@sjcrh/proteinpaint-client 2.219.1 → 2.221.0

package/dist/cellTypeBubbleHeatmap-RQINXXTK.js

@@ -1,274 +0,0 @@
-import {
-  LegendCircleReference,
-  PlotBase,
-  addGeneSearchbox
-} from "./chunk-BKW35Z4U.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-ETXOEP4N.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-5NI77Z3O.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-CJHNPYFQ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-NR6WFCPF.js";
-import "./chunk-GN2A5NL5.js";
-import "./chunk-ME3HB3V6.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  linear,
-  sqrt
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/cellTypeBubbleHeatmap.ts
-var defaultConfig = { chartType: "cellTypeBubbleHeatmap" };
-var CELL_W = 84;
-var CELL_H = 60;
-var ROW_LABEL_W = 74;
-var GROUP_LABEL_H = 22;
-var GENO_LABEL_H = 40;
-var COL_LABEL_H = GROUP_LABEL_H + GENO_LABEL_H;
-var MIN_DOT_R = 8;
-var MAX_DOT_R = 22;
-var NEG_LOG_FDR_CAP = 10;
-var COLOR_NEG = "#762a83";
-var COLOR_ZERO = "#f7f7f7";
-var COLOR_POS = "#2166ac";
-var CellTypeBubbleHeatmap = class _CellTypeBubbleHeatmap extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.currentIsoform = "";
-    this.type = _CellTypeBubbleHeatmap.type;
-  }
-  static {
-    this.type = "cellTypeBubbleHeatmap";
-  }
-  async init() {
-    const holder = this.opts.holder.append("div").style("padding", "10px");
-    this.dom = {
-      holder,
-      body: holder.append("div"),
-      tip: new Menu({ padding: "" }),
-      header: this.opts.header
-    };
-    if (this.dom.header) this.dom.header.html("Cell-type Bubble Heatmap");
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return { config };
-  }
-  async main() {
-    const gene = this.state.config?.gene;
-    if (!gene) throw new Error("cellTypeBubbleHeatmap: gene is missing");
-    if (this.dom.header) this.dom.header.text(`Cell-type Bubble Heatmap: ${gene}`);
-    const body = {
-      genome: this.app.opts.state.vocab.genome,
-      dslabel: this.app.opts.state.vocab.dslabel,
-      gene
-    };
-    const data = await dofetch3("termdb/cellTypeBubbleHeatmap", { body });
-    if (data.error) throw data.error;
-    this.data = data;
-    this.dom.body.selectAll("*").remove();
-    const isoformIds = Object.keys(data.isoforms);
-    if (isoformIds.length === 0) {
-      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text(`No data found for gene "${gene}" in any cohort DAPfile.`);
-      return;
-    }
-    this.currentIsoform = isoformIds[0];
-    const isoBlock = this.dom.body.append("div").style("margin-bottom", "12px");
-    isoBlock.append("span").style("font-weight", "bold").text("Isoform: ");
-    if (isoformIds.length > 1) {
-      const sel = isoBlock.append("select").style("margin-left", "5px").style("padding", "3px 6px").on("change", () => {
-        this.currentIsoform = sel.node().value;
-        this.renderGrid();
-      });
-      sel.selectAll("option").data(isoformIds).enter().append("option").attr("value", (d) => d).text((d) => `${data.isoforms[d].gene_name} \u2014 ${d}`);
-    } else {
-      isoBlock.append("span").style("margin-left", "5px").text(`${data.isoforms[this.currentIsoform].gene_name} \u2014 ${this.currentIsoform}`);
-    }
-    this.gridHolder = this.dom.body.append("div");
-    this.renderGrid();
-  }
-  renderGrid() {
-    const data = this.data;
-    const selectedIsoform = this.currentIsoform;
-    const threshold = data.fdrThreshold;
-    this.gridHolder.selectAll("*").remove();
-    const container = this.gridHolder.append("div").style("display", "flex").style("gap", "24px").style("align-items", "flex-start").style("flex-wrap", "wrap");
-    const isoformData = data.isoforms[selectedIsoform];
-    if (!isoformData) return;
-    const columns = data.columns;
-    const rows = data.rows;
-    const nCols = columns.length;
-    const nRows = rows.length;
-    const negLogFdr = (fdr) => fdr > 0 ? Math.min(-Math.log10(fdr), NEG_LOG_FDR_CAP) : NEG_LOG_FDR_CAP;
-    const cellOf = (colKey, rowKey) => isoformData.data[colKey]?.[rowKey];
-    let maxAbs = 0;
-    const thresholdNegLog = negLogFdr(threshold);
-    let maxNegLog = thresholdNegLog;
-    for (const col of columns) {
-      for (const row of rows) {
-        const s = cellOf(col.key, row.key);
-        if (!s) continue;
-        const v = Math.abs(s.log2FC);
-        if (v > maxAbs) maxAbs = v;
-        const nl = negLogFdr(s.fdr);
-        if (nl > maxNegLog) maxNegLog = nl;
-      }
-    }
-    if (maxAbs === 0) maxAbs = 1;
-    if (maxNegLog <= thresholdNegLog) maxNegLog = thresholdNegLog + 1;
-    const colorScale = linear().domain([-maxAbs, 0, maxAbs]).range([COLOR_NEG, COLOR_ZERO, COLOR_POS]).clamp(true);
-    const sizeScale = sqrt().domain([thresholdNegLog, maxNegLog]).range([MIN_DOT_R, MAX_DOT_R]).clamp(true);
-    const gridW = ROW_LABEL_W + nCols * CELL_W + 20;
-    const gridH = COL_LABEL_H + nRows * CELL_H + 20;
-    const svg = container.append("svg").attr("width", gridW).attr("height", gridH).style("flex", "0 0 auto");
-    const grid = svg.append("g");
-    let c = 0;
-    while (c < nCols) {
-      const cellType = columns[c].cellType;
-      let end = c;
-      while (end + 1 < nCols && columns[end + 1].cellType === cellType) end++;
-      const xStart = ROW_LABEL_W + c * CELL_W;
-      const xEnd = ROW_LABEL_W + (end + 1) * CELL_W;
-      const xMid = (xStart + xEnd) / 2;
-      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);
-      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);
-      c = end + 1;
-    }
-    for (let col = 0; col < nCols; col++) {
-      const cx = ROW_LABEL_W + col * CELL_W + CELL_W / 2;
-      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);
-    }
-    for (let r = 0; r < nRows; r++) {
-      const cy = COL_LABEL_H + r * CELL_H + CELL_H / 2;
-      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);
-    }
-    for (let r = 0; r < nRows; r++) {
-      for (let col = 0; col < nCols; col++) {
-        const x0 = ROW_LABEL_W + col * CELL_W;
-        const y0 = COL_LABEL_H + r * CELL_H;
-        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);
-        const s = cellOf(columns[col].key, rows[r].key);
-        if (!s) continue;
-        const cx = x0 + CELL_W / 2;
-        const cy = y0 + CELL_H / 2;
-        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(
-          "mouseover",
-          (event) => this.showCellTip(event, isoformData.gene_name, selectedIsoform, columns[col], rows[r], s)
-        ).on("mouseout", () => this.dom.tip.hide());
-      }
-    }
-    this.renderLegend(container, colorScale, maxAbs, threshold, maxNegLog);
-  }
-  fmtFdr(v) {
-    return v >= 1e-4 ? v.toFixed(4) : v.toExponential(2);
-  }
-  showCellTip(event, geneName, isoform, col, row, s) {
-    this.dom.tip.clear().show(event.clientX, event.clientY);
-    const t = this.dom.tip.d.append("div").style("padding", "8px").style("font-size", "13px");
-    t.append("div").style("font-weight", "bold").style("margin-bottom", "4px").text(`${geneName} \u2014 ${isoform}`);
-    t.append("div").text(`Cell type: ${col.cellType}`);
-    t.append("div").text(`Genotype: ${col.genotype}`);
-    t.append("div").text(`Timepoint: ${row.label}`);
-    t.append("div").text(`Protein: ${s.id}`);
-    t.append("div").text(`log\u2082FC: ${s.log2FC.toFixed(3)}`);
-    t.append("div").text(`FDR: ${this.fmtFdr(s.fdr)}${s.significant ? "" : " (n.s.)"}`);
-    t.append("div").style("color", "#666").style("margin-top", "4px").text("Color = log\u2082FC (blue up / purple down). Size = \u2212log\u2081\u2080 FDR.");
-  }
-  renderLegend(container, colorScale, maxAbs, threshold, maxNegLog) {
-    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");
-    const colorBlock = legend.append("div");
-    colorBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("log\u2082FC");
-    const cW = 22;
-    const cH = 130;
-    const cSvg = colorBlock.append("svg").attr("width", cW + 80).attr("height", cH + 16);
-    const gid = `ctbh-grad-${this.id}`;
-    const grad = cSvg.append("defs").append("linearGradient").attr("id", gid).attr("x1", "0").attr("y1", "0").attr("x2", "0").attr("y2", "1");
-    const steps = 10;
-    for (let i = 0; i <= steps; i++) {
-      const t = i / steps;
-      grad.append("stop").attr("offset", `${t * 100}%`).attr("stop-color", colorScale(maxAbs * (1 - 2 * t)));
-    }
-    cSvg.append("rect").attr("x", 0).attr("y", 8).attr("width", cW).attr("height", cH).style("fill", `url(#${gid})`).attr("stroke", "#999");
-    const cScale = linear().domain([maxAbs, -maxAbs]).range([8, cH + 8]);
-    for (const tick of [maxAbs, maxAbs / 2, 0, -maxAbs / 2, -maxAbs]) {
-      const y = cScale(tick);
-      cSvg.append("line").attr("x1", cW).attr("y1", y).attr("x2", cW + 5).attr("y2", y).attr("stroke", "#666");
-      cSvg.append("text").attr("x", cW + 8).attr("y", y).attr("dominant-baseline", "central").attr("font-size", "10px").text(`${tick > 0 ? "+" : ""}${tick.toFixed(2)}`);
-    }
-    colorBlock.append("div").style("font-size", "11px").style("color", "#666").style("margin-top", "2px").text("blue = up (+), purple = down (\u2212)");
-    const sizeBlock = legend.append("div");
-    sizeBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("Dot size: significance (\u2212log\u2081\u2080 FDR)");
-    const sSvg = sizeBlock.append("svg");
-    const sG = sSvg.append("g");
-    new LegendCircleReference({
-      g: sG,
-      inputMin: 0,
-      inputMax: MAX_DOT_R * 2,
-      minRadius: MIN_DOT_R,
-      maxRadius: MAX_DOT_R,
-      minLabel: Number(Math.min(-Math.log10(threshold), NEG_LOG_FDR_CAP).toFixed(1)),
-      maxLabel: Number(maxNegLog.toFixed(1))
-    });
-    const sPad = 4;
-    const sBox = sG.node().getBBox();
-    sG.attr("transform", `translate(${sPad - sBox.x}, ${sPad - sBox.y})`);
-    sSvg.attr("width", Math.ceil(sBox.width + 2 * sPad)).attr("height", Math.ceil(sBox.height + 2 * sPad));
-    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");
-    notes.append("div").text(
-      `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.`
-    );
-    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.");
-  }
-};
-var componentInit = getCompInit(CellTypeBubbleHeatmap);
-async function getPlotConfig(opts) {
-  const config = structuredClone(defaultConfig);
-  if (!opts.gene) throw new Error("cellTypeBubbleHeatmap requires opts.gene");
-  return copyMerge(config, opts);
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  const row = holder.append("div").style("padding", "5px");
-  row.append("span").style("font-weight", "bold").text("Enter a gene name:");
-  const geneSearch = addGeneSearchbox({
-    row,
-    genome: chartsInstance.app.opts.genome,
-    tip: new Menu({ padding: "0px" }),
-    searchOnly: "gene",
-    callback: async () => {
-      if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
-      chartsInstance.dom.tip.hide();
-      chartsInstance.app.dispatch({
-        type: "plot_create",
-        config: {
-          chartType: "cellTypeBubbleHeatmap",
-          gene: geneSearch.geneSymbol
-        }
-      });
-    }
-  });
-}
-export {
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=cellTypeBubbleHeatmap-RQINXXTK.js.map

package/dist/chunk-24ZS2XWC.js

@@ -1,176 +0,0 @@
-import {
-  appInit
-} from "./chunk-MVSUESEV.js";
-import {
-  showErrorsWithCounter
-} from "./chunk-BKW35Z4U.js";
-import {
-  mclass
-} from "./chunk-ME3HB3V6.js";
-
-// plots/disco/launch.adhoc.ts
-async function launch(arg, genomeObj, holder) {
-  const [mlst, errors] = await getMlst(arg);
-  if (errors?.length) {
-    return showErrorsWithCounter(errors, holder);
-  }
-  const opts = {
-    holder,
-    vocabApi: {
-      // api is required by plot.app.js, so create a mock one for the adhoc data
-      vocab: { terms: [] },
-      main: () => {
-        return;
-      },
-      getTermdbConfig: () => {
-        return {};
-      }
-    },
-    state: {
-      args: {
-        data: mlst,
-        genome: genomeObj
-      },
-      plots: [
-        {
-          chartType: "Disco",
-          subfolder: "disco",
-          extension: "ts",
-          /** NOTE: Users should only override the settings in the default
-           * settings.Disco:{}, not the entire settings:{} object.*/
-          overrides: { Disco: arg?.settings || {} }
-        }
-      ]
-    }
-  };
-  const plotAppApi = await appInit(opts);
-  return plotAppApi;
-}
-async function getMlst(arg) {
-  if (Array.isArray(arg.mlst)) {
-    return [arg.mlst, null];
-  }
-  const mlst = [];
-  const errors = [];
-  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
-  if (arg.svText) parseSvText(arg.svText, mlst, errors);
-  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
-  return [mlst, errors];
-}
-function parseSnvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (![5, 7, 9].includes(l.length)) {
-      errors.push("snv input not equal to 5, 7, or 9 columns");
-      continue;
-    }
-    let m;
-    try {
-      m = {
-        dt: 1,
-        chr: l[0],
-        position: Number(l[1]),
-        gene: l[2],
-        mname: l[3],
-        class: validateMutation(l[4], errors)
-      };
-      const vafs = parseOptionalVafs(l, errors);
-      if (vafs.length) m.vafs = vafs;
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function parseOptionalVafs(line, errors) {
-  const vafs = [];
-  const addVaf = (id, totalIndex, altIndex) => {
-    if (line.length <= altIndex) return;
-    const totalCount = Number(line[totalIndex]);
-    const altCount = Number(line[altIndex]);
-    if (!Number.isInteger(totalCount) || !Number.isInteger(altCount) || totalCount <= 0 || altCount < 0 || altCount > totalCount) {
-      errors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`);
-      return;
-    }
-    vafs.push({ id, totalCount, altCount });
-  };
-  addVaf("DNA", 5, 6);
-  addVaf("RNA", 7, 8);
-  return vafs;
-}
-function parseSvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (l.length < 4 || l.length > 6) {
-      errors.push("sv input not equal to 4 or 6 columns");
-      continue;
-    }
-    let m;
-    try {
-      const length = l.length;
-      if (length == 4) {
-        m = {
-          dt: 2,
-          chrA: l[0],
-          posA: Number(l[1]),
-          chrB: l[2],
-          posB: Number(l[3])
-        };
-      } else {
-        m = {
-          dt: 2,
-          chrA: l[0],
-          posA: Number(l[1]),
-          geneA: l[2],
-          chrB: l[3],
-          posB: Number(l[4]),
-          geneB: l[5]
-        };
-      }
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function parseCnvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (l.length != 4) {
-      errors.push("cnv input not equal to 4 columns");
-      continue;
-    }
-    let m;
-    try {
-      m = {
-        dt: 4,
-        chr: l[0],
-        start: Number(l[1]),
-        stop: Number(l[2]),
-        value: Number(l[3])
-      };
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function validateMutation(mutation, errors) {
-  const mut2check = mutation.toLowerCase();
-  const foundMutation = Object.values(mclass).find(
-    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
-  );
-  if (foundMutation) {
-    return foundMutation.key;
-  } else {
-    errors.push(`Invalid mutation class: ${mutation}`);
-  }
-}
-
-export {
-  launch
-};
-//# sourceMappingURL=chunk-24ZS2XWC.js.map