@sjcrh/proteinpaint-client 2.211.0 → 2.212.0

package/dist/chunk-QWCKIRW2.js

@@ -0,0 +1,237 @@
+import {
+  DataPointInteractions,
+  axisstyle,
+  createLollipopFromGene,
+  drawHoverShapes,
+  showResultsTable,
+  table2col,
+  to_svg
+} from "./chunk-VHDYIOWU.js";
+import {
+  Menu
+} from "./chunk-7XZA2XR2.js";
+import {
+  icons
+} from "./chunk-6RRZRISL.js";
+import {
+  axisLeft
+} from "./chunk-Z2ZITHT4.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/manhattan/manhattan.ts
+var manhattanLayoutDefaults = {
+  plotWidth: 1e3,
+  plotHeight: 400,
+  pngDotRadius: 2,
+  yAxisX: 70,
+  yAxisY: 40,
+  yAxisSpace: 20,
+  xAxisLabelPad: 30,
+  yAxisPad: 5,
+  axisColor: "#545454",
+  showYAxisLine: true,
+  fontSize: 12,
+  showLegend: true,
+  legendItemWidth: 80,
+  legendDotRadius: 3,
+  legendRightOffset: 15,
+  legendTextOffset: 12,
+  legendVerticalOffset: 4,
+  legendFontSize: 12,
+  showInteractiveDots: true,
+  interactiveDotRadius: 2,
+  interactiveDotStrokeWidth: 1,
+  showDownload: true,
+  interactiveDotsCap: 5e3,
+  maxTooltipGenes: 5
+};
+function plotManhattan(div, data, settings, app, custom = {}) {
+  const handle = { points: [], highlight: () => {
+  } };
+  settings = {
+    ...settings
+  };
+  let interactivePoints = data.plotData.points;
+  if (data.plotData.points.length > settings.interactiveDotsCap) {
+    interactivePoints = data.plotData.points.sort((a, b) => Math.abs(b.y) - Math.abs(a.y)).slice(0, settings.interactiveDotsCap);
+  }
+  const signed = data.plotData.y_min < 0;
+  div.style("position", "relative");
+  const geneTip = new Menu({ padding: "" });
+  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
+  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
+  const yPad = data.plotData.y_pad ?? settings.pngDotRadius;
+  const yAxisLow = signed ? data.plotData.y_min + yPad : 0;
+  const yAxisScale = linear().domain([yAxisLow, data.plotData.y_max - yPad]).range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)]);
+  const axisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`);
+  axisG.call(
+    axisLeft(yAxisScale).tickSizeOuter(0)
+    // removes top/bottom cap lines for clean look
+  );
+  axisstyle({
+    axis: axisG,
+    color: settings.axisColor,
+    fontsize: settings.fontSize + 2,
+    showline: settings.showYAxisLine
+  });
+  svg.append("text").attr("x", -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text((custom.yAxisLabel ?? "-log\u2081\u2080(q-value)") + (data.plotData.has_capped_points ? " [capped]" : ""));
+  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", settings.plotWidth + 2 * settings.pngDotRadius).attr("height", settings.plotHeight + 2 * settings.pngDotRadius).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
+  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
+  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
+    const hoverLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
+    const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
+    const circlePath = (r) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`;
+    const linkedLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
+    handle.points = interactivePoints;
+    handle.highlight = (dots) => drawHoverShapes(
+      linkedLayer,
+      dots.map((d) => ({
+        path: circlePath(settings.pngDotRadius + 2),
+        transform: `translate(${d.pixel_x},${d.pixel_y})`,
+        stroke: "black",
+        strokeWidth: 2
+      }))
+    );
+    const grin2Hover = (d, container) => {
+      const table = table2col({ holder: container.append("div"), margin: "10px" });
+      table.addRow("Gene", d.gene);
+      table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
+      const [t1, t2] = table.addRow();
+      t1.text("Type");
+      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
+      table.addRow("Q-value", d.q_value.toPrecision(3));
+      table.addRow("Subject count", d.nsubj);
+    };
+    const grin2Table = (dots) => ({
+      columns: [
+        { label: "Gene" },
+        { label: "Position" },
+        { label: "Type" },
+        { label: "Q-value", sortable: true },
+        { label: "Subject count", sortable: true }
+      ],
+      rows: dots.map((d) => [
+        { value: d.gene },
+        { value: `${d.chrom}:${d.start}-${d.end}` },
+        {
+          html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`
+        },
+        { value: d.q_value.toPrecision(3) },
+        { value: d.nsubj }
+      ])
+    });
+    const interactions = new DataPointInteractions({
+      cover,
+      hoverLayer,
+      hoverTip: geneTip,
+      points: interactivePoints,
+      getX: (d) => d.pixel_x,
+      getY: (d) => d.pixel_y,
+      hitRadius: settings.pngDotRadius + 3,
+      toHoverSpec: (d) => ({
+        path: circlePath(settings.pngDotRadius),
+        transform: `translate(${d.pixel_x},${d.pixel_y})`,
+        fill: "none",
+        stroke: "black",
+        strokeWidth: settings.interactiveDotStrokeWidth
+      }),
+      maxTooltipRows: settings.maxTooltipGenes,
+      onHover: custom.onHover,
+      itemNoun: custom.itemNoun ?? "gene",
+      renderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,
+      buildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,
+      // A caller with actions gets the module's standard click flow: an action menu for one
+      // dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.
+      ...custom.getActions ? {
+        getActions: custom.getActions,
+        renderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,
+        getRowKey: custom.getRowKey
+      } : {
+        // Manhattan single-click goes straight to a lollipop launch — no menu.
+        // Release hover-suppression immediately so the cursor's next move re-engages.
+        onSingleClick: (d, _event, ctx) => {
+          ctx.dismiss();
+          if (app && d.gene) createLollipopFromGene(d.gene, app);
+        },
+        // Manhattan multi-click shows showResultsTable directly with `app + clickMenu`
+        // so the table renders inline Matrix/Lollipop buttons. Reuses the module's
+        // clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.
+        // Content is built BEFORE show2 so Menu can measure the populated rect for
+        // its right-edge clamp — otherwise the wide table is placed at cursor+offsetX
+        // and extends off the right edge of the viewport.
+        onMultiClick: (dots, event, ctx) => {
+          if (!app) {
+            ctx.dismiss();
+            return;
+          }
+          ctx.clickMenu.clear();
+          const holder = ctx.clickMenu.d.append("div").style("margin", "10px");
+          showResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu });
+          ctx.clickMenu.show2(event.clientX, event.clientY);
+        }
+      }
+    });
+    interactions.attach();
+  }
+  if (data.plotData.chrom_data) {
+    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
+    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
+      const chromLabel = chrom.replace("chr", "");
+      if (chromLabel === "M") return;
+      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
+      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 2}px`).text(chromLabel);
+    });
+  }
+  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2).attr("y", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text("Chromosomes");
+  const title = svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).text(custom.title ?? "Manhattan Plot");
+  const titleWidth = title.node().getBBox?.().width || 100;
+  if (settings.showDownload) {
+    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + titleWidth + 8}px`);
+    icons["download"](downloadDiv, {
+      width: 16,
+      height: 16,
+      title: "Download Manhattan plot",
+      handler: () => {
+        const svgNode = svg.node();
+        const clone = svgNode.cloneNode(true);
+        const bbox = svgNode.getBBox();
+        clone.setAttribute("width", bbox.width.toString());
+        clone.setAttribute("height", bbox.height.toString());
+        clone.setAttribute("viewBox", `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`);
+        to_svg(clone, `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`, {
+          apply_dom_styles: true
+        });
+      }
+    });
+  }
+  const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type).filter(Boolean))];
+  const legendData = custom.legend?.map((l) => ({ type: l.label, color: l.color, hollow: l.hollow })) ?? mutationTypes.map((type) => {
+    const point = data.plotData.points.find((p) => p.type === type);
+    return {
+      type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
+      color: point?.color
+    };
+  });
+  if (settings.showLegend && legendData.length > 0) {
+    const legendY = settings.yAxisY / 2;
+    const totalWidth = legendData.length * settings.legendItemWidth;
+    const legendX = settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) - totalWidth - settings.legendRightOffset;
+    legendData.forEach((item, i) => {
+      const x = legendX + i * settings.legendItemWidth;
+      svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.hollow ? "none" : item.color).attr("stroke", item.hollow ? item.color : "none");
+      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize + 2}px`).text(item.type);
+    });
+  }
+  return handle;
+}
+
+export {
+  manhattanLayoutDefaults,
+  plotManhattan
+};
+//# sourceMappingURL=chunk-QWCKIRW2.js.map

package/dist/chunk-R3LWGFGS.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox
+} from "./chunk-VHDYIOWU.js";
+import {
+  Menu
+} from "./chunk-7XZA2XR2.js";
+
+// termdb/handlers/snp.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: opts.holder,
+      searchOnly: "snp",
+      allowVariant: true,
+      callback: () => this.selectSnp(geneSearch)
+    });
+  }
+  async selectSnp(geneSearch) {
+    const { chr, ref, alt, fromWhat } = geneSearch;
+    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
+    let start, stop;
+    if (!geneSearch.start && !geneSearch.stop) {
+      if (geneSearch.pos) {
+        start = geneSearch.pos - 1;
+        stop = geneSearch.pos;
+      } else {
+        throw "missing coordinate of snp";
+      }
+    } else {
+      start = geneSearch.start;
+      stop = geneSearch.stop;
+    }
+    const term = {
+      id: fromWhat,
+      chr,
+      start,
+      stop,
+      name: fromWhat,
+      ref,
+      alt: typeof alt == "string" ? [alt] : alt,
+      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
+      type: "snp"
+    };
+    this.callback(term);
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-R3LWGFGS.js.map