@sjcrh/proteinpaint-client 2.209.0 → 2.210.0

package/dist/chunk-V3SOBDIT.js

@@ -1,255 +0,0 @@
-import {
-  first_genetrack_tolist
-} from "./chunk-C3HEDQPT.js";
-import {
-  HYPER_COLOR,
-  HYPO_COLOR
-} from "./chunk-OBDIJ4QS.js";
-
-// plots/dmr/settings/defaults.ts
-function getDefaultDMRSettings(opts) {
-  const overrides = opts.settings || {};
-  const dm = opts?.app?.vocabApi?.termdbConfig?.queries?.dnaMethylation;
-  const chr = opts?.coordinateOverride?.chr;
-  const elementScale = dm?.regionAnalysis == "element" || Array.isArray(dm?.cpgChroms) && !!chr && !dm.cpgChroms.includes(chr);
-  const defaults = {
-    blockWidth: 800,
-    pad: elementScale ? 1e5 : 2e3,
-    lambda: elementScale ? 5e4 : 1e3,
-    C: 2,
-    fdr_cutoff: 0.05,
-    colors: {
-      group1: "#3b5ee6",
-      group2: "#c04e00",
-      hyper: HYPER_COLOR,
-      hypo: HYPO_COLOR
-    },
-    maxLoessRegion: 25e4,
-    minProbesForCi: 10,
-    backend: "rust",
-    maxRegionSize: 5e6
-  };
-  if (overrides.colors) {
-    Object.assign(defaults.colors, overrides.colors);
-    delete overrides.colors;
-  }
-  return Object.assign(defaults, overrides);
-}
-
-// plots/dmr/viewModel/DmrViewModel.ts
-var CCRE_TRACK_NAME = "ENCODE cCREs";
-var DmrViewModel = class {
-  constructor(dmrResult, config, genomeObj, queryChr, queryStart, queryStop) {
-    const { settings } = config;
-    const dmrBedItems = this.makeDmrBedItems(dmrResult, settings);
-    const sigCpgBedItems = this.makeSigCpgBedItems(dmrResult, settings, queryChr, queryStart, queryStop);
-    const xRange = (queryStop ?? 0) - (queryStart ?? 0);
-    const loess = dmrResult.diagnostic?.loess;
-    const showLoess = !!(loess && loess.group1_fitted.length > 0 && loess.group2_fitted.length > 0);
-    const showDots = xRange <= settings.dmr.maxLoessRegion;
-    const betaTrackResult = dmrResult.diagnostic ? this.renderBetaTrack(
-      dmrResult.diagnostic,
-      config,
-      settings.dmr.blockWidth,
-      showLoess,
-      showDots,
-      queryStart,
-      queryStop
-    ) : void 0;
-    this.viewData = {
-      tklst: this.buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackResult?.img),
-      legendRows: this.buildLegendData(
-        config,
-        dmrResult.dmrs,
-        sigCpgBedItems,
-        showLoess,
-        showDots,
-        betaTrackResult?.showCi ?? false
-      ),
-      diagnostic: dmrResult.diagnostic,
-      dmrs: dmrResult.dmrs,
-      dmrBedItems,
-      showLoess,
-      showDots
-    };
-  }
-  buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackImg) {
-    const tklst = [];
-    first_genetrack_tolist(genomeObj, tklst);
-    const ccre = (genomeObj?.tracks || []).find((t) => t.name == CCRE_TRACK_NAME);
-    if (ccre) tklst.push(structuredClone(ccre));
-    tklst.push({ type: "bedj", name: "DMRs", bedItems: dmrBedItems });
-    tklst.push({ type: "bedj", name: "Sig. CpGs", bedItems: sigCpgBedItems });
-    if (betaTrackImg) {
-      tklst.push({
-        type: "bigwig",
-        name: "Per-CpG Means",
-        height: 150,
-        imgData: betaTrackImg
-      });
-    }
-    return tklst;
-  }
-  buildLegendData(config, dmrs, sigCpgBedItems, showLoess, showDots, showCi) {
-    const { colors } = config.settings.dmr;
-    const g1 = config.group1Name || "Group 1";
-    const g2 = config.group2Name || "Group 2";
-    const meansItems = [];
-    if (showDots) {
-      meansItems.push({ text: `${g1} (control)`, color: colors.group1 }, { text: `${g2} (case)`, color: colors.group2 });
-    }
-    if (showLoess) {
-      const ciLabel = showCi ? " + 95% CI" : "";
-      meansItems.push(
-        { text: `${g1} LOESS trend${ciLabel}`, color: colors.group1, style: showCi ? "shaded" : "dashed" },
-        { text: `${g2} LOESS trend${ciLabel}`, color: colors.group2, style: showCi ? "shaded" : "dashed" }
-      );
-    }
-    const rows = [{ label: "Per-CpG Means", items: meansItems }];
-    const hasHyper = dmrs.some((d) => d.direction === "hyper");
-    const hasHypo = dmrs.some((d) => d.direction === "hypo");
-    if (hasHyper || hasHypo) {
-      const items = [];
-      if (hasHyper) items.push({ text: "Hypermethylated", color: colors.hyper });
-      if (hasHypo) items.push({ text: "Hypomethylated", color: colors.hypo });
-      rows.push({ label: "DMR", items });
-    }
-    if (sigCpgBedItems.length) {
-      const items = [];
-      const hasHyperCpg = sigCpgBedItems.some((b) => b.color === colors.hyper);
-      const hasHypoCpg = sigCpgBedItems.some((b) => b.color === colors.hypo);
-      if (hasHyperCpg) items.push({ text: "Hyper (FDR sig.)", color: colors.hyper });
-      if (hasHypoCpg) items.push({ text: "Hypo (FDR sig.)", color: colors.hypo });
-      rows.push({ label: "Sig. CpGs", items });
-    }
-    return rows;
-  }
-  /**
-   * Render the per-CpG means scatter plot to an offscreen canvas and return
-   * a data URI suitable for the bigwig imgData track.
-   */
-  renderBetaTrack(diagnostic, config, blockWidth, showLoess, showDots, queryStart, queryStop) {
-    const { probes } = diagnostic;
-    if (!probes.positions.length) return void 0;
-    const { colors, fdr_cutoff, minProbesForCi } = config.settings.dmr;
-    const dpr = typeof window !== "undefined" && window.devicePixelRatio > 1 ? window.devicePixelRatio : 1;
-    const width = blockWidth;
-    const height = 150;
-    const canvas = document.createElement("canvas");
-    canvas.width = width * dpr;
-    canvas.height = height * dpr;
-    const ctx = canvas.getContext("2d");
-    if (!ctx) return void 0;
-    ctx.scale(dpr, dpr);
-    const xMin = queryStart ?? probes.positions[0];
-    const xMax = queryStop ?? probes.positions[probes.positions.length - 1];
-    const xRange = xMax - xMin || 1;
-    const scaleX = (val) => (val - xMin) / xRange * width;
-    const scaleY = (val) => height - val * height;
-    ctx.clearRect(0, 0, width, height);
-    let showCi = false;
-    if (showLoess && diagnostic.loess) {
-      const { loess } = diagnostic;
-      const firstProbePos = probes.positions[0];
-      const lastProbePos = probes.positions[probes.positions.length - 1];
-      showCi = probes.positions.length >= minProbesForCi;
-      for (const [fitted, ciLower, ciUpper, color] of [
-        [loess.group1_fitted, loess.group1_ci_lower, loess.group1_ci_upper, colors.group1],
-        [loess.group2_fitted, loess.group2_ci_lower, loess.group2_ci_upper, colors.group2]
-      ]) {
-        if (!fitted.length) continue;
-        const lPos = loess.positions;
-        let iStart = 0;
-        let iEnd = lPos.length - 1;
-        while (iStart < lPos.length && lPos[iStart] < firstProbePos) iStart++;
-        while (iEnd >= 0 && lPos[iEnd] > lastProbePos) iEnd--;
-        if (iStart > iEnd) continue;
-        if (showCi) {
-          ctx.globalAlpha = 0.12;
-          ctx.fillStyle = color;
-          ctx.beginPath();
-          for (let i = iStart; i <= iEnd; i++) {
-            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciUpper[i]))));
-          }
-          for (let i = iEnd; i >= iStart; i--) {
-            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciLower[i]))));
-          }
-          ctx.closePath();
-          ctx.fill();
-        }
-        ctx.globalAlpha = 0.8;
-        ctx.strokeStyle = color;
-        ctx.lineWidth = 2;
-        ctx.setLineDash(showCi ? [] : [6, 4]);
-        ctx.beginPath();
-        for (let i = iStart; i <= iEnd; i++) {
-          ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, fitted[i]))));
-        }
-        ctx.stroke();
-        ctx.setLineDash([]);
-      }
-    }
-    if (!showDots) {
-      ctx.globalAlpha = 1;
-      return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
-    }
-    for (let i = 0; i < probes.positions.length; i++) {
-      const x = scaleX(probes.positions[i]);
-      const isSig = probes.fdr[i] < fdr_cutoff;
-      const alpha = isSig ? 0.85 : 0.3;
-      ctx.globalAlpha = alpha;
-      ctx.fillStyle = colors.group1;
-      const m1 = probes.mean_group1[i];
-      if (m1 != null) {
-        ctx.beginPath();
-        ctx.arc(x, scaleY(m1), 4, 0, Math.PI * 2);
-        ctx.fill();
-      }
-      ctx.fillStyle = colors.group2;
-      const m2 = probes.mean_group2[i];
-      if (m2 != null) {
-        ctx.beginPath();
-        ctx.arc(x, scaleY(m2), 4, 0, Math.PI * 2);
-        ctx.fill();
-      }
-    }
-    ctx.globalAlpha = 1;
-    return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
-  }
-  makeDmrBedItems(dmrResult, settings) {
-    return dmrResult.dmrs.map((dmr) => {
-      const negLog = -Math.log10(Math.max(dmr.min_smoothed_fdr, 1e-300));
-      const alpha = Math.round(Math.min(255, Math.max(50, negLog / 10 * 255)));
-      const hex = alpha.toString(16).padStart(2, "0");
-      const base = dmr.direction === "hyper" ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
-      return { chr: dmr.chr, start: dmr.start, stop: dmr.stop, color: base + hex };
-    });
-  }
-  makeSigCpgBedItems(dmrResult, settings, chr, queryStart, queryStop) {
-    const diag = dmrResult.diagnostic;
-    if (!diag) return [];
-    const { probes } = diag;
-    const items = [];
-    const minDeltaBeta = 0.05;
-    for (let i = 0; i < probes.positions.length; i++) {
-      if (probes.fdr[i] >= settings.dmr.fdr_cutoff) continue;
-      const pos = probes.positions[i];
-      if (queryStart != null && queryStop != null && (pos < queryStart || pos > queryStop)) continue;
-      const mg1 = probes.mean_group1[i];
-      const mg2 = probes.mean_group2[i];
-      if (mg1 == null || mg2 == null) continue;
-      const deltaBeta = mg2 - mg1;
-      if (Math.abs(deltaBeta) < minDeltaBeta) continue;
-      const color = deltaBeta >= 0 ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
-      items.push({ chr, start: pos, stop: pos + 1, color });
-    }
-    return items;
-  }
-};
-
-export {
-  getDefaultDMRSettings,
-  CCRE_TRACK_NAME,
-  DmrViewModel
-};
-//# sourceMappingURL=chunk-V3SOBDIT.js.map

package/dist/chunk-VFUSBU43.js

@@ -1,14 +0,0 @@
-// src/block.lazyload.js
-var Block;
-async function blocklazyload(arg) {
-  if (!Block) {
-    const b = await import("./block-XGK6TEGH.js");
-    Block = b.Block;
-  }
-  return new Block(arg);
-}
-
-export {
-  blocklazyload
-};
-//# sourceMappingURL=chunk-VFUSBU43.js.map

package/dist/chunk-VOF6NWTS.js

@@ -1,274 +0,0 @@
-import {
-  termType2label
-} from "./chunk-3XBG5HIV.js";
-import {
-  TermTypes
-} from "./chunk-SB36AUG7.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/hierCluster.renderers.js
-var hierCluster_renderers_exports = {};
-__export(hierCluster_renderers_exports, {
-  maySetSandboxHeader: () => maySetSandboxHeader,
-  plotDendrogramHclust: () => plotDendrogramHclust,
-  renderImage: () => renderImage
-});
-function maySetSandboxHeader(appState) {
-  if (!this.dom.header) return;
-  const dataType = this.config.dataType;
-  const headerText = this.config?.headerText ? `${this.config.headerText} ` : "";
-  let title;
-  if (this.config.preBuiltPlotTitle) {
-    title = this.config.preBuiltPlotTitle;
-  } else if (this.config.appName) {
-    title = `${headerText}${this.config.appName} Clustering`;
-  } else if (dataType == TermTypes.PROTEOME_ABUNDANCE) {
-    title = this.config.assayCohortTitle ? `Protein Abundance Clustering (${this.config.assayCohortTitle})` : "Protein Abundance Clustering";
-  } else {
-    title = `${headerText}${termType2label(dataType)} Clustering`;
-  }
-  this.dom.header.text(title);
-}
-function plotDendrogramHclust(plotOnly) {
-  const d = this.dimensions;
-  const s = this.config.settings.matrix;
-  const xOffset = d.seriesXoffset;
-  const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
-  const obj = this.hierClusterData.clustering;
-  const row = obj.row;
-  const col = obj.col;
-  const rowHeight = this.settings.matrix.clusterRowh, { xDendrogramHeight, yDendrogramHeight } = this.settings.hierCluster, colWidth = this.dimensions.dx;
-  if (plotOnly !== "left") {
-    if (!this.settings.hierCluster.clusterSamples) {
-      this.dom.topDendrogram.selectAll("*").remove();
-    } else {
-      const height2px = getHclustHeightScalefactor(col.height, yDendrogramHeight);
-      const height = yDendrogramHeight + 1e-7;
-      const width = Math.min(colWidth * col.inputOrder.length, s.imgWMax);
-      if (width <= 0 || height <= 0) {
-        console.warn(
-          "Skipping top dendrogram render: invalid dimensions.",
-          "This may indicate a zoom feedback loop issue.",
-          {
-            width,
-            height,
-            colWidth,
-            sampleCount: col.inputOrder.length,
-            yDendrogramHeight
-          }
-        );
-        this.dom.topDendrogram.selectAll("*").remove();
-        return;
-      }
-      const canvas = new OffscreenCanvas(width * pxr, height * pxr);
-      const ctx = canvas.getContext("2d");
-      ctx.scale(pxr, pxr);
-      ctx.translate(-d.xMin, 0);
-      ctx.imageSmoothingEnabled = false;
-      ctx.imageSmoothingQuality = "high";
-      ctx.strokeStyle = "black";
-      const mergedClusters = /* @__PURE__ */ new Map();
-      for (const [clusterid0, pair] of col.merge.entries()) {
-        const clusterid = clusterid0 + 1;
-        const children = [];
-        const childrenClusters = [];
-        let x1, x2, y1, y2;
-        if (pair.n1 < 0) {
-          const [name, columnNumber] = getLeafNumber(pair.n1, col.inputOrder, col.order);
-          x1 = colWidth * (columnNumber + 0.5);
-          y1 = yDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n1);
-          x1 = c.x;
-          y1 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n1);
-        }
-        if (pair.n2 < 0) {
-          const [name, columnNumber] = getLeafNumber(pair.n2, col.inputOrder, col.order);
-          x2 = colWidth * (columnNumber + 0.5);
-          y2 = yDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n2);
-          x2 = c.x;
-          y2 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n2);
-        }
-        const clusterY = yDendrogramHeight - col.height[clusterid0].height * height2px;
-        const highlight = this.clickedClusterIds?.includes(clusterid);
-        ctx.strokeStyle = highlight ? "red" : "black";
-        ctx.beginPath();
-        ctx.moveTo(x1, y1);
-        ctx.lineTo(x1, clusterY);
-        ctx.lineTo(x2, clusterY);
-        ctx.lineTo(x2, y2);
-        ctx.stroke();
-        ctx.closePath();
-        mergedClusters.set(clusterid, {
-          x: (x1 + x2) / 2,
-          y: clusterY,
-          children,
-          childrenClusters,
-          clusterPosition: {
-            x1,
-            x2,
-            y1,
-            y2,
-            clusterY
-          }
-        });
-      }
-      this.renderImage(
-        this.api,
-        this.dom.topDendrogram,
-        canvas,
-        width,
-        height,
-        xDendrogramHeight + 0.5 * colWidth + d.xMin,
-        s.margin.top + s.scrollHeight
-      );
-      col.mergedClusters = mergedClusters;
-    }
-  }
-  if (plotOnly !== "top") {
-    if (!this.settings.hierCluster.clusterRows) {
-      this.dom.leftDendrogram.selectAll("*").remove();
-    } else {
-      const height2px = getHclustHeightScalefactor(row.height, xDendrogramHeight);
-      const width = xDendrogramHeight + 1e-7;
-      const height = rowHeight * row.inputOrder.length;
-      const canvasWidthPx = Number.isFinite(width) && Number.isFinite(pxr) ? Math.max(0, Math.floor(width * pxr)) : 0;
-      const canvasHeightPx = Number.isFinite(height) && Number.isFinite(pxr) ? Math.max(0, Math.floor(height * pxr)) : 0;
-      if (!Number.isFinite(width) || !Number.isFinite(height) || !Number.isFinite(pxr) || width <= 0 || height <= 0 || pxr <= 0 || canvasWidthPx < 1 || canvasHeightPx < 1) {
-        console.warn(
-          "Skipping left dendrogram render: invalid dimensions.",
-          "This may indicate a zoom feedback loop issue.",
-          {
-            width,
-            height,
-            pxr,
-            canvasWidthPx,
-            canvasHeightPx,
-            rowHeight,
-            termCount: row.inputOrder.length,
-            xDendrogramHeight
-          }
-        );
-        this.dom.leftDendrogram.selectAll("*").remove();
-        return;
-      }
-      const canvas = new OffscreenCanvas(canvasWidthPx, canvasHeightPx);
-      const ctx = canvas.getContext("2d");
-      ctx.scale(pxr, pxr);
-      ctx.imageSmoothingEnabled = false;
-      ctx.imageSmoothingQuality = "high";
-      ctx.strokeStyle = "black";
-      const mergedClusters = /* @__PURE__ */ new Map();
-      for (const [clusterid0, pair] of row.merge.entries()) {
-        const clusterid = clusterid0 + 1;
-        const children = [];
-        const childrenClusters = [];
-        let x1, x2, y1, y2;
-        if (pair.n1 < 0) {
-          const [name, rowNumber] = getLeafNumber(pair.n1, row.inputOrder, row.order);
-          y1 = rowHeight * (rowNumber + 0.5);
-          x1 = xDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n1);
-          x1 = c.x;
-          y1 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n1);
-        }
-        if (pair.n2 < 0) {
-          const [name, rowNumber] = getLeafNumber(pair.n2, row.inputOrder, row.order);
-          y2 = rowHeight * (rowNumber + 0.5);
-          x2 = xDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n2);
-          x2 = c.x;
-          y2 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n2);
-        }
-        const clusterX = xDendrogramHeight - row.height[clusterid0].height * height2px;
-        const highlight = this.clickedLeftClusterIds?.includes(clusterid);
-        ctx.strokeStyle = highlight ? "red" : "black";
-        ctx.beginPath();
-        ctx.moveTo(x1, y1);
-        ctx.lineTo(clusterX, y1);
-        ctx.lineTo(clusterX, y2);
-        ctx.lineTo(x2, y2);
-        ctx.stroke();
-        ctx.closePath();
-        mergedClusters.set(clusterid, {
-          x: clusterX,
-          y: (y1 + y2) / 2,
-          children,
-          childrenClusters,
-          clusterPosition: {
-            x1,
-            x2,
-            y1,
-            y2,
-            clusterX
-          }
-        });
-      }
-      const t = this.termOrder.find((t2) => t2.grp.type == "hierCluster" || t2.grp.name == this.hcTermGroup.name);
-      const y = (
-        // t.labelOffset is commented out because it is already handled in adjustSvgDimensions
-        t.grpIndex * s.rowgspace + t.prevGrpTotalIndex * s.rowh + t.totalHtAdjustments + s.margin.top + s.scrollHeight + // left dendrogram image must be lower than the top dendrogram image height
-        yDendrogramHeight
-      );
-      this.renderImage(this.api, this.dom.leftDendrogram, canvas, width, height, 0, y);
-      row.mergedClusters = mergedClusters;
-    }
-  }
-}
-async function renderImage(componentApi, g, canvas, width, height, x, y) {
-  const sequenceId = componentApi.getSequenceId();
-  const reader = new FileReader();
-  reader.addEventListener(
-    "load",
-    () => {
-      if (componentApi.isStaleSequenceId(sequenceId)) return;
-      g.selectAll("*").remove();
-      g.append("image").attr("x", x + 0.033).attr("y", y + 0.033).attr("xlink:href", reader.result).attr("width", width).attr("height", height);
-    },
-    false
-  );
-  const blob = await canvas.convertToBlob({ quality: 1 });
-  reader.readAsDataURL(blob);
-}
-function getHclustHeightScalefactor(lst, ph) {
-  let max = lst[0].height;
-  for (const h of lst) max = Math.max(max, h.height);
-  return ph / max;
-}
-function getLeafNumber(minus, inputOrder, order) {
-  const name = inputOrder[-minus - 1];
-  if (!name) throw "minus not in inputOrder";
-  const i = order.findIndex((j) => j.name == name);
-  if (i == -1) throw "name not found in hc$order";
-  return [name, i];
-}
-
-export {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage,
-  hierCluster_renderers_exports
-};
-//# sourceMappingURL=chunk-VOF6NWTS.js.map