";
22
+ import "./chunk-NGMM2MNC.js";
23
+ import "./chunk-AVCEHJG7.js";
24
+ import "./chunk-V2OJLJSK.js";
25
+ import "./chunk-C3HEDQPT.js";
26
+ import "./chunk-HJ6L54YS.js";
27
+ import "./chunk-KV4W2ACA.js";
28
+ import "./chunk-B6UXFX73.js";
29
+ import "./chunk-ELJX3QIQ.js";
30
+ import "./chunk-3FEP6B5T.js";
31
+ import "./chunk-EEB5VE2A.js";
32
+ import "./chunk-6RRZRISL.js";
33
+ import "./chunk-2KM4PRQM.js";
34
+ import "./chunk-OBDIJ4QS.js";
35
+ import "./chunk-6FG6JFZP.js";
36
+ import "./chunk-3XBG5HIV.js";
37
+ import "./chunk-SB36AUG7.js";
38
+ import "./chunk-WINIL2KN.js";
39
+ import "./chunk-PF4DSFDR.js";
40
+ import "./chunk-7X6NF7NI.js";
41
+ import "./chunk-W5J3LTYS.js";
42
+ import "./chunk-Z2ZITHT4.js";
43
+ import "./chunk-4OLM3KSB.js";
44
+ import "./chunk-FXQXCOII.js";
45
+ import "./chunk-TLT4YIG3.js";
46
+ import "./chunk-5R63Q5KH.js";
47
+ import "./chunk-I6Y4O3RR.js";
48
+ import "./chunk-Q5RDQNIT.js";
49
+ import "./chunk-DQC5FFGV.js";
50
+ import "./chunk-HS5PO5ZQ.js";
51
+ export {
52
+ Matrix,
53
+ componentInit,
54
+ getPlotConfig,
55
+ makeChartBtnMenu,
56
+ matrixInit,
57
+ setComputedConfig
58
+ };
59
+ //# sourceMappingURL=matrix-XT7LUV5K.js.map