@sjcrh/proteinpaint-client 2.224.2 → 2.225.0

package/dist/cohort-2DQOQ5AO.js

@@ -1,66 +0,0 @@
-import {
-  appInit,
-  vocabInit
-} from "./chunk-ZIMAIUZD.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-AQSZLUDV.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-BOQYGAYA.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-ZUXXBQ7D.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-ZUG4EY4T.js";
-import "./chunk-5FD6NRGE.js";
-import {
-  TermTypes
-} from "./chunk-R2H22S4J.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// termdb/handlers/cohort.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const cohorts = this.app.vocabApi.app?.opts?.opts?.cohorts0;
-    if (!cohorts?.length) return;
-    const terms = cohorts.map((cohort) => {
-      const term = {
-        id: cohort.id,
-        name: cohort.name,
-        type: TermTypes.COHORT,
-        filter0: cohort.filter,
-        isleaf: true,
-        parent_id: null
-      };
-      return term;
-    });
-    const vocabApi = vocabInit({ vocab: { terms } });
-    appInit({
-      holder,
-      vocabApi,
-      state: {
-        nav: { header_mode: "hide_search" }
-      },
-      tree: {
-        click_term: (term) => {
-          this.callback(term);
-        }
-      }
-    });
-  }
-};
-export {
-  SearchHandler
-};
-//# sourceMappingURL=cohort-2DQOQ5AO.js.map

package/dist/cohortSunburst-W6XC7VD6.js

@@ -1,402 +0,0 @@
-import {
-  LINK,
-  RULE,
-  SIZE,
-  SunburstRenderer,
-  TEXT_DARK,
-  TEXT_MUTED,
-  WARN,
-  badge,
-  card,
-  icon,
-  pill
-} from "./chunk-T2DORAV4.js";
-import {
-  catalogRowKey,
-  cohortMatches,
-  deriveCatalogRows
-} from "./chunk-ZX75ZAUG.js";
-import {
-  PlotBase
-} from "./chunk-ZIMAIUZD.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-AQSZLUDV.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-BOQYGAYA.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-ZUXXBQ7D.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-ZUG4EY4T.js";
-import "./chunk-5FD6NRGE.js";
-import "./chunk-R2H22S4J.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/cohortSunburst.ts
-var defaultConfig = { chartType: "cohortSunburst" };
-var CohortSunburst = class _CohortSunburst extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    /** selected cohorts by key, in selection order */
-    this.selected = /* @__PURE__ */ new Map();
-    /** leaf node of each cohort by key, for its hue and ring label */
-    this.leafNode = /* @__PURE__ */ new Map();
-    this.type = _CohortSunburst.type;
-  }
-  static {
-    this.type = "cohortSunburst";
-  }
-  async init() {
-    const holder = this.opts.holder.append("div").style("padding", "10px").style("white-space", "normal");
-    const body = holder.append("div");
-    this.dom = {
-      holder,
-      body,
-      sel: void 0,
-      selectAll: void 0,
-      header: this.opts.header
-    };
-    if (this.dom.header) this.dom.header.html("Explore cohorts");
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return { config };
-  }
-  async main() {
-    const proteome = this.app.vocabApi.termdbConfig?.queries?.proteome;
-    const ui = proteome?.cohortSunburst;
-    this.dom.body.selectAll("*").remove();
-    this.renderer?.destroy();
-    if (!ui?.levels?.length || !proteome?.organisms) {
-      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text("No cohort sunburst is configured.");
-      return;
-    }
-    this.ui = ui;
-    const tree = buildTree(deriveCatalogRows(proteome.organisms), ui);
-    this.renderer = new SunburstRenderer({
-      holder: this.dom.body,
-      unit: { one: "sample set", many: "sample sets" },
-      rootName: "All sample sets",
-      rootPathTitle: `${ui.levels[0]?.name || ""} selection`.trim(),
-      colors: ui.colors,
-      statLabels: (ui.stats || []).map((s) => s.label),
-      hooks: {
-        onClick: (d) => this.onWedgeClick(d),
-        isSelected: (d) => this.isSelected(d),
-        isDimmed: (d) => this.selectedKind() !== void 0 && !leavesOf(d.data).some((l) => this.compatible(l.cohort)),
-        cursor: (d) => d.dim && this.terminalLeaf(d) ? "not-allowed" : "pointer",
-        tooltip: (d, box) => this.tooltip(d, box),
-        onFocus: () => {
-          this.renderStats();
-          this.renderToolbar();
-          this.renderSidebar();
-        }
-      }
-    });
-    this.dom.selectAll = this.renderer.addControl().on("click", () => this.toggleSelectAll());
-    this.dom.sel = card(this.renderer.dom.right, "Selected sample sets");
-    this.renderer.setTree(tree);
-    this.leafNode = new Map(this.renderer.root.leaves().map((l) => [cohortKey(l.data.cohort), l]));
-    this.renderSidebar();
-  }
-  /** selection strokes on the wedges plus the selection panel; no geometry changes */
-  refreshSelection() {
-    this.renderer.refresh();
-    this.renderToolbar();
-    this.renderSidebar();
-  }
-  /************ selection kind ************/
-  kindKeys() {
-    return this.ui?.selectionKind?.keys || [];
-  }
-  /** the kind of the current selection; undefined when nothing is selected */
-  selectedKind() {
-    const first = this.selected.values().next();
-    return first.done ? void 0 : kindOf(first.value, this.kindKeys());
-  }
-  /** whether a cohort could be added to the current selection */
-  compatible(r) {
-    const kind = this.selectedKind();
-    return kind === void 0 || kindOf(r, this.kindKeys()) === kind;
-  }
-  /** stat boxes for the sample sets under the centre */
-  renderStats() {
-    const leaves = leavesOf(this.renderer.focus.data);
-    const values = /* @__PURE__ */ new Map();
-    for (const def of this.ui.stats || []) values.set(def.label, computeStat(leaves, def));
-    const keyOf = new Map((this.ui.stats || []).map((def) => [def.label, def.key || ""]));
-    this.renderer.setStats(values, (label) => `No ${keyOf.get(label)} counts in the dataset yet`);
-  }
-  /** the sample sets Select all would take under the centre: those of the selected kind,
-   *  or, with nothing selected, of the largest kind there; and whether all are selected */
-  underFocus() {
-    const leaves = leavesOf(this.renderer.focus.data);
-    const keys = this.kindKeys();
-    const kind = this.selectedKind() ?? largestKind(leaves, keys);
-    const under = leaves.filter((l) => kindOf(l.cohort, keys) === kind);
-    const allIn = under.length > 0 && under.every((l) => this.selected.has(cohortKey(l.cohort)));
-    return { under, allIn, kind };
-  }
-  toggleSelectAll() {
-    const { under, allIn } = this.underFocus();
-    if (!under.length) return;
-    for (const l of under) {
-      if (allIn) this.selected.delete(cohortKey(l.cohort));
-      else this.selected.set(cohortKey(l.cohort), l.cohort);
-    }
-    this.refreshSelection();
-  }
-  /** select all follows the centre and flips to deselect once everything under it is selected */
-  renderToolbar() {
-    const { under, allIn, kind } = this.underFocus();
-    const what = kind ? `${kind} sample sets` : "sample sets";
-    const none = !under.length;
-    this.dom.selectAll.style("opacity", none ? 0.35 : 1).style("cursor", none ? "default" : "pointer").attr(
-      "title",
-      none ? `No ${what} under the centre; clear the selection to pick other kinds` : allIn ? `Deselect every ${what.replace(/s$/, "")} under the centre` : `Select every ${what.replace(/s$/, "")} under the centre`
-    ).html(
-      allIn ? `${icon('<circle cx="12" cy="12" r="9"/><path d="M8 12h8"/>')}DESELECT ALL` : `${icon('<circle cx="12" cy="12" r="9"/><path d="M12 8v8M8 12h8"/>')}SELECT ALL ${under.length}${kind ? ` \xB7 ${kind.toUpperCase()}` : ""}`
-    );
-  }
-  /** the selected-sample-sets card: count in the head, one line per set with its hue
-   *  badge, and the analyze/compare action as the footer */
-  renderSidebar() {
-    const { title, headRight, body } = this.dom.sel;
-    headRight.selectAll("*").remove();
-    body.selectAll("*").remove();
-    headRight.style("margin-bottom", "8px");
-    const n = this.selected.size;
-    title.text(n ? "Selected sample sets" : "No sample sets selected");
-    if (n) {
-      pill(headRight).text(n);
-      headRight.append("span").style("font-size", "11px").style("color", LINK).style("cursor", "pointer").text("Clear").on("click", () => {
-        this.selected.clear();
-        this.refreshSelection();
-      });
-    }
-    const kind = this.selectedKind();
-    if (kind) {
-      body.append("div").style("font-size", "0.75em").style("color", TEXT_MUTED).style("margin-bottom", "4px").text(`${kind} only \xB7 clear the selection to pick another kind`);
-    }
-    const list = body.append("div").style("max-height", `${SIZE - 200}px`).style("overflow-y", "auto");
-    if (!n) {
-      list.append("div").style("font-size", "0.85em").style("color", TEXT_MUTED).style("padding", "4px 0").text("Click a sample-set wedge, or Select all above the chart.");
-    }
-    for (const [k, r] of this.selected) {
-      const leaf = this.leafNode.get(k);
-      const line = list.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("padding", "3px 6px").style("margin", "2px 0").style("border-radius", "6px").on("mouseenter", (event) => {
-        select_default(event.currentTarget).style("background", "#f3f4f6").select(".sjpp-sunburst-remove").style("opacity", 1);
-      }).on("mouseleave", (event) => {
-        select_default(event.currentTarget).style("background", "transparent").select(".sjpp-sunburst-remove").style("opacity", 0);
-      });
-      badge(line, leaf?.data.name || r.cohort, leaf ? this.renderer.hue(leaf) : "#9ca3af", 24);
-      const text = line.append("div").style("flex", "1 1 auto").style("min-width", "0").style("line-height", "1.2");
-      text.append("div").style("font-size", "0.9em").style("color", TEXT_DARK).style("overflow", "hidden").style("text-overflow", "ellipsis").style("white-space", "nowrap").text(this.selectionLabel(r));
-      text.append("div").style("font-size", "0.7em").style("color", "#6b7280").text(r.proteome + (r.placeholder ? " \xB7 placeholder data" : ""));
-      line.append("span").attr("class", "sjpp-sunburst-remove").style("opacity", 0).style("cursor", "pointer").style("color", "#9ca3af").style("font-size", "0.85em").attr("title", "Remove").text("\u2715").on("click", () => {
-        this.selected.delete(k);
-        this.refreshSelection();
-      });
-    }
-    const types = new Set([...this.selected.values()].map((r) => r.dataType));
-    if (types.size > 1) {
-      body.append("div").style("font-size", "0.8em").style("color", WARN).style("margin-top", "6px").text("Selection mixes PTM (site-level) and protein-level assays; their log2FC-z are not directly comparable.");
-    }
-    const footer = body.append("div").style("margin-top", "10px").style("padding-top", "10px").style("border-top", `1px solid ${RULE}`);
-    pill(footer, { button: true }).property("disabled", n === 0).style("opacity", n ? 1 : 0.3).style("cursor", n ? "pointer" : "default").text(n >= 2 ? `Compare ${n} cohorts` : "Analyze cohort").on("click", () => this.onAction());
-  }
-  /************ interaction ************/
-  /** the single sample set a wedge stands for: the leaf itself, or the only leaf beneath an
-   *  inner wedge (e.g. a human assay wedge with one cohort), so it can be selected without
-   *  zooming down to a lone full-circle wedge */
-  terminalLeaf(d) {
-    if (d.data.cohort) return d.data.cohort;
-    if (d.value !== 1) return void 0;
-    return leavesOf(d.data)[0].cohort;
-  }
-  isSelected(d) {
-    const r = this.terminalLeaf(d);
-    return !!r && this.selected.has(cohortKey(r));
-  }
-  onWedgeClick(d) {
-    const r = this.terminalLeaf(d);
-    if (r) {
-      if (!this.compatible(r)) return;
-      const k = cohortKey(r);
-      if (this.selected.has(k)) this.selected.delete(k);
-      else this.selected.set(k, r);
-      this.refreshSelection();
-    } else this.renderer.zoomTo(d);
-  }
-  tooltip(d, box) {
-    const r = this.terminalLeaf(d);
-    const stat = (label, value) => {
-      const line = box.append("div").style("color", "#374151");
-      line.append("span").text(`${label}: `);
-      line.append("b").text(String(value));
-    };
-    const note = (text, color) => box.append("div").style("margin-top", "4px").style("color", color).text(text);
-    const kind = this.selectedKind();
-    if (r) {
-      box.append("div").style("color", "#6b7280").text(`${r.species} \xB7 ${r.proteome} \xB7 ${r.cohort}`);
-      if (r.placeholder) box.append("div").style("color", WARN).text("placeholder data");
-      if (!this.compatible(r))
-        note(`Clear the ${kind} selection to select a ${kindOf(r, this.kindKeys())} sample set`, WARN);
-      else note(this.selected.has(cohortKey(r)) ? "click to deselect" : "click to select", LINK);
-    } else {
-      box.append("div").style("color", "#6b7280").text(d.data.level);
-      stat("Sample sets", d.value);
-      if (d.dim) note(`No ${kind} sample sets here; clear the selection to pick from these`, WARN);
-      note("click to zoom in", LINK);
-    }
-  }
-  /** label for the selection list / compare plot; adds the assay when several are selected */
-  selectionLabel(r) {
-    const species = r.species;
-    const leaf = this.leafNode.get(cohortKey(r));
-    const base = `${species} ${leaf?.data.name || r.cohort}`;
-    const assays = new Set([...this.selected.values()].map((x) => x.proteome));
-    return assays.size > 1 ? `${base} (${r.proteome})` : base;
-  }
-  onAction() {
-    const sel = [...this.selected.values()];
-    if (sel.length === 1) {
-      const c = sel[0];
-      this.app.dispatch({
-        type: "plot_create",
-        config: {
-          chartType: "ProteomeInput",
-          proteomeDetails: { organism: c.organism, assay: c.assay, cohort: c.cohort },
-          hidePlotFilter: true
-        }
-      });
-    } else if (sel.length >= 2) {
-      this.app.dispatch({
-        type: "plot_create",
-        config: {
-          chartType: "proteomeCohortCompare",
-          cohorts: sel.map((c) => ({
-            organism: c.organism,
-            assay: c.assay,
-            cohort: c.cohort,
-            label: this.selectionLabel(c)
-          }))
-        }
-      });
-    }
-  }
-  destroy() {
-    this.renderer?.destroy();
-  }
-};
-function levelValue(row, level) {
-  for (const v of level.values) {
-    if (v.when && !cohortMatches(v.when, row.organism, row.assay, row)) continue;
-    if (v.const) return v.const;
-    if (v.key && row[v.key]) return String(row[v.key]);
-  }
-  return "";
-}
-function leafLabel(row, cfg) {
-  const pick = (keys) => keys.map((k) => row[k]).filter(Boolean).map(String);
-  const a = pick(cfg.keys);
-  if (a.length) return a.join(" ");
-  const b = pick(cfg.fallbackKeys || []);
-  return b.length ? b.join(" ") : row.cohort;
-}
-function buildTree(rows, ui, rootName = "All sample sets") {
-  const root = { name: rootName, children: [] };
-  for (const r of rows) {
-    let node = root;
-    for (const level of ui.levels) {
-      const v = levelValue(r, level);
-      if (!v) continue;
-      if (!node.children) node.children = [];
-      let child = node.children.find((c) => c.name === v && c.level === level.name);
-      if (!child) {
-        child = { name: v, level: level.name, children: [] };
-        node.children.push(child);
-      }
-      node = child;
-    }
-    if (!node.children) node.children = [];
-    node.children.push({ name: leafLabel(r, ui.leafLabel), cohort: r, value: 1 });
-  }
-  disambiguateLeaves(root);
-  return root;
-}
-function disambiguateLeaves(node) {
-  const leaves = (node.children || []).filter((c) => c.cohort);
-  const seen = /* @__PURE__ */ new Map();
-  for (const l of leaves) seen.set(l.name, (seen.get(l.name) || 0) + 1);
-  for (const l of leaves) if (seen.get(l.name) > 1) l.name = `${l.name} (${l.cohort.cohort})`;
-  for (const c of node.children || []) if (!c.cohort) disambiguateLeaves(c);
-}
-function leavesOf(n) {
-  if (n.cohort) return [n];
-  const out = [];
-  for (const c of n.children || []) out.push(...leavesOf(c));
-  return out;
-}
-var cohortKey = (r) => catalogRowKey(r.organism, r.assay, r.cohort);
-function kindOf(r, keys = []) {
-  return keys.map((k) => r[k]).filter(Boolean).map(String).join(" ");
-}
-function largestKind(leaves, keys = []) {
-  const counts = /* @__PURE__ */ new Map();
-  for (const l of leaves) {
-    const k = kindOf(l.cohort, keys);
-    counts.set(k, (counts.get(k) || 0) + 1);
-  }
-  let best = "";
-  let bestN = 0;
-  for (const [k, n] of counts) {
-    if (n > bestN) {
-      best = k;
-      bestN = n;
-    }
-  }
-  return best;
-}
-function computeStat(leaves, def) {
-  const rows = leaves.map((l) => l.cohort).filter((r) => !def.where || cohortMatches(def.where, r.organism, r.assay, r));
-  if (def.kind === "count") return rows.length;
-  if (def.kind === "distinct") {
-    const vals = new Set(rows.map((r) => r[def.key || ""]).filter((v) => v !== void 0 && v !== null && v !== ""));
-    return vals.size;
-  }
-  let total = 0;
-  let seen = false;
-  for (const r of rows) {
-    const v = Number(r[def.key || ""]);
-    if (!Number.isFinite(v) || r[def.key || ""] === void 0 || r[def.key || ""] === "") continue;
-    total += v;
-    seen = true;
-  }
-  return seen ? total : null;
-}
-var componentInit = getCompInit(CohortSunburst);
-async function getPlotConfig(opts) {
-  const config = structuredClone(defaultConfig);
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=cohortSunburst-W6XC7VD6.js.map