@sjcrh/proteinpaint-client 2.216.0 → 2.217.0

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 (956) hide show
  1. package/dist/2dmaf-RRHATFHO.js +1362 -0
  2. package/dist/AggMatrixInput-4UHBCXYH.js +402 -0
  3. package/dist/AggregateMatrix-IJE5CM5Y.js +37 -0
  4. package/dist/AppHeader-UXGLRW6C.js +826 -0
  5. package/dist/BoxPlot-GQYC22KY.js +1233 -0
  6. package/dist/CorrelationVolcano-5CWRWZTI.js +613 -0
  7. package/dist/Cuminc-TYHKAPRK.js +1217 -0
  8. package/dist/DE-UUFQGSOI.js +85 -0
  9. package/dist/DEinput-DU7MF4YY.js +497 -0
  10. package/dist/DM-SSI5KUBC.js +86 -0
  11. package/dist/DifferentialAnalysis-G6FE2MXY.js +235 -0
  12. package/dist/Disco-B3KGNEAW.js +3384 -0
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  14. package/dist/DmrPlot-27NGDMT4.js +358 -0
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  17. package/dist/GeneExpInput-NDXISF2U.js +38 -0
  18. package/dist/Geomap-3CNT227W.js +80 -0
  19. package/dist/HicApp-VQBUB6EZ.js +2240 -0
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  21. package/dist/NumBinaryEditor-IVZ4MMQT.js +274 -0
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  25. package/dist/NumCustomBinEditor-UEEYZ4ZO.js +29 -0
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  37. package/dist/ProteomeInput-NYPUYVN5.js +610 -0
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  166. package/dist/condition-SGJIDZNB.js +323 -0
  167. package/dist/controls-JQCMGPXP.js +30 -0
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  170. package/dist/customdata.inputui-LGTGMJBZ.js +280 -0
  171. package/dist/dataDownload-FAWN2WKE.js +325 -0
  172. package/dist/databrowser.ui-KF3LWQXG.js +421 -0
  173. package/dist/dictionary-EVLEOT72.js +109 -0
  174. package/dist/dnaMethylation-J3SPEM4S.js +29 -0
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  181. package/dist/gb-YDEOK7NW.js +77 -0
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  841. /package/dist/{junction.unit.spec-VU665JWH.js.map → junction.unit.spec-F35E3GJW.js.map} +0 -0
  842. /package/dist/{launch.adhoc-PG2VDOP5.js.map → launch.adhoc-V2HTCQGD.js.map} +0 -0
  843. /package/dist/{leftlabel.sample-O4EI4FEW.js.map → leftlabel.sample-V7O2EC36.js.map} +0 -0
  844. /package/dist/{lollipop-LWQ3ZPUC.js.map → lollipop-RNRZLG64.js.map} +0 -0
  845. /package/dist/{maf-Z7IN4HAW.js.map → maf-W6SF6BJS.js.map} +0 -0
  846. /package/dist/{maftimeline-AQLIVUW3.js.map → maftimeline-NABCAMHG.js.map} +0 -0
  847. /package/dist/{matrix-LTXFBGFW.js.map → matrix-JC6AJT2N.js.map} +0 -0
  848. /package/dist/{matrix-W2XR54DY.js.map → matrix-UCHESWVK.js.map} +0 -0
  849. /package/dist/{matrix.cells-F44JHGOO.js.map → matrix.cells-B4L42TBM.js.map} +0 -0
  850. /package/dist/{matrix.config-Y5OUBSEC.js.map → matrix.config-6US3AAH7.js.map} +0 -0
  851. /package/dist/{matrix.data-VLIW75OR.js.map → matrix.data-FYFXYDA3.js.map} +0 -0
  852. /package/dist/{matrix.groups-QEWUDMPF.js.map → matrix.groups-Y7DEG3GS.js.map} +0 -0
  853. /package/dist/{matrix.integration.spec-24DH4HNF.js.map → matrix.integration.spec-KXX7SFX5.js.map} +0 -0
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  857. /package/dist/{matrix.renderers-CMPAIUYT.js.map → matrix.renderers-GYOXGHPU.js.map} +0 -0
  858. /package/dist/{matrix.serieses-GXVQBJML.js.map → matrix.serieses-657TLDAV.js.map} +0 -0
  859. /package/dist/{matrix.sort-VQS6E6S5.js.map → matrix.sort-IMA2ES3T.js.map} +0 -0
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  862. /package/dist/{matrix.sorterUi.unit.spec-UMI2N2OG.js.map → matrix.sorterUi.unit.spec-V5NVQGD5.js.map} +0 -0
  863. /package/dist/{matrix.unit.spec-HSA7OWME.js.map → matrix.unit.spec-R4NMTZYQ.js.map} +0 -0
  864. /package/dist/{mavb-ZARQZJJR.js.map → mavb-MRCVMBPD.js.map} +0 -0
  865. /package/dist/{mds.fimo-YRNNY5KA.js.map → mds.fimo-5DCH5BEM.js.map} +0 -0
  866. /package/dist/{mds.samplescatterplot-ESIALOMA.js.map → mds.samplescatterplot-VIBCS5M6.js.map} +0 -0
  867. /package/dist/{mds.survivalplot-5E6ITKIU.js.map → mds.survivalplot-AZ7LJDZZ.js.map} +0 -0
  868. /package/dist/{multivalue-CT2QWWB4.js.map → multivalue-4QKGYYW2.js.map} +0 -0
  869. /package/dist/{numericDictTermCluster-CRVSJ6PI.js.map → numericDictTermCluster-GLLG6IK2.js.map} +0 -0
  870. /package/dist/{oncomatrix-MX5EHBNW.js.map → oncomatrix-R32ZPMX7.js.map} +0 -0
  871. /package/dist/{oncomatrix.spec-DN2RAWGZ.js.map → oncomatrix.spec-BMK6LMBS.js.map} +0 -0
  872. /package/dist/{plot.2dvaf-B5QAKDTK.js.map → plot.2dvaf-46FT53MF.js.map} +0 -0
  873. /package/dist/{plot.app-V5DZWC6N.js.map → plot.app-7EE4YCV4.js.map} +0 -0
  874. /package/dist/{plot.barplot-VAJLAU7H.js.map → plot.barplot-FK4J2G7K.js.map} +0 -0
  875. /package/dist/{plot.boxplot-PT3BUNVT.js.map → plot.boxplot-ATY4LK3X.js.map} +0 -0
  876. /package/dist/{plot.brainImaging-2WB7XJJM.js.map → plot.brainImaging-S7B547V4.js.map} +0 -0
  877. /package/dist/{plot.disco-64IPBCII.js.map → plot.disco-K5MMC2GD.js.map} +0 -0
  878. /package/dist/{plot.ssgq-ET4OBMUM.js.map → plot.ssgq-B3OVMZFD.js.map} +0 -0
  879. /package/dist/{plot.vaf2cov-DGMVJ7UN.js.map → plot.vaf2cov-RBHDQULW.js.map} +0 -0
  880. /package/dist/{polar2-CWWDVNZQ.js.map → polar2-GECELCTG.js.map} +0 -0
  881. /package/dist/{profileForms-FM7D4WO2.js.map → profileForms-2USYOA34.js.map} +0 -0
  882. /package/dist/{profilePlot-LQ6K4EXX.js.map → profilePlot-YGD2CF6P.js.map} +0 -0
  883. /package/dist/{pseudbulk.unit.spec-IAONX4QR.js.map → pseudbulk.unit.spec-UVVRP6NR.js.map} +0 -0
  884. /package/dist/{pseudobulk-NIX4JOOZ.js.map → pseudobulk-ZIN5VJGB.js.map} +0 -0
  885. /package/dist/{qualitative-M3XSQZA2.js.map → qualitative-27BZGASV.js.map} +0 -0
  886. /package/dist/{qualitative-GLTKWA6H.js.map → qualitative-N4F6NITI.js.map} +0 -0
  887. /package/dist/{radar2-JBULXNFQ.js.map → radar2-X465RPJX.js.map} +0 -0
  888. /package/dist/{radarFacility2-YYIBHZCY.js.map → radarFacility2-AE7BA62N.js.map} +0 -0
  889. /package/dist/{rememberedGvQ.unit.spec-YJV6DVPN.js.map → rememberedGvQ.unit.spec-4PDIU5RY.js.map} +0 -0
  890. /package/dist/{render-ZCH7R3WL.js.map → render-TD2QWOHT.js.map} +0 -0
  891. /package/dist/{report-YPIAIMND.js.map → report-3Y2OWDF7.js.map} +0 -0
  892. /package/dist/{sampleView-K4GSYMAE.js.map → sampleView-BUMMYRHJ.js.map} +0 -0
  893. /package/dist/{samplelst-F2SLVHFP.js.map → samplelst-BWK53BLI.js.map} +0 -0
  894. /package/dist/{samplematrix-Z6F4F7YN.js.map → samplematrix-RQU43UYR.js.map} +0 -0
  895. /package/dist/{sc-UM7SEGED.js.map → sc-LCBFWCZZ.js.map} +0 -0
  896. /package/dist/{scatter-63XRRLGP.js.map → scatter-6S5I7OW3.js.map} +0 -0
  897. /package/dist/{scatter-HFTYLGDP.js.map → scatter-MJELX75N.js.map} +0 -0
  898. /package/dist/{selectGenomeWithTklst-PJNALPM2.js.map → selectGenomeWithTklst-WAVXHXR5.js.map} +0 -0
  899. /package/dist/{singleCellCellType-HR3R6KBD.js.map → singleCellCellType-WMCAJ7JF.js.map} +0 -0
  900. /package/dist/{singleCellCellType.unit.spec-VK57HQ2O.js.map → singleCellCellType.unit.spec-4Z46ZT5Q.js.map} +0 -0
  901. /package/dist/{singleCellGeneExpression-VWOA7MLN.js.map → singleCellGeneExpression-7Q5ZJT4R.js.map} +0 -0
  902. /package/dist/{singleCellGeneExpression.unit.spec-YP64T3XD.js.map → singleCellGeneExpression.unit.spec-6C7PDGRH.js.map} +0 -0
  903. /package/dist/{singleCellNumericValue-3VIUPYPB.js.map → singleCellNumericValue-QGYITZRC.js.map} +0 -0
  904. /package/dist/{singleCellNumericValue.unit.spec-VR5ICRQA.js.map → singleCellNumericValue.unit.spec-MQUKPEZJ.js.map} +0 -0
  905. /package/dist/{singleCellPlot-36QDY7VL.js.map → singleCellPlot-JJMFJ2KQ.js.map} +0 -0
  906. /package/dist/{singlecell-EXEOLJ3J.js.map → singlecell-J23S3JR2.js.map} +0 -0
  907. /package/dist/{singlecell-D2MZVFR4.js.map → singlecell-Y4OGUWEC.js.map} +0 -0
  908. /package/dist/{snp-XHEHXZMB.js.map → snp-IO6TKWGD.js.map} +0 -0
  909. /package/dist/{snp.unit.spec-YR6IDLL7.js.map → snp.unit.spec-X7ILEEPO.js.map} +0 -0
  910. /package/dist/{snplocus-BM7LUK2U.js.map → snplocus-Z2NGIKMO.js.map} +0 -0
  911. /package/dist/{snplst-22VSEZ7R.js.map → snplst-XCS2FCQV.js.map} +0 -0
  912. /package/dist/{spliceevent.a53ss.diagram-KERTJ3QA.js.map → spliceevent.a53ss.diagram-F3S4BRVG.js.map} +0 -0
  913. /package/dist/{spliceevent.exonskip.diagram-K74VIUA4.js.map → spliceevent.exonskip.diagram-AXCDJKH4.js.map} +0 -0
  914. /package/dist/{spliceevent.noeventdiagram-W7WGSVVL.js.map → spliceevent.noeventdiagram-UK3X667E.js.map} +0 -0
  915. /package/dist/{ssGSEA-XDEA5TVX.js.map → ssGSEA-ZRPNQKJ5.js.map} +0 -0
  916. /package/dist/{ssGSEA.unit.spec-RDCPXJ5S.js.map → ssGSEA.unit.spec-DG5ZHLC7.js.map} +0 -0
  917. /package/dist/{stattable-HZ3DOUEM.js.map → stattable-XYSC3CYU.js.map} +0 -0
  918. /package/dist/{summarizeCnvGeneexp-VB4SOJHT.js.map → summarizeCnvGeneexp-H2NP7VLU.js.map} +0 -0
  919. /package/dist/{summarizeGeneexpSurvival-5ZWIJ6O4.js.map → summarizeGeneexpSurvival-HTCD3VQQ.js.map} +0 -0
  920. /package/dist/{summarizeMutationCnv-MBPU64C5.js.map → summarizeMutationCnv-UEGXWK2P.js.map} +0 -0
  921. /package/dist/{summarizeMutationDiagnosis-QRP4ITNL.js.map → summarizeMutationDiagnosis-MJGWP7IT.js.map} +0 -0
  922. /package/dist/{summarizeMutationSurvival-SSXAY5W4.js.map → summarizeMutationSurvival-55JW5LA6.js.map} +0 -0
  923. /package/dist/{summary-SRESZS4Z.js.map → summary-HJO23RGB.js.map} +0 -0
  924. /package/dist/{summary.integration.spec-3V2CEPJM.js.map → summary.integration.spec-OWI2C2N5.js.map} +0 -0
  925. /package/dist/{summaryInput-3VD4KBCU.js.map → summaryInput-RL2JXRDE.js.map} +0 -0
  926. /package/dist/{sunburst-E5IEQQUV.js.map → sunburst-JFY6V5E2.js.map} +0 -0
  927. /package/dist/{survival-H4HYC6GC.js.map → survival-6FLR4YCJ.js.map} +0 -0
  928. /package/dist/{survival-K5WWAELO.js.map → survival-PBBU6PA5.js.map} +0 -0
  929. /package/dist/{survival.integration.spec-SPN2TSQW.js.map → survival.integration.spec-WAKTGYGP.js.map} +0 -0
  930. /package/dist/{svgraph-USRAYSBN.js.map → svgraph-WD3DUZV7.js.map} +0 -0
  931. /package/dist/{svmr-MOKLLJKJ.js.map → svmr-AP6ZFO7S.js.map} +0 -0
  932. /package/dist/{table-WD3P3WL2.js.map → table-GX3VJLPZ.js.map} +0 -0
  933. /package/dist/{termCollection-JU4OJRWD.js.map → termCollection-QE7U5QBD.js.map} +0 -0
  934. /package/dist/{termCollection-VWS5CKVH.js.map → termCollection-YQ332WKB.js.map} +0 -0
  935. /package/dist/{termCollection.unit.spec-TPUJWKKW.js.map → termCollection.unit.spec-ELLN7VRA.js.map} +0 -0
  936. /package/dist/{termCollectionFractionSelection-UWLHDPX2.js.map → termCollectionFractionSelection-V3RP5KAT.js.map} +0 -0
  937. /package/dist/{termCollectionFractionSelection.unit.spec-RBHJY34K.js.map → termCollectionFractionSelection.unit.spec-JR7Q7TJI.js.map} +0 -0
  938. /package/dist/{tk-OAOVCATS.js.map → tk-GD2KJM5W.js.map} +0 -0
  939. /package/dist/{tk-SMOGJUD7.js.map → tk-J5VPFEX6.js.map} +0 -0
  940. /package/dist/{tp.ui-EMWJCGRX.js.map → tp.ui-5K3AAXDW.js.map} +0 -0
  941. /package/dist/{tvs.categorical-A7J4RIKL.js.map → tvs.categorical-RPACB4VU.js.map} +0 -0
  942. /package/dist/{tvs.condition-HFLZES5E.js.map → tvs.condition-O6JBUM6D.js.map} +0 -0
  943. /package/dist/{tvs.dt-GBYX2RWX.js.map → tvs.dt-5EVBSRX3.js.map} +0 -0
  944. /package/dist/{tvs.dtcnv.categorical-X2K3MIPG.js.map → tvs.dtcnv.categorical-Y5YHBZNC.js.map} +0 -0
  945. /package/dist/{tvs.dtcnv.continuous-5EMX4PBP.js.map → tvs.dtcnv.continuous-WP322QUP.js.map} +0 -0
  946. /package/dist/{tvs.dtfusion-7VVSPNRK.js.map → tvs.dtfusion-CCMUFDMQ.js.map} +0 -0
  947. /package/dist/{tvs.dtitd-2YGFPXOY.js.map → tvs.dtitd-P3ED3MWA.js.map} +0 -0
  948. /package/dist/{tvs.dtsnvindel-EISO52O6.js.map → tvs.dtsnvindel-X2MXPLC6.js.map} +0 -0
  949. /package/dist/{tvs.dtsv-RTAMAW3G.js.map → tvs.dtsv-4FOWFNVV.js.map} +0 -0
  950. /package/dist/{tvs.multivalue-5N6PSG4L.js.map → tvs.multivalue-IRF467ZK.js.map} +0 -0
  951. /package/dist/{tvs.numeric-R5UT7ARM.js.map → tvs.numeric-C7FDCGCS.js.map} +0 -0
  952. /package/dist/{tvs.samplelst-SZDNNFK5.js.map → tvs.samplelst-CBU6ATI5.js.map} +0 -0
  953. /package/dist/{tvs.survival-EUUDDXP7.js.map → tvs.survival-3K5ASAXV.js.map} +0 -0
  954. /package/dist/{tvs.termCollection-DAHEYZK2.js.map → tvs.termCollection-MXEWO6KJ.js.map} +0 -0
  955. /package/dist/{vocabulary-P4XRHR34.js.map → vocabulary-GQBHDP3K.js.map} +0 -0
  956. /package/dist/{wsi.direct-J7VX5EMI.js.map → wsi.direct-25JUHWEF.js.map} +0 -0
@@ -1,274 +0,0 @@
1
- import {
2
- LegendCircleReference,
3
- PlotBase,
4
- addGeneSearchbox
5
- } from "./chunk-FIFNXVTS.js";
6
- import "./chunk-HJ6L54YS.js";
7
- import "./chunk-N2FCAFJH.js";
8
- import "./chunk-OH33WT6Q.js";
9
- import {
10
- Menu
11
- } from "./chunk-CNFTQSNE.js";
12
- import "./chunk-EEB5VE2A.js";
13
- import "./chunk-3CIL7KH7.js";
14
- import "./chunk-T4XPCSLP.js";
15
- import {
16
- dofetch3
17
- } from "./chunk-5MHE7AIV.js";
18
- import "./chunk-6WYKPBZI.js";
19
- import "./chunk-W5J3LTYS.js";
20
- import "./chunk-DBOJ3TMI.js";
21
- import "./chunk-EZFO5UYD.js";
22
- import {
23
- copyMerge,
24
- getCompInit
25
- } from "./chunk-HBNB5TRH.js";
26
- import "./chunk-PF4DSFDR.js";
27
- import {
28
- linear,
29
- sqrt
30
- } from "./chunk-4OLM3KSB.js";
31
- import "./chunk-6XKAOSQE.js";
32
- import "./chunk-TLT4YIG3.js";
33
- import "./chunk-5R63Q5KH.js";
34
- import "./chunk-I6Y4O3RR.js";
35
- import "./chunk-Q5RDQNIT.js";
36
- import "./chunk-HS5PO5ZQ.js";
37
-
38
- // plots/cellTypeBubbleHeatmap.ts
39
- var defaultConfig = { chartType: "cellTypeBubbleHeatmap" };
40
- var CELL_W = 84;
41
- var CELL_H = 60;
42
- var ROW_LABEL_W = 74;
43
- var GROUP_LABEL_H = 22;
44
- var GENO_LABEL_H = 40;
45
- var COL_LABEL_H = GROUP_LABEL_H + GENO_LABEL_H;
46
- var MIN_DOT_R = 8;
47
- var MAX_DOT_R = 22;
48
- var NEG_LOG_FDR_CAP = 10;
49
- var COLOR_NEG = "#762a83";
50
- var COLOR_ZERO = "#f7f7f7";
51
- var COLOR_POS = "#2166ac";
52
- var CellTypeBubbleHeatmap = class _CellTypeBubbleHeatmap extends PlotBase {
53
- constructor(opts, api) {
54
- super(opts, api);
55
- this.currentIsoform = "";
56
- this.type = _CellTypeBubbleHeatmap.type;
57
- }
58
- static {
59
- this.type = "cellTypeBubbleHeatmap";
60
- }
61
- async init() {
62
- const holder = this.opts.holder.append("div").style("padding", "10px");
63
- this.dom = {
64
- holder,
65
- body: holder.append("div"),
66
- tip: new Menu({ padding: "" }),
67
- header: this.opts.header
68
- };
69
- if (this.dom.header) this.dom.header.html("Cell-type Bubble Heatmap");
70
- }
71
- getState(appState) {
72
- const config = appState.plots.find((p) => p.id === this.id);
73
- if (!config) throw `No plot with id='${this.id}' found`;
74
- return { config };
75
- }
76
- async main() {
77
- const gene = this.state.config?.gene;
78
- if (!gene) throw new Error("cellTypeBubbleHeatmap: gene is missing");
79
- if (this.dom.header) this.dom.header.text(`Cell-type Bubble Heatmap: ${gene}`);
80
- const body = {
81
- genome: this.app.opts.state.vocab.genome,
82
- dslabel: this.app.opts.state.vocab.dslabel,
83
- gene
84
- };
85
- const data = await dofetch3("termdb/cellTypeBubbleHeatmap", { body });
86
- if (data.error) throw data.error;
87
- this.data = data;
88
- this.dom.body.selectAll("*").remove();
89
- const isoformIds = Object.keys(data.isoforms);
90
- if (isoformIds.length === 0) {
91
- this.dom.body.append("div").style("padding", "20px").style("color", "#666").text(`No data found for gene "${gene}" in any cohort DAPfile.`);
92
- return;
93
- }
94
- this.currentIsoform = isoformIds[0];
95
- const isoBlock = this.dom.body.append("div").style("margin-bottom", "12px");
96
- isoBlock.append("span").style("font-weight", "bold").text("Isoform: ");
97
- if (isoformIds.length > 1) {
98
- const sel = isoBlock.append("select").style("margin-left", "5px").style("padding", "3px 6px").on("change", () => {
99
- this.currentIsoform = sel.node().value;
100
- this.renderGrid();
101
- });
102
- sel.selectAll("option").data(isoformIds).enter().append("option").attr("value", (d) => d).text((d) => `${data.isoforms[d].gene_name} \u2014 ${d}`);
103
- } else {
104
- isoBlock.append("span").style("margin-left", "5px").text(`${data.isoforms[this.currentIsoform].gene_name} \u2014 ${this.currentIsoform}`);
105
- }
106
- this.gridHolder = this.dom.body.append("div");
107
- this.renderGrid();
108
- }
109
- renderGrid() {
110
- const data = this.data;
111
- const selectedIsoform = this.currentIsoform;
112
- const threshold = data.fdrThreshold;
113
- this.gridHolder.selectAll("*").remove();
114
- const container = this.gridHolder.append("div").style("display", "flex").style("gap", "24px").style("align-items", "flex-start").style("flex-wrap", "wrap");
115
- const isoformData = data.isoforms[selectedIsoform];
116
- if (!isoformData) return;
117
- const columns = data.columns;
118
- const rows = data.rows;
119
- const nCols = columns.length;
120
- const nRows = rows.length;
121
- const negLogFdr = (fdr) => fdr > 0 ? Math.min(-Math.log10(fdr), NEG_LOG_FDR_CAP) : NEG_LOG_FDR_CAP;
122
- const cellOf = (colKey, rowKey) => isoformData.data[colKey]?.[rowKey];
123
- let maxAbs = 0;
124
- const thresholdNegLog = negLogFdr(threshold);
125
- let maxNegLog = thresholdNegLog;
126
- for (const col of columns) {
127
- for (const row of rows) {
128
- const s = cellOf(col.key, row.key);
129
- if (!s) continue;
130
- const v = Math.abs(s.log2FC);
131
- if (v > maxAbs) maxAbs = v;
132
- const nl = negLogFdr(s.fdr);
133
- if (nl > maxNegLog) maxNegLog = nl;
134
- }
135
- }
136
- if (maxAbs === 0) maxAbs = 1;
137
- if (maxNegLog <= thresholdNegLog) maxNegLog = thresholdNegLog + 1;
138
- const colorScale = linear().domain([-maxAbs, 0, maxAbs]).range([COLOR_NEG, COLOR_ZERO, COLOR_POS]).clamp(true);
139
- const sizeScale = sqrt().domain([thresholdNegLog, maxNegLog]).range([MIN_DOT_R, MAX_DOT_R]).clamp(true);
140
- const gridW = ROW_LABEL_W + nCols * CELL_W + 20;
141
- const gridH = COL_LABEL_H + nRows * CELL_H + 20;
142
- const svg = container.append("svg").attr("width", gridW).attr("height", gridH).style("flex", "0 0 auto");
143
- const grid = svg.append("g");
144
- let c = 0;
145
- while (c < nCols) {
146
- const cellType = columns[c].cellType;
147
- let end = c;
148
- while (end + 1 < nCols && columns[end + 1].cellType === cellType) end++;
149
- const xStart = ROW_LABEL_W + c * CELL_W;
150
- const xEnd = ROW_LABEL_W + (end + 1) * CELL_W;
151
- const xMid = (xStart + xEnd) / 2;
152
- grid.append("text").attr("x", xMid).attr("y", GROUP_LABEL_H - 7).attr("text-anchor", "middle").attr("font-size", "13px").attr("font-weight", "bold").text(cellType);
153
- grid.append("line").attr("x1", xStart + 4).attr("y1", GROUP_LABEL_H - 3).attr("x2", xEnd - 4).attr("y2", GROUP_LABEL_H - 3).attr("stroke", "#bbb").attr("stroke-width", 1);
154
- c = end + 1;
155
- }
156
- for (let col = 0; col < nCols; col++) {
157
- const cx = ROW_LABEL_W + col * CELL_W + CELL_W / 2;
158
- grid.append("text").attr("x", cx).attr("y", COL_LABEL_H - 14).attr("text-anchor", "middle").attr("font-size", "12px").attr("font-weight", "600").text(columns[col].genotype);
159
- }
160
- for (let r = 0; r < nRows; r++) {
161
- const cy = COL_LABEL_H + r * CELL_H + CELL_H / 2;
162
- grid.append("text").attr("x", ROW_LABEL_W - 12).attr("y", cy).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("font-size", "13px").attr("font-weight", "bold").text(rows[r].label);
163
- }
164
- for (let r = 0; r < nRows; r++) {
165
- for (let col = 0; col < nCols; col++) {
166
- const x0 = ROW_LABEL_W + col * CELL_W;
167
- const y0 = COL_LABEL_H + r * CELL_H;
168
- grid.append("rect").attr("x", x0).attr("y", y0).attr("width", CELL_W).attr("height", CELL_H).attr("fill", "none").attr("stroke", "#eee").attr("stroke-width", 1);
169
- const s = cellOf(columns[col].key, rows[r].key);
170
- if (!s) continue;
171
- const cx = x0 + CELL_W / 2;
172
- const cy = y0 + CELL_H / 2;
173
- grid.append("circle").attr("cx", cx).attr("cy", cy).attr("r", sizeScale(negLogFdr(s.fdr))).attr("fill", colorScale(s.log2FC)).attr("stroke", "#888").attr("stroke-width", 0.8).style("opacity", s.significant ? 1 : 0.35).on(
174
- "mouseover",
175
- (event) => this.showCellTip(event, isoformData.gene_name, selectedIsoform, columns[col], rows[r], s)
176
- ).on("mouseout", () => this.dom.tip.hide());
177
- }
178
- }
179
- this.renderLegend(container, colorScale, maxAbs, threshold, maxNegLog);
180
- }
181
- fmtFdr(v) {
182
- return v >= 1e-4 ? v.toFixed(4) : v.toExponential(2);
183
- }
184
- showCellTip(event, geneName, isoform, col, row, s) {
185
- this.dom.tip.clear().show(event.clientX, event.clientY);
186
- const t = this.dom.tip.d.append("div").style("padding", "8px").style("font-size", "13px");
187
- t.append("div").style("font-weight", "bold").style("margin-bottom", "4px").text(`${geneName} \u2014 ${isoform}`);
188
- t.append("div").text(`Cell type: ${col.cellType}`);
189
- t.append("div").text(`Genotype: ${col.genotype}`);
190
- t.append("div").text(`Timepoint: ${row.label}`);
191
- t.append("div").text(`Protein: ${s.id}`);
192
- t.append("div").text(`log\u2082FC: ${s.log2FC.toFixed(3)}`);
193
- t.append("div").text(`FDR: ${this.fmtFdr(s.fdr)}${s.significant ? "" : " (n.s.)"}`);
194
- t.append("div").style("color", "#666").style("margin-top", "4px").text("Color = log\u2082FC (blue up / purple down). Size = \u2212log\u2081\u2080 FDR.");
195
- }
196
- renderLegend(container, colorScale, maxAbs, threshold, maxNegLog) {
197
- const legend = container.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "16px").style("padding", "8px 0").style("min-width", "180px").style("max-width", "260px");
198
- const colorBlock = legend.append("div");
199
- colorBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("log\u2082FC");
200
- const cW = 22;
201
- const cH = 130;
202
- const cSvg = colorBlock.append("svg").attr("width", cW + 80).attr("height", cH + 16);
203
- const gid = `ctbh-grad-${this.id}`;
204
- const grad = cSvg.append("defs").append("linearGradient").attr("id", gid).attr("x1", "0").attr("y1", "0").attr("x2", "0").attr("y2", "1");
205
- const steps = 10;
206
- for (let i = 0; i <= steps; i++) {
207
- const t = i / steps;
208
- grad.append("stop").attr("offset", `${t * 100}%`).attr("stop-color", colorScale(maxAbs * (1 - 2 * t)));
209
- }
210
- cSvg.append("rect").attr("x", 0).attr("y", 8).attr("width", cW).attr("height", cH).style("fill", `url(#${gid})`).attr("stroke", "#999");
211
- const cScale = linear().domain([maxAbs, -maxAbs]).range([8, cH + 8]);
212
- for (const tick of [maxAbs, maxAbs / 2, 0, -maxAbs / 2, -maxAbs]) {
213
- const y = cScale(tick);
214
- cSvg.append("line").attr("x1", cW).attr("y1", y).attr("x2", cW + 5).attr("y2", y).attr("stroke", "#666");
215
- cSvg.append("text").attr("x", cW + 8).attr("y", y).attr("dominant-baseline", "central").attr("font-size", "10px").text(`${tick > 0 ? "+" : ""}${tick.toFixed(2)}`);
216
- }
217
- colorBlock.append("div").style("font-size", "11px").style("color", "#666").style("margin-top", "2px").text("blue = up (+), purple = down (\u2212)");
218
- const sizeBlock = legend.append("div");
219
- sizeBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("Dot size: significance (\u2212log\u2081\u2080 FDR)");
220
- const sSvg = sizeBlock.append("svg");
221
- const sG = sSvg.append("g");
222
- new LegendCircleReference({
223
- g: sG,
224
- inputMin: 0,
225
- inputMax: MAX_DOT_R * 2,
226
- minRadius: MIN_DOT_R,
227
- maxRadius: MAX_DOT_R,
228
- minLabel: Number(Math.min(-Math.log10(threshold), NEG_LOG_FDR_CAP).toFixed(1)),
229
- maxLabel: Number(maxNegLog.toFixed(1))
230
- });
231
- const sPad = 4;
232
- const sBox = sG.node().getBBox();
233
- sG.attr("transform", `translate(${sPad - sBox.x}, ${sPad - sBox.y})`);
234
- sSvg.attr("width", Math.ceil(sBox.width + 2 * sPad)).attr("height", Math.ceil(sBox.height + 2 * sPad));
235
- const notes = legend.append("div").style("font-size", "11px").style("color", "#666").style("line-height", "1.5").style("max-width", "240px").style("overflow-wrap", "break-word");
236
- notes.append("div").text(
237
- `Color = log\u2082FC (blue up, purple down). Dot size = significance, \u2212log\u2081\u2080 FDR; the smallest size marks the FDR < ${threshold} cutoff. Non-significant dots (FDR \u2265 ${threshold}) are faded.`
238
- );
239
- notes.append("div").style("margin-top", "4px").text("An empty cell means the cohort was not assayed (e.g. OPC has no 4m) or the protein was not detected.");
240
- }
241
- };
242
- var componentInit = getCompInit(CellTypeBubbleHeatmap);
243
- async function getPlotConfig(opts) {
244
- const config = structuredClone(defaultConfig);
245
- if (!opts.gene) throw new Error("cellTypeBubbleHeatmap requires opts.gene");
246
- return copyMerge(config, opts);
247
- }
248
- function makeChartBtnMenu(holder, chartsInstance) {
249
- const row = holder.append("div").style("padding", "5px");
250
- row.append("span").style("font-weight", "bold").text("Enter a gene name:");
251
- const geneSearch = addGeneSearchbox({
252
- row,
253
- genome: chartsInstance.app.opts.genome,
254
- tip: new Menu({ padding: "0px" }),
255
- searchOnly: "gene",
256
- callback: async () => {
257
- if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
258
- chartsInstance.dom.tip.hide();
259
- chartsInstance.app.dispatch({
260
- type: "plot_create",
261
- config: {
262
- chartType: "cellTypeBubbleHeatmap",
263
- gene: geneSearch.geneSymbol
264
- }
265
- });
266
- }
267
- });
268
- }
269
- export {
270
- componentInit,
271
- getPlotConfig,
272
- makeChartBtnMenu
273
- };
274
- //# sourceMappingURL=cellTypeBubbleHeatmap-H7VHFQFD.js.map
@@ -1,176 +0,0 @@
1
- import {
2
- appInit
3
- } from "./chunk-DURCB2KS.js";
4
- import {
5
- showErrorsWithCounter
6
- } from "./chunk-FIFNXVTS.js";
7
- import {
8
- mclass
9
- } from "./chunk-EZFO5UYD.js";
10
-
11
- // plots/disco/launch.adhoc.ts
12
- async function launch(arg, genomeObj, holder) {
13
- const [mlst, errors] = await getMlst(arg);
14
- if (errors?.length) {
15
- return showErrorsWithCounter(errors, holder);
16
- }
17
- const opts = {
18
- holder,
19
- vocabApi: {
20
- // api is required by plot.app.js, so create a mock one for the adhoc data
21
- vocab: { terms: [] },
22
- main: () => {
23
- return;
24
- },
25
- getTermdbConfig: () => {
26
- return {};
27
- }
28
- },
29
- state: {
30
- args: {
31
- data: mlst,
32
- genome: genomeObj
33
- },
34
- plots: [
35
- {
36
- chartType: "Disco",
37
- subfolder: "disco",
38
- extension: "ts",
39
- /** NOTE: Users should only override the settings in the default
40
- * settings.Disco:{}, not the entire settings:{} object.*/
41
- overrides: { Disco: arg?.settings || {} }
42
- }
43
- ]
44
- }
45
- };
46
- const plotAppApi = await appInit(opts);
47
- return plotAppApi;
48
- }
49
- async function getMlst(arg) {
50
- if (Array.isArray(arg.mlst)) {
51
- return [arg.mlst, null];
52
- }
53
- const mlst = [];
54
- const errors = [];
55
- if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
56
- if (arg.svText) parseSvText(arg.svText, mlst, errors);
57
- if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
58
- return [mlst, errors];
59
- }
60
- function parseSnvText(text, mlst, errors) {
61
- for (const line of text.trim().split("\n")) {
62
- const l = line.trim().split(" ");
63
- if (![5, 7, 9].includes(l.length)) {
64
- errors.push("snv input not equal to 5, 7, or 9 columns");
65
- continue;
66
- }
67
- let m;
68
- try {
69
- m = {
70
- dt: 1,
71
- chr: l[0],
72
- position: Number(l[1]),
73
- gene: l[2],
74
- mname: l[3],
75
- class: validateMutation(l[4], errors)
76
- };
77
- const vafs = parseOptionalVafs(l, errors);
78
- if (vafs.length) m.vafs = vafs;
79
- } catch (e) {
80
- errors.push(e);
81
- continue;
82
- }
83
- mlst.push(m);
84
- }
85
- }
86
- function parseOptionalVafs(line, errors) {
87
- const vafs = [];
88
- const addVaf = (id, totalIndex, altIndex) => {
89
- if (line.length <= altIndex) return;
90
- const totalCount = Number(line[totalIndex]);
91
- const altCount = Number(line[altIndex]);
92
- if (!Number.isInteger(totalCount) || !Number.isInteger(altCount) || totalCount <= 0 || altCount < 0 || altCount > totalCount) {
93
- errors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`);
94
- return;
95
- }
96
- vafs.push({ id, totalCount, altCount });
97
- };
98
- addVaf("DNA", 5, 6);
99
- addVaf("RNA", 7, 8);
100
- return vafs;
101
- }
102
- function parseSvText(text, mlst, errors) {
103
- for (const line of text.trim().split("\n")) {
104
- const l = line.trim().split(" ");
105
- if (l.length < 4 || l.length > 6) {
106
- errors.push("sv input not equal to 4 or 6 columns");
107
- continue;
108
- }
109
- let m;
110
- try {
111
- const length = l.length;
112
- if (length == 4) {
113
- m = {
114
- dt: 2,
115
- chrA: l[0],
116
- posA: Number(l[1]),
117
- chrB: l[2],
118
- posB: Number(l[3])
119
- };
120
- } else {
121
- m = {
122
- dt: 2,
123
- chrA: l[0],
124
- posA: Number(l[1]),
125
- geneA: l[2],
126
- chrB: l[3],
127
- posB: Number(l[4]),
128
- geneB: l[5]
129
- };
130
- }
131
- } catch (e) {
132
- errors.push(e);
133
- continue;
134
- }
135
- mlst.push(m);
136
- }
137
- }
138
- function parseCnvText(text, mlst, errors) {
139
- for (const line of text.trim().split("\n")) {
140
- const l = line.trim().split(" ");
141
- if (l.length != 4) {
142
- errors.push("cnv input not equal to 4 columns");
143
- continue;
144
- }
145
- let m;
146
- try {
147
- m = {
148
- dt: 4,
149
- chr: l[0],
150
- start: Number(l[1]),
151
- stop: Number(l[2]),
152
- value: Number(l[3])
153
- };
154
- } catch (e) {
155
- errors.push(e);
156
- continue;
157
- }
158
- mlst.push(m);
159
- }
160
- }
161
- function validateMutation(mutation, errors) {
162
- const mut2check = mutation.toLowerCase();
163
- const foundMutation = Object.values(mclass).find(
164
- (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
165
- );
166
- if (foundMutation) {
167
- return foundMutation.key;
168
- } else {
169
- errors.push(`Invalid mutation class: ${mutation}`);
170
- }
171
- }
172
-
173
- export {
174
- launch
175
- };
176
- //# sourceMappingURL=chunk-2XH5T5HA.js.map
@@ -1,102 +0,0 @@
1
- import {
2
- addGeneSearchbox,
3
- first_genetrack_tolist,
4
- getDNAMethUnit,
5
- sayerror
6
- } from "./chunk-FIFNXVTS.js";
7
- import {
8
- Menu
9
- } from "./chunk-CNFTQSNE.js";
10
- import {
11
- DNA_METHYLATION
12
- } from "./chunk-EZFO5UYD.js";
13
-
14
- // termdb/handlers/dnaMethylation.ts
15
- var SearchHandler = class {
16
- init(opts) {
17
- this.opts = opts;
18
- this.callback = opts.callback;
19
- this.app = opts.app;
20
- const holder = opts.holder.append("div").style("margin", "10px 0px");
21
- this.dom = {};
22
- this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
23
- this.dom.geneSearchDiv = holder.append("div");
24
- this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
25
- const geneSearch = addGeneSearchbox({
26
- tip: new Menu({ padding: "0px" }),
27
- genome: opts.genomeObj,
28
- row: this.dom.geneSearchDiv,
29
- callback: async () => {
30
- try {
31
- this.dom.errDiv.style("display", "none");
32
- await this.handleGeneSearch(geneSearch);
33
- } catch (e) {
34
- this.dom.errDiv.style("display", "block");
35
- sayerror(this.dom.errDiv, "Error: " + (e.message || e));
36
- if (e.stack) console.log(e.stack);
37
- }
38
- }
39
- });
40
- }
41
- async handleGeneSearch(geneSearch) {
42
- if (geneSearch.geneSymbol) {
43
- const { chr, start, stop } = geneSearch;
44
- if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
45
- throw new Error("unable to retrieve gene coordinate");
46
- this.dom.blockDiv.selectAll("*").remove();
47
- this.dom.blockDiv.style("display", "block");
48
- this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
49
- const arg = {
50
- holder: this.dom.blockDiv,
51
- genome: this.opts.genomeObj,
52
- // genome obj
53
- chr,
54
- start,
55
- stop,
56
- tklst: [],
57
- nobox: true,
58
- width: 500,
59
- hidegenelegend: true,
60
- debugmode: this.opts.debug
61
- };
62
- first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
63
- const _ = await import("./block-NVXPY2IK.js");
64
- this.blockInstance = new _.Block(arg);
65
- this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
66
- const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
67
- const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
68
- await this.callback(term);
69
- });
70
- } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
71
- const { chr } = geneSearch;
72
- let { start, stop } = geneSearch;
73
- if (geneSearch.actualposition?.len <= 1) {
74
- start = geneSearch.actualposition.position;
75
- stop = start + 1;
76
- }
77
- const term = this.makeTerm({ chr, start, stop });
78
- await this.callback(term);
79
- } else {
80
- throw new Error("invalid gene search input");
81
- }
82
- }
83
- makeTerm(opts) {
84
- const { chr, start, stop } = opts;
85
- if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
86
- const unit = getDNAMethUnit("region", this.app.vocabApi);
87
- const term = {
88
- chr,
89
- start,
90
- stop,
91
- type: DNA_METHYLATION,
92
- unit,
93
- genomicFeatureType: "region"
94
- };
95
- return term;
96
- }
97
- };
98
-
99
- export {
100
- SearchHandler
101
- };
102
- //# sourceMappingURL=chunk-3Z7FX6GQ.js.map
@@ -1,14 +0,0 @@
1
- // src/block.lazyload.js
2
- var Block;
3
- async function blocklazyload(arg) {
4
- if (!Block) {
5
- const b = await import("./block-NVXPY2IK.js");
6
- Block = b.Block;
7
- }
8
- return new Block(arg);
9
- }
10
-
11
- export {
12
- blocklazyload
13
- };
14
- //# sourceMappingURL=chunk-42II4FNQ.js.map