@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (957) hide show
  1. package/dist/2dmaf-BNMEUJVM.js +1373 -0
  2. package/dist/AIProjectAdmin-AEXQY5LY.js +958 -0
  3. package/dist/AIProjectAdmin-AEXQY5LY.js.map +7 -0
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  7. package/dist/CorrelationVolcano-V2E566XL.js +619 -0
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  851. /package/dist/{importPlot-YH7ZY6RJ.js.map → importPlot-DQFWY5A7.js.map} +0 -0
  852. /package/dist/{isoformExpression-EV27MKYZ.js.map → isoformExpression-2KANPCBH.js.map} +0 -0
  853. /package/dist/{isoformExpression.unit.spec-7T2GOHH3.js.map → isoformExpression.unit.spec-6FSMHT4K.js.map} +0 -0
  854. /package/dist/{launch.adhoc-NOISOX5E.js.map → launch.adhoc-ZYTIRVIC.js.map} +0 -0
  855. /package/dist/{leftlabel.sample-42AX4KTV.js.map → leftlabel.sample-66U6MHPN.js.map} +0 -0
  856. /package/dist/{legacyDataset-SWJCAWIR.js.map → legacyDataset-TNIIJABK.js.map} +0 -0
  857. /package/dist/{lollipop-LQCQBTSX.js.map → lollipop-PJDUFWEY.js.map} +0 -0
  858. /package/dist/{maf-U237OWZ3.js.map → maf-DLJHCKHJ.js.map} +0 -0
  859. /package/dist/{maftimeline-NLZLMHT2.js.map → maftimeline-NK5QYJMJ.js.map} +0 -0
  860. /package/dist/{matrix-DZJXYRYN.js.map → matrix-7BFYR6QL.js.map} +0 -0
  861. /package/dist/{matrix-Y5345QQG.js.map → matrix-USAB2CHO.js.map} +0 -0
  862. /package/dist/{matrix.cells-PT7S74QP.js.map → matrix.cells-OTAXAJ4N.js.map} +0 -0
  863. /package/dist/{matrix.config-2ORCUWKX.js.map → matrix.config-AL4WSFZ7.js.map} +0 -0
  864. /package/dist/{matrix.data-C6VPQJJ4.js.map → matrix.data-BDHCSN2G.js.map} +0 -0
  865. /package/dist/{matrix.groups-CEOCG2CT.js.map → matrix.groups-MV2D2636.js.map} +0 -0
  866. /package/dist/{matrix.integration.spec-U4B3JB6N.js.map → matrix.integration.spec-DESORC2Y.js.map} +0 -0
  867. /package/dist/{matrix.interactivity-GFLIFIER.js.map → matrix.interactivity-H7EJW3P2.js.map} +0 -0
  868. /package/dist/{matrix.layout-DOVDHTDX.js.map → matrix.layout-7CAS2IBO.js.map} +0 -0
  869. /package/dist/{matrix.legend-JE4ZSLP7.js.map → matrix.legend-JDVG2JDF.js.map} +0 -0
  870. /package/dist/{matrix.renderers-GPUJQ7KF.js.map → matrix.renderers-PDR5FIBC.js.map} +0 -0
  871. /package/dist/{matrix.serieses-REE4DCSR.js.map → matrix.serieses-QVDS5HKK.js.map} +0 -0
  872. /package/dist/{matrix.sort-VD5URUWY.js.map → matrix.sort-HCK4CSTJ.js.map} +0 -0
  873. /package/dist/{matrix.sort.unit.spec-4IOFVHJN.js.map → matrix.sort.unit.spec-2GC4E26N.js.map} +0 -0
  874. /package/dist/{matrix.sorterUi-VQYY6KBK.js.map → matrix.sorterUi-XGBQOPG4.js.map} +0 -0
  875. /package/dist/{matrix.sorterUi.unit.spec-V5O2EJBX.js.map → matrix.sorterUi.unit.spec-BJQKDU2F.js.map} +0 -0
  876. /package/dist/{mavb-SQDA3B2B.js.map → mavb-6E6Z4LPK.js.map} +0 -0
  877. /package/dist/{mds.fimo-ZJSEPLD7.js.map → mds.fimo-5P2TK5U4.js.map} +0 -0
  878. /package/dist/{mds.samplescatterplot-Y5V73GOY.js.map → mds.samplescatterplot-KLKOD4AS.js.map} +0 -0
  879. /package/dist/{mds.survivalplot-CZBRMHYN.js.map → mds.survivalplot-SWQCOFIU.js.map} +0 -0
  880. /package/dist/{numericDictTermCluster-TFXBBUVI.js.map → numericDictTermCluster-WIVO33AV.js.map} +0 -0
  881. /package/dist/{oncomatrix-ZILACPPI.js.map → oncomatrix-SDUUQZCK.js.map} +0 -0
  882. /package/dist/{oncomatrix.spec-RLIVVVD6.js.map → oncomatrix.spec-YGQYIUDT.js.map} +0 -0
  883. /package/dist/{plot.2dvaf-BNRZPIKU.js.map → plot.2dvaf-K53KTP5W.js.map} +0 -0
  884. /package/dist/{plot.app-NRUARQCN.js.map → plot.app-FNJVWLPQ.js.map} +0 -0
  885. /package/dist/{plot.barplot-342AYQC7.js.map → plot.barplot-VTC3N6BR.js.map} +0 -0
  886. /package/dist/{plot.boxplot-OHEJDPTW.js.map → plot.boxplot-RJFGQSLA.js.map} +0 -0
  887. /package/dist/{plot.brainImaging-KV72PAON.js.map → plot.brainImaging-6KVNPPMT.js.map} +0 -0
  888. /package/dist/{plot.disco-OUE4RFHL.js.map → plot.disco-ZFH5RK6B.js.map} +0 -0
  889. /package/dist/{plot.dzi-T3GPUH36.js.map → plot.dzi-IA2SOFUD.js.map} +0 -0
  890. /package/dist/{plot.ssgq-WJHGMXW5.js.map → plot.ssgq-QARGQVKB.js.map} +0 -0
  891. /package/dist/{plot.vaf2cov-NGD5PCV4.js.map → plot.vaf2cov-2JUXYCPG.js.map} +0 -0
  892. /package/dist/{plot.wsi-2MU5BDG3.js.map → plot.wsi-C2DULA7U.js.map} +0 -0
  893. /package/dist/{profilePlot-OMVO3K4H.js.map → profilePlot-SVI3QKMD.js.map} +0 -0
  894. /package/dist/{qualitative-MEYBRUC6.js.map → qualitative-AQFKAZID.js.map} +0 -0
  895. /package/dist/{regression-ZPDPLI6G.js.map → regression-DLPBCDZT.js.map} +0 -0
  896. /package/dist/{regression.inputs-QOSBAGL6.js.map → regression.inputs-42LY4MEZ.js.map} +0 -0
  897. /package/dist/{regression.inputs.term-HMUMPY7X.js.map → regression.inputs.term-TTUFFPG6.js.map} +0 -0
  898. /package/dist/{regression.inputs.values.table-VMCTZHLG.js.map → regression.inputs.values.table-CJAPTSMS.js.map} +0 -0
  899. /package/dist/{regression.integration.spec-RP74JTAA.js.map → regression.integration.spec-UDA26OGS.js.map} +0 -0
  900. /package/dist/{regression.results-5XC6M67C.js.map → regression.results-IA3C7SHR.js.map} +0 -0
  901. /package/dist/{regression.spec-EZYM24J7.js.map → regression.spec-HEXCL3QV.js.map} +0 -0
  902. /package/dist/{report-ZOVQCOGQ.js.map → report-4CFOWNPJ.js.map} +0 -0
  903. /package/dist/{sampleScatter.spec-CD52FEOC.js.map → sampleScatter.spec-N6V4BQ5Q.js.map} +0 -0
  904. /package/dist/{sampleView-SVTLSWRG.js.map → sampleView-CZF7U23I.js.map} +0 -0
  905. /package/dist/{samplelst-HXF5POJD.js.map → samplelst-XUGDS5TU.js.map} +0 -0
  906. /package/dist/{samplematrix-NYDAH74I.js.map → samplematrix-R5PZLZDE.js.map} +0 -0
  907. /package/dist/{sc-JIDT4W4K.js.map → sc-WTZZA5J5.js.map} +0 -0
  908. /package/dist/{selectGenomeWithTklst-OSB7B6L3.js.map → selectGenomeWithTklst-2S2MXVCI.js.map} +0 -0
  909. /package/dist/{singleCellCellType-3BH7LWQ6.js.map → singleCellCellType-LJWFG7MY.js.map} +0 -0
  910. /package/dist/{singleCellCellType.unit.spec-RU4RJXFF.js.map → singleCellCellType.unit.spec-RGN2XVUR.js.map} +0 -0
  911. /package/dist/{singleCellGeneExpression-3UA4YER7.js.map → singleCellGeneExpression-IW2QXTTU.js.map} +0 -0
  912. /package/dist/{singleCellGeneExpression.unit.spec-4ZTBG37H.js.map → singleCellGeneExpression.unit.spec-4PO3Q7TM.js.map} +0 -0
  913. /package/dist/{singleCellPlot-ZUAWK5RE.js.map → singleCellPlot-6EZ6JXCM.js.map} +0 -0
  914. /package/dist/{singlecell-BGJZB7MF.js.map → singlecell-3LFPQ6KO.js.map} +0 -0
  915. /package/dist/{singlecell-RO3BL5OO.js.map → singlecell-NTTAVVMR.js.map} +0 -0
  916. /package/dist/{snp-HD7VQKBR.js.map → snp-XB4IBG4Z.js.map} +0 -0
  917. /package/dist/{snp.unit.spec-ISXCLMWW.js.map → snp.unit.spec-HAJPM53L.js.map} +0 -0
  918. /package/dist/{snplocus-IL5Z4XWV.js.map → snplocus-HE6TITSX.js.map} +0 -0
  919. /package/dist/{spliceevent.a53ss.diagram-LLJSPV7M.js.map → spliceevent.a53ss.diagram-TCZMBMD7.js.map} +0 -0
  920. /package/dist/{spliceevent.exonskip.diagram-LAOIOIST.js.map → spliceevent.exonskip.diagram-VESOF6UC.js.map} +0 -0
  921. /package/dist/{spliceevent.noeventdiagram-MVA7Q3HT.js.map → spliceevent.noeventdiagram-4K7FMO4F.js.map} +0 -0
  922. /package/dist/{ssGSEA-7T6S3DSE.js.map → ssGSEA-2XYMX36P.js.map} +0 -0
  923. /package/dist/{ssGSEA.unit.spec-XJ3W4NWX.js.map → ssGSEA.unit.spec-J36KM2HO.js.map} +0 -0
  924. /package/dist/{summarizeCnvGeneexp-RRP6JUV6.js.map → summarizeCnvGeneexp-LYVDZXXD.js.map} +0 -0
  925. /package/dist/{summarizeGeneexpSurvival-AFLHDD6Q.js.map → summarizeGeneexpSurvival-Y52TGAHF.js.map} +0 -0
  926. /package/dist/{summarizeMutationCnv-NABUYHMX.js.map → summarizeMutationCnv-6EEJT3PV.js.map} +0 -0
  927. /package/dist/{summarizeMutationDiagnosis-2LQ7JU3K.js.map → summarizeMutationDiagnosis-HZKXHOOQ.js.map} +0 -0
  928. /package/dist/{summarizeMutationSurvival-3WBT5TXG.js.map → summarizeMutationSurvival-TU7TQYFQ.js.map} +0 -0
  929. /package/dist/{summary-FRDKOFXW.js.map → summary-4QQZUAMU.js.map} +0 -0
  930. /package/dist/{summary.integration.spec-ZLRIA7G2.js.map → summary.integration.spec-SLIIM4HN.js.map} +0 -0
  931. /package/dist/{summaryInput-4JO6MHP4.js.map → summaryInput-6HROPKCE.js.map} +0 -0
  932. /package/dist/{sunburst-DRCVSC2X.js.map → sunburst-MBJJPERL.js.map} +0 -0
  933. /package/dist/{survival-AK75COPY.js.map → survival-CXLMQSV2.js.map} +0 -0
  934. /package/dist/{survival-IF5NI3A6.js.map → survival-QSL2KDKD.js.map} +0 -0
  935. /package/dist/{survival.integration.spec-7IWBTPJG.js.map → survival.integration.spec-EUAAALVW.js.map} +0 -0
  936. /package/dist/{svgraph-QBDF2SLB.js.map → svgraph-JM5MHQDX.js.map} +0 -0
  937. /package/dist/{svmr-O4GJJUT2.js.map → svmr-MCMST2FL.js.map} +0 -0
  938. /package/dist/{table-FQAIXKLE.js.map → table-MVX3IMAL.js.map} +0 -0
  939. /package/dist/{termCollection-ZO5PZ7E3.js.map → termCollection-FZ2SCVA7.js.map} +0 -0
  940. /package/dist/{termCollection-GMDDL3L7.js.map → termCollection-IGC7REFK.js.map} +0 -0
  941. /package/dist/{termCollection.unit.spec-5JBCTXHX.js.map → termCollection.unit.spec-VY2EZZIP.js.map} +0 -0
  942. /package/dist/{tk-GJX23IV7.js.map → tk-5F3TWZ2G.js.map} +0 -0
  943. /package/dist/{tp.ui-T7FVMTGQ.js.map → tp.ui-IURWTMAS.js.map} +0 -0
  944. /package/dist/{tvs.dt-X7L7NSU6.js.map → tvs.dt-BPZCFPYK.js.map} +0 -0
  945. /package/dist/{tvs.dtcnv.categorical-73G2V6CH.js.map → tvs.dtcnv.categorical-UFS62DTR.js.map} +0 -0
  946. /package/dist/{tvs.dtcnv.continuous-DWFJL3X7.js.map → tvs.dtcnv.continuous-R6YXNNLA.js.map} +0 -0
  947. /package/dist/{tvs.dtfusion-HQADHCSV.js.map → tvs.dtfusion-FGXXS4XX.js.map} +0 -0
  948. /package/dist/{tvs.dtsnvindel-PY5OBMGW.js.map → tvs.dtsnvindel-DR43K7X3.js.map} +0 -0
  949. /package/dist/{tvs.dtsv-OTBEEWSW.js.map → tvs.dtsv-NO34GIOL.js.map} +0 -0
  950. /package/dist/{tvs.numeric-WGDHEBJV.js.map → tvs.numeric-KYAU5OV3.js.map} +0 -0
  951. /package/dist/{tvs.samplelst-LCXSU5MG.js.map → tvs.samplelst-2QP7IV2Y.js.map} +0 -0
  952. /package/dist/{tvs.termCollection-L527XN4X.js.map → tvs.termCollection-UEJDG22G.js.map} +0 -0
  953. /package/dist/{violin-6VKRUQV3.js.map → violin-NBZTGGYF.js.map} +0 -0
  954. /package/dist/{violin.integration.spec-RJATDLQH.js.map → violin.integration.spec-5CLYJSAR.js.map} +0 -0
  955. /package/dist/{violin.interactivity-SKF5H7MN.js.map → violin.interactivity-KXVKTT22.js.map} +0 -0
  956. /package/dist/{violin.renderer-GB4TPX3B.js.map → violin.renderer-37OF6K7Q.js.map} +0 -0
  957. /package/dist/{vocabulary-D3W44IWE.js.map → vocabulary-GR6J3VKW.js.map} +0 -0
@@ -0,0 +1,593 @@
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-KUZPTJJO.js";
11
+ import "./chunk-HJ6L54YS.js";
12
+ import "./chunk-LSEFWW72.js";
13
+ import "./chunk-C4BCMAIK.js";
14
+ import {
15
+ Menu
16
+ } from "./chunk-HYOEWQ5P.js";
17
+ import "./chunk-HBW42TDT.js";
18
+ import "./chunk-LQJMCE7G.js";
19
+ import "./chunk-FN5XPUPH.js";
20
+ import "./chunk-IIT367QZ.js";
21
+ import "./chunk-RZGEKL77.js";
22
+ import "./chunk-Z457XQSX.js";
23
+ import "./chunk-AI2LUQS6.js";
24
+ import "./chunk-2JR7RPB6.js";
25
+ import "./chunk-7IYJZZQI.js";
26
+ import "./chunk-M3J4MINX.js";
27
+ import "./chunk-PF4DSFDR.js";
28
+ import "./chunk-TLTS33EY.js";
29
+ import "./chunk-2U2CP2Y2.js";
30
+ import "./chunk-ZF6HNVYD.js";
31
+ import "./chunk-BKPDYW5T.js";
32
+ import "./chunk-JNITUVXP.js";
33
+ import {
34
+ category10_default
35
+ } from "./chunk-TJYRBEBK.js";
36
+ import {
37
+ axisBottom,
38
+ axisLeft
39
+ } from "./chunk-LOZEKOES.js";
40
+ import "./chunk-VQZ2Z5YU.js";
41
+ import {
42
+ format,
43
+ linear,
44
+ log,
45
+ ordinal,
46
+ time,
47
+ timeParse
48
+ } from "./chunk-SOTB4FRE.js";
49
+ import "./chunk-TLT4YIG3.js";
50
+ import "./chunk-KYBIQBXE.js";
51
+ import {
52
+ select_default
53
+ } from "./chunk-I6Y4O3RR.js";
54
+ import "./chunk-OMR2DT66.js";
55
+ import "./chunk-DQC5FFGV.js";
56
+ import "./chunk-HFNDKYVF.js";
57
+
58
+ // src/maftimeline.js
59
+ var zerovalue = 1e-5;
60
+ var showcircle = true;
61
+ var maflogscale = true;
62
+ var tip = new Menu();
63
+ function maftimelineui(genomes, holder, sandbox_header) {
64
+ let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
65
+ if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
66
+ else {
67
+ ;
68
+ [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
69
+ pane.header.text("MAF timeline plot");
70
+ }
71
+ inputdiv.append("p").html(
72
+ "<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
73
+ );
74
+ inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
75
+ {
76
+ const id = Math.random().toString();
77
+ const p = inputdiv.append("p");
78
+ p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
79
+ maflogscale = !maflogscale;
80
+ });
81
+ p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
82
+ }
83
+ const fileui = () => {
84
+ filediv.selectAll("*").remove();
85
+ const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
86
+ saydiv.text("");
87
+ const file = event.target.files[0];
88
+ if (!file) {
89
+ fileui();
90
+ return;
91
+ }
92
+ if (file.size == 0) {
93
+ saydiv.text("Wrong file: " + file.name);
94
+ fileui();
95
+ return;
96
+ }
97
+ const reader = new FileReader();
98
+ reader.onload = (event2) => {
99
+ const lines = event2.target.result.trim().split(/\r?\n/);
100
+ const [err, header] = parseheader(lines[0].trim());
101
+ if (err) {
102
+ saydiv.text("File header error: " + err);
103
+ fileui();
104
+ return;
105
+ }
106
+ const badlines = [];
107
+ const data = {};
108
+ let good = 0;
109
+ for (let i = 1; i < lines.length; i++) {
110
+ if (lines[i] == "") continue;
111
+ if (lines[i][0] == "#") continue;
112
+ const m = parseline(i, lines[i], header, badlines, data);
113
+ if (m) {
114
+ good++;
115
+ }
116
+ }
117
+ if (badlines.length) {
118
+ bulk_badline(header, badlines);
119
+ }
120
+ if (good == 0) {
121
+ fileui();
122
+ return;
123
+ }
124
+ let visual_holder;
125
+ if (pane) {
126
+ disappear(pane.pane);
127
+ const pane2 = newpane({ x: 100, y: 100, toshrink: true });
128
+ pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
129
+ visual_holder = pane2.body;
130
+ }
131
+ if (holder !== void 0) {
132
+ visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
133
+ inputdiv.selectAll("*").remove();
134
+ saydiv.text("");
135
+ }
136
+ render(data, header, visual_holder);
137
+ };
138
+ reader.onerror = function() {
139
+ saydiv.text("Error reading file " + file.name);
140
+ fileui();
141
+ return;
142
+ };
143
+ saydiv.text("Parsing file " + file.name + " ...");
144
+ reader.readAsText(file, "utf8");
145
+ });
146
+ setTimeout(() => butt.node().focus(), 1100);
147
+ };
148
+ fileui();
149
+ }
150
+ function parseheader(line) {
151
+ const header = line.toLowerCase().split(" ");
152
+ if (header.length <= 1) return ["columns must be separated by tab"];
153
+ const htry = (...lst) => {
154
+ for (const i2 of lst) {
155
+ const j = header.indexOf(i2);
156
+ if (j != -1) return j;
157
+ }
158
+ return -1;
159
+ };
160
+ let i = htry("person", "patient", "caseid");
161
+ if (i == -1) return ["person missing"];
162
+ header[i] = "patient";
163
+ i = htry("sample", "sampleid");
164
+ if (i == -1) return ["sample missing"];
165
+ header[i] = "sample";
166
+ i = htry("snv4");
167
+ if (i == -1) return ["snv4 missing"];
168
+ header[i] = "snv4";
169
+ i = htry("date", "dateofsample");
170
+ if (i == -1) return ["date missing"];
171
+ header[i] = "date";
172
+ i = htry("mutant_readcount", "mutantcount");
173
+ if (i != -1) header[i] = "mutant_readcount";
174
+ i = htry("ref_readcount", "refcount");
175
+ if (i != -1) header[i] = "ref_readcount";
176
+ i = htry("total_readcount", "coveragecount");
177
+ if (i == -1) return ["total_readcount missing"];
178
+ header[i] = "coverage";
179
+ i = htry("maf");
180
+ if (i == -1) return ["maf missing"];
181
+ header[i] = "maf";
182
+ i = htry("call_manual");
183
+ if (i != -1) header[i] = "call_manual";
184
+ return [null, header];
185
+ }
186
+ function parseline(i, line, header, badlines, data) {
187
+ const lst = line.split(" ");
188
+ const m = {};
189
+ for (let j = 0; j < header.length; j++) {
190
+ m[header[j]] = lst[j];
191
+ }
192
+ if (!m.patient) {
193
+ badlines.push([i, "missing patient", lst]);
194
+ return;
195
+ }
196
+ if (!data[m.patient]) {
197
+ data[m.patient] = {
198
+ snv4: {},
199
+ show: false
200
+ };
201
+ }
202
+ if (!m.snv4) {
203
+ badlines.push([i, "missing snv4", lst]);
204
+ return;
205
+ }
206
+ if (!data[m.patient].snv4[m.snv4]) {
207
+ data[m.patient].snv4[m.snv4] = {
208
+ mutationname: m.snv4,
209
+ samples: [],
210
+ subidx: void 0
211
+ };
212
+ }
213
+ if (m.gene) {
214
+ data[m.patient].snv4[m.snv4].gene = m.gene;
215
+ }
216
+ if (!m.maf) {
217
+ badlines.push([i, "missing maf", lst]);
218
+ return;
219
+ }
220
+ let v = Number.parseFloat(m.maf);
221
+ if (Number.isNaN(v)) {
222
+ badlines.push([i, "invalid maf", lst]);
223
+ return;
224
+ }
225
+ if (v < zerovalue) {
226
+ v = zerovalue;
227
+ }
228
+ m.maf = v;
229
+ if (!m.coverage) {
230
+ badlines.push([i, "missing total_readcount", lst]);
231
+ return;
232
+ }
233
+ if (m.call_manual && m.call_manual == "wildtype") {
234
+ m.maf = zerovalue;
235
+ }
236
+ v = Number.parseInt(m.coverage);
237
+ if (Number.isNaN(v)) {
238
+ badlines.push([i, "invalid total_readcount", lst]);
239
+ return;
240
+ }
241
+ m.coverage = v;
242
+ let date;
243
+ if (m.date) {
244
+ const f = timeParse("%m/%d/%Y");
245
+ date = f(m.date);
246
+ m.Date = m.date;
247
+ } else {
248
+ badlines.push([i, "missing date", lst]);
249
+ return;
250
+ }
251
+ if (date == null) {
252
+ badlines.push([i, "cannot parse date", lst]);
253
+ return;
254
+ }
255
+ m.date = date;
256
+ if (!m.sample) {
257
+ badlines.push([i, "missing sample", lst]);
258
+ return;
259
+ }
260
+ data[m.patient].snv4[m.snv4].samples.push(m);
261
+ return true;
262
+ }
263
+ function render(data, header, holder) {
264
+ const table = holder.append("table").style("margin", "20px");
265
+ const tr1 = table.append("tr");
266
+ let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
267
+ td.append("button").text("Toggle circle visibility").on("click", () => {
268
+ showcircle = !showcircle;
269
+ for (const n in data) {
270
+ if (data[n].show) {
271
+ data[n].handle.node().click();
272
+ break;
273
+ }
274
+ }
275
+ });
276
+ const patientholder = td.append("div").style("margin-top", "10px");
277
+ const td1 = tr1.append("td").style("vertical-align", "top");
278
+ const graphholder = td1.append("div").style("display", "inline-block");
279
+ const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
280
+ const tr2 = table.append("tr");
281
+ const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
282
+ const gtr1 = tiantable.append("tr");
283
+ td = gtr1.append("td").style("vertical-align", "top");
284
+ td.append("div").text("Shared").style("font-size", "2em");
285
+ const graph1holder = td.append("div").style("border", "solid 1px black");
286
+ td = gtr1.append("td").style("vertical-align", "top");
287
+ td.append("div").text("Rising").style("font-size", "2em");
288
+ const graph2holder = td.append("div").style("border", "solid 1px black");
289
+ const gtr2 = tiantable.append("tr");
290
+ td = gtr2.append("td").style("vertical-align", "top");
291
+ td.append("div").text("Falling").style("font-size", "2em");
292
+ const graph3holder = td.append("div").style("border", "solid 1px black");
293
+ td = gtr2.append("td").style("vertical-align", "top");
294
+ td.append("div").text("R-only").style("font-size", "2em");
295
+ const graph4holder = td.append("div").style("border", "solid 1px black");
296
+ for (const patient in data) {
297
+ const snvlst = [];
298
+ const colors = ordinal(category10_default);
299
+ for (const x in data[patient].snv4) {
300
+ const snv = data[patient].snv4[x];
301
+ snv.show = true;
302
+ snv.color = colors(snv.mutationname);
303
+ snv.samples.sort((a, b) => a.date - b.date);
304
+ for (const s of snv.samples) {
305
+ s.color = snv.color;
306
+ }
307
+ snvlst.push(snv);
308
+ }
309
+ const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
310
+ for (const pn in data) {
311
+ data[pn].handle.style("color", "black");
312
+ data[pn].show = false;
313
+ }
314
+ data[patient].handle.style("color", "red");
315
+ data[patient].show = true;
316
+ makegraph(snvlst, header, graphholder);
317
+ makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
318
+ makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
319
+ });
320
+ data[patient].handle = div;
321
+ }
322
+ for (const n in data) {
323
+ data[n].handle.node().click();
324
+ break;
325
+ }
326
+ }
327
+ function makesubgraph(snvlst, g1, g2, g3, g4) {
328
+ g1.selectAll("*").remove();
329
+ g2.selectAll("*").remove();
330
+ g3.selectAll("*").remove();
331
+ g4.selectAll("*").remove();
332
+ const l1 = [];
333
+ const l2 = [];
334
+ const l3 = [];
335
+ const l4 = [];
336
+ for (const snv of snvlst) {
337
+ switch (snv.subidx) {
338
+ case 1:
339
+ l1.push(snv);
340
+ break;
341
+ case 2:
342
+ l2.push(snv);
343
+ break;
344
+ case 3:
345
+ l3.push(snv);
346
+ break;
347
+ case 4:
348
+ l4.push(snv);
349
+ break;
350
+ }
351
+ }
352
+ if (l1.length) {
353
+ makegraph(l1, null, g1, true);
354
+ } else {
355
+ g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
356
+ }
357
+ if (l2.length) {
358
+ makegraph(l2, null, g2, true);
359
+ } else {
360
+ g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
361
+ }
362
+ if (l3.length) {
363
+ makegraph(l3, null, g3, true);
364
+ } else {
365
+ g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
366
+ }
367
+ if (l4.length) {
368
+ makegraph(l4, null, g4, true);
369
+ } else {
370
+ g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
371
+ }
372
+ }
373
+ function makegraph(snvlst0, header, holder, issub) {
374
+ holder.selectAll("*").remove();
375
+ const samples = [];
376
+ const snvlst = [];
377
+ for (const snv of snvlst0) {
378
+ if (!issub && !snv.show) continue;
379
+ snvlst.push(snv);
380
+ for (const s of snv.samples) {
381
+ samples.push(s);
382
+ }
383
+ }
384
+ if (snvlst.length == 0) return;
385
+ let mindate = snvlst[0].samples[0].date;
386
+ let maxdate = snvlst[0].samples[0].date;
387
+ let maxmaf = snvlst[0].samples[0].maf;
388
+ let maxcoverage = snvlst[0].samples[0].coverage;
389
+ for (const snv of snvlst) {
390
+ for (const s of snv.samples) {
391
+ mindate = Math.min(mindate, s.date);
392
+ maxdate = Math.max(maxdate, s.date);
393
+ maxmaf = Math.max(maxmaf, s.maf);
394
+ maxcoverage = Math.max(maxcoverage, s.coverage);
395
+ }
396
+ }
397
+ const svg = holder.append("svg");
398
+ const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
399
+ let width = 600;
400
+ let height = 400;
401
+ let xpad, ypad, minradius;
402
+ const xaxisg = svg.append("g");
403
+ const yaxisg = svg.append("g");
404
+ const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
405
+ event.preventDefault();
406
+ const x = event.clientX;
407
+ const y = event.clientY;
408
+ const w0 = width;
409
+ const h0 = height;
410
+ const body = select_default(document.body);
411
+ body.on("mousemove", (event2) => {
412
+ setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
413
+ }).on("mouseup", () => {
414
+ body.on("mousemove", null).on("mouseup", null);
415
+ });
416
+ });
417
+ const xscale = time().domain([mindate, maxdate]);
418
+ const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
419
+ const rscale = linear().domain([1, maxcoverage]);
420
+ const g = svg.append("g");
421
+ const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
422
+ let circles;
423
+ if (showcircle) {
424
+ circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
425
+ event.target.setAttribute("fill-opacity", 0.4);
426
+ tip.clear();
427
+ tip.show(event.clientX, event.clientY);
428
+ const lst = [];
429
+ for (const k in d) {
430
+ if (k == "color") continue;
431
+ if (k == "gene") {
432
+ lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
433
+ continue;
434
+ }
435
+ if (k == "date") continue;
436
+ if (k == "url") {
437
+ lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
438
+ continue;
439
+ }
440
+ lst.push({ k, v: d[k] });
441
+ }
442
+ make_table_2col(tip.d, lst);
443
+ }).on("mouseout", (event) => {
444
+ event.target.setAttribute("fill-opacity", 0.1);
445
+ });
446
+ }
447
+ const legend = svg.append("g");
448
+ const setsize = (w, h) => {
449
+ width = w;
450
+ height = h;
451
+ minradius = 2;
452
+ const maxradius = Math.max(width, height) / 30;
453
+ xpad = maxradius;
454
+ ypad = maxradius;
455
+ rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
456
+ xscale.range([0, width]);
457
+ yscale.range([height, 0]);
458
+ svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
459
+ xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
460
+ yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
461
+ drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
462
+ axisstyle({
463
+ axis: xaxisg.call(axisBottom().scale(xscale)),
464
+ showline: true,
465
+ color: "black",
466
+ fontsize: Math.max(12, Math.min(20, width / 100))
467
+ });
468
+ axisstyle({
469
+ axis: yaxisg.call(
470
+ axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
471
+ ),
472
+ showline: true,
473
+ color: "black",
474
+ fontsize: Math.max(12, Math.min(20, height / 100))
475
+ });
476
+ g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
477
+ lines.attr("d", (d) => {
478
+ const lst = [];
479
+ for (let i = 0; i < d.samples.length; i++) {
480
+ const s = d.samples[i];
481
+ lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
482
+ }
483
+ return lst.join(" ");
484
+ });
485
+ if (showcircle) {
486
+ circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
487
+ }
488
+ legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
489
+ legend.selectAll("*").remove();
490
+ let y = minradius;
491
+ if (showcircle) {
492
+ legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
493
+ legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
494
+ y += 5 + minradius + maxradius;
495
+ legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
496
+ legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
497
+ y += 15 + maxradius;
498
+ }
499
+ const fontsize = 12;
500
+ for (const snv of snvlst) {
501
+ legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
502
+ if (showcircle) {
503
+ legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
504
+ }
505
+ legend.append("text").text(snv.gene).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("x", 30 + 10).attr("y", y).attr("fill", snv.color).style("cursor", "default").on("mouseover", (event) => {
506
+ event.target.setAttribute("font-weight", "bold");
507
+ lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
508
+ }).on("mouseout", (event) => {
509
+ event.target.setAttribute("font-weight", "normal");
510
+ lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
511
+ });
512
+ y += fontsize + 10;
513
+ }
514
+ };
515
+ setsize(width, height);
516
+ holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
517
+ to_svg(svg.node(), "maf-timeline");
518
+ });
519
+ }
520
+ function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
521
+ holder.selectAll("*").remove();
522
+ const table = holder.append("table");
523
+ for (const snv of snvlst) {
524
+ const tr = table.append("tr");
525
+ const td1 = tr.append("td");
526
+ td1.text(snv.gene).style("color", snv.color);
527
+ const td2 = tr.append("td");
528
+ const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
529
+ snv.checkbox = checkbox;
530
+ checkbox.on("change", (event) => {
531
+ snv.show = event.target.checked;
532
+ makegraph(snvlst, header, graphholder);
533
+ });
534
+ const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
535
+ for (const s2 of snvlst) {
536
+ s2.show = false;
537
+ s2.checkbox.property("checked", false);
538
+ }
539
+ snv.show = true;
540
+ snv.checkbox.property("checked", true);
541
+ makegraph(snvlst, header, graphholder);
542
+ });
543
+ let cname = Math.random();
544
+ const td11 = tr.append("td");
545
+ const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
546
+ td11.append("label").html("&nbsp;shared").attr("for", cname);
547
+ cname = Math.random();
548
+ const td22 = tr.append("td");
549
+ const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
550
+ td22.append("label").html("&nbsp;rising").attr("for", cname);
551
+ cname = Math.random();
552
+ const td33 = tr.append("td");
553
+ const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
554
+ td33.append("label").html("&nbsp;falling").attr("for", cname);
555
+ cname = Math.random();
556
+ const td44 = tr.append("td");
557
+ const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
558
+ td44.append("label").html("&nbsp;R-only").attr("for", cname);
559
+ if (snv.subidx == 1) c1.property("checked", true);
560
+ if (snv.subidx == 2) c2.property("checked", true);
561
+ if (snv.subidx == 3) c3.property("checked", true);
562
+ if (snv.subidx == 4) c4.property("checked", true);
563
+ const cchange = (which, check) => {
564
+ if (!check.checked) {
565
+ snv.subidx = -1;
566
+ } else {
567
+ snv.subidx = which;
568
+ if (which == 1) {
569
+ c2.property("checked", false);
570
+ c3.property("checked", false);
571
+ c4.property("checked", false);
572
+ } else if (which == 2) {
573
+ c1.property("checked", false);
574
+ c3.property("checked", false);
575
+ c4.property("checked", false);
576
+ } else if (which == 3) {
577
+ c1.property("checked", false);
578
+ c2.property("checked", false);
579
+ c4.property("checked", false);
580
+ } else {
581
+ c1.property("checked", false);
582
+ c2.property("checked", false);
583
+ c3.property("checked", false);
584
+ }
585
+ }
586
+ makesubgraph(snvlst, g1, g2, g3, g4);
587
+ };
588
+ }
589
+ }
590
+ export {
591
+ maftimelineui as default
592
+ };
593
+ //# sourceMappingURL=maftimeline-NK5QYJMJ.js.map
@@ -0,0 +1,63 @@
1
+ import {
2
+ Matrix,
3
+ componentInit,
4
+ makeChartBtnMenu,
5
+ matrixInit
6
+ } from "./chunk-F2WPS7VY.js";
7
+ import {
8
+ getPlotConfig,
9
+ setComputedConfig
10
+ } from "./chunk-CJPGYPI3.js";
11
+ import "./chunk-TMM7BWW7.js";
12
+ import "./chunk-LHKDLWG5.js";
13
+ import "./chunk-PTQ774XH.js";
14
+ import "./chunk-VIUATDO2.js";
15
+ import "./chunk-G6RZYGWY.js";
16
+ import "./chunk-3K2O2NIH.js";
17
+ import "./chunk-W5OEFZCR.js";
18
+ import "./chunk-WXSRK3XR.js";
19
+ import "./chunk-HUBO743S.js";
20
+ import "./chunk-3RSJU6YM.js";
21
+ import "./chunk-OH5I6I2D.js";
22
+ import "./chunk-DDKS3MV3.js";
23
+ import "./chunk-V2OJLJSK.js";
24
+ import "./chunk-KUZPTJJO.js";
25
+ import "./chunk-HJ6L54YS.js";
26
+ import "./chunk-LSEFWW72.js";
27
+ import "./chunk-C4BCMAIK.js";
28
+ import "./chunk-HYOEWQ5P.js";
29
+ import "./chunk-HBW42TDT.js";
30
+ import "./chunk-LQJMCE7G.js";
31
+ import "./chunk-FN5XPUPH.js";
32
+ import "./chunk-IIT367QZ.js";
33
+ import "./chunk-RZGEKL77.js";
34
+ import "./chunk-Z457XQSX.js";
35
+ import "./chunk-AI2LUQS6.js";
36
+ import "./chunk-2JR7RPB6.js";
37
+ import "./chunk-7IYJZZQI.js";
38
+ import "./chunk-M3J4MINX.js";
39
+ import "./chunk-PF4DSFDR.js";
40
+ import "./chunk-TLTS33EY.js";
41
+ import "./chunk-2U2CP2Y2.js";
42
+ import "./chunk-ZF6HNVYD.js";
43
+ import "./chunk-BKPDYW5T.js";
44
+ import "./chunk-JNITUVXP.js";
45
+ import "./chunk-TJYRBEBK.js";
46
+ import "./chunk-LOZEKOES.js";
47
+ import "./chunk-VQZ2Z5YU.js";
48
+ import "./chunk-SOTB4FRE.js";
49
+ import "./chunk-TLT4YIG3.js";
50
+ import "./chunk-KYBIQBXE.js";
51
+ import "./chunk-I6Y4O3RR.js";
52
+ import "./chunk-OMR2DT66.js";
53
+ import "./chunk-DQC5FFGV.js";
54
+ import "./chunk-HFNDKYVF.js";
55
+ export {
56
+ Matrix,
57
+ componentInit,
58
+ getPlotConfig,
59
+ makeChartBtnMenu,
60
+ matrixInit,
61
+ setComputedConfig
62
+ };
63
+ //# sourceMappingURL=matrix-7BFYR6QL.js.map