@sjcrh/proteinpaint-client 2.207.1 → 2.209.0

package/dist/block.tk.ase-V3AJRYT6.js

@@ -0,0 +1,360 @@
+import {
+  configPanel_rnabam,
+  rnabamtk_initparam
+} from "./chunk-X4MV2M5F.js";
+import {
+  ase_color,
+  init_config,
+  measure,
+  showsingleitem_table
+} from "./chunk-7FFTAYT4.js";
+import {
+  axisstyle,
+  keyupEnter,
+  make_table_2col
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import {
+  dofetch
+} from "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import {
+  bplen
+} from "./chunk-SB36AUG7.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import {
+  axisLeft
+} from "./chunk-Z2ZITHT4.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/block.tk.ase.js
+async function loadTk(tk, block) {
+  block.tkcloakon(tk);
+  block.block_setheight();
+  if (tk.uninitialized) {
+    makeTk(tk, block);
+  }
+  const regions = [];
+  let xoff = 0;
+  for (let i = block.startidx; i <= block.stopidx; i++) {
+    const r = block.rglst[i];
+    regions.push({
+      chr: r.chr,
+      start: r.start,
+      stop: r.stop,
+      width: r.width,
+      x: xoff
+    });
+    xoff += r.width + block.regionspace;
+  }
+  if (block.subpanels.length == tk.subpanels.length) {
+    for (const [idx, r] of block.subpanels.entries()) {
+      xoff += r.leftpad;
+      regions.push({
+        chr: r.chr,
+        start: r.start,
+        stop: r.stop,
+        width: r.width,
+        exonsf: r.exonsf,
+        subpanelidx: idx,
+        x: xoff
+      });
+      xoff += r.width;
+    }
+  }
+  tk.regions = regions;
+  try {
+    tk.dna.coveragemax = 0;
+    if (tk.rna.coverageauto) tk.rna.coveragemax = 0;
+    for (const r of regions) {
+      await getdata_region(r, tk, block);
+    }
+    renderTk(tk, block);
+    block.tkcloakoff(tk, {});
+  } catch (e) {
+    if (e.stack) console.log(e.stack);
+    tk.height_main = tk.height = 100;
+    block.tkcloakoff(tk, { error: e.message || e });
+  }
+  block.block_setheight();
+}
+function getdata_region(r, tk, block) {
+  const arg = {
+    genome: block.genome.name,
+    samplename: tk.samplename,
+    rnabamfile: tk.rnabamfile,
+    rnabamurl: tk.rnabamurl,
+    rnabamindexURL: tk.rnabamindexURL,
+    rnabamtotalreads: tk.rnabamtotalreads,
+    rnabamispairedend: tk.rnabamispairedend,
+    vcffile: tk.vcffile,
+    vcfurl: tk.vcfurl,
+    vcfindexURL: tk.vcfindexURL,
+    rnabarheight: tk.rna.coveragebarh,
+    dnabarheight: tk.dna.coveragebarh,
+    barypad: tk.barypad,
+    chr: r.chr,
+    start: r.start,
+    stop: r.stop,
+    width: r.width,
+    checkrnabam: tk.checkrnabam,
+    refcolor: tk.dna.refcolor,
+    altcolor: tk.dna.altcolor,
+    devicePixelRatio: window.devicePixelRatio > 1 ? window.devicePixelRatio : 1
+  };
+  if (!tk.rna.coverageauto) {
+    arg.rnamax = tk.rna.coveragemax;
+  }
+  return dofetch("ase", arg).then((data) => {
+    if (data.error) throw data.error;
+    r.genes = data.genes;
+    r.fpkmrangelimit = data.fpkmrangelimit;
+    if (data.covplotrangelimit) {
+      r.covplotrangelimit = data.covplotrangelimit;
+    } else {
+      r.coveragesrc = data.coveragesrc;
+      tk.dna.coveragemax = Math.max(tk.dna.coveragemax, data.dnamax);
+      if (tk.rna.coverageauto) {
+        tk.rna.coveragemax = Math.max(tk.rna.coveragemax, data.rnamax);
+      }
+    }
+  });
+}
+function renderTk(tk, block) {
+  tk.glider.selectAll("*").remove();
+  for (const p of tk.subpanels) {
+    p.glider.attr("transform", "translate(0,0)").selectAll("*").remove();
+  }
+  renderTk_covplot(tk, block);
+  renderTk_fpkm(tk, block);
+  block.setllabel();
+  tk.height_main += tk.toppad + tk.bottompad;
+}
+function renderTk_covplot(tk, block) {
+  const noploth = 30;
+  const anyregionwithcovplot = tk.regions.find((r) => r.coveragesrc);
+  if (anyregionwithcovplot) {
+    axisstyle({
+      axis: tk.rna.coverageaxisg.attr("transform", "scale(1) translate(0,0)").call(
+        axisLeft().scale(linear().domain([0, tk.rna.coveragemax]).range([tk.rna.coveragebarh, 0])).tickValues([0, tk.rna.coveragemax])
+      ),
+      showline: true
+    });
+    tk.tklabel.attr("y", tk.rna.coveragebarh / 2 - 7);
+    tk.rna.coveragelabel.attr("y", tk.rna.coveragebarh / 2 + 2).attr("transform", "scale(1)");
+    axisstyle({
+      axis: tk.dna.coverageaxisg.attr("transform", "scale(1) translate(0," + (tk.rna.coveragebarh + tk.barypad) + ")").call(
+        axisLeft().scale(linear().domain([0, tk.dna.coveragemax]).range([0, tk.dna.coveragebarh])).tickValues([0, tk.dna.coveragemax])
+      ),
+      showline: true
+    });
+    tk.dna.coveragelabel.attr("transform", "scale(1)").attr("y", tk.rna.coveragebarh + tk.barypad + tk.dna.coveragebarh / 2).each(function() {
+      tk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, this.getBBox().width);
+    });
+    tk.height_main = tk.rna.coveragebarh + tk.barypad + tk.dna.coveragebarh;
+  } else {
+    tk.dna.coverageaxisg.attr("transform", "scale(0)");
+    tk.rna.coverageaxisg.attr("transform", "scale(0)");
+    tk.dna.coveragelabel.attr("transform", "scale(0)");
+    tk.rna.coveragelabel.attr("transform", "scale(0)");
+    tk.height_main = noploth;
+  }
+  for (const r of tk.regions) {
+    if (r.covplotrangelimit) {
+      tk.glider.append("text").text("Zoom in under " + bplen(r.covplotrangelimit) + " to show coverage plot").attr("font-size", block.laelfontsize).attr("text-anchor", "middle").attr("x", r.x + r.width / 2).attr("y", noploth / 2);
+      continue;
+    }
+    tk.glider.append("image").attr("x", r.x).attr("width", r.width).attr("height", tk.rna.coveragebarh + tk.barypad + tk.dna.coveragebarh).attr("xlink:href", r.coveragesrc);
+  }
+}
+function renderTk_fpkm(tk, block) {
+  const noploth = 30;
+  const anyregionwithfpkm = tk.regions.find((r) => !r.fpkmrangelimit);
+  let maxfpkm = 0;
+  for (const r of tk.regions) {
+    if (r.fpkmrangelimit) continue;
+    if (r.genes) {
+      for (const g of r.genes) {
+        if (Number.isFinite(g.fpkm)) maxfpkm = Math.max(maxfpkm, g.fpkm);
+        measure(g, tk.gecfg);
+      }
+    }
+  }
+  const y = tk.height_main + tk.yspace1;
+  if (anyregionwithfpkm && maxfpkm > 0) {
+    axisstyle({
+      axis: tk.fpkm.axisg.attr("transform", "scale(1) translate(0," + y + ")").call(
+        axisLeft().scale(linear().domain([0, maxfpkm]).range([tk.fpkm.barh, 0])).tickValues([0, maxfpkm])
+      ),
+      showline: true
+    });
+    tk.fpkm.label.attr("y", y + tk.fpkm.barh / 2).attr("transform", "scale(1)");
+    tk.height_main += tk.yspace1 + tk.fpkm.barh;
+  } else {
+    tk.fpkm.axisg.attr("transform", "scale(0)");
+    tk.fpkm.label.attr("transform", "scale(0)");
+    tk.height_main += noploth;
+  }
+  for (const r of tk.regions) {
+    if (r.fpkmrangelimit) {
+      tk.glider.append("text").text("Zoom in under " + bplen(r.fpkmrangelimit) + " to show gene " + tk.gecfg.datatype + " values").attr("font-size", block.laelfontsize).attr("text-anchor", "middle").attr("x", r.x + r.width / 2).attr("y", y + noploth / 2);
+      continue;
+    }
+    if (!r.genes) continue;
+    if (maxfpkm == 0) {
+      continue;
+    }
+    const rsf = r.width / (r.stop - r.start);
+    for (const gene of r.genes) {
+      if (!Number.isFinite(gene.fpkm)) continue;
+      const color = ase_color(gene, tk.gecfg);
+      const boxh = tk.fpkm.barh * gene.fpkm / maxfpkm;
+      let x1, x2;
+      if (r.reverse) {
+        x1 = r.x + rsf * (r.stop - Math.min(r.stop, gene.stop));
+        x2 = r.x + rsf * (r.stop - Math.max(r.start, gene.start));
+      } else {
+        x1 = r.x + rsf * (Math.max(r.start, gene.start) - r.start);
+        x2 = r.x + rsf * (Math.min(r.stop, gene.stop) - r.start);
+      }
+      const line = tk.glider.append("line").attr("x1", x1).attr("x2", x2).attr("y1", y + tk.fpkm.barh - boxh).attr("y2", y + tk.fpkm.barh - boxh).attr("stroke", color).attr("stroke-width", 2).attr("stroke-opacity", 0.4);
+      const box = tk.glider.append("rect").attr("x", x1).attr("y", y + tk.fpkm.barh - boxh).attr("width", x2 - x1).attr("height", boxh).attr("fill", color).attr("fill-opacity", 0.2);
+      tk.glider.append("rect").attr("x", x1).attr("y", y + tk.fpkm.barh - boxh - 2).attr("width", x2 - x1).attr("height", boxh + 2).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event2) => {
+        line.attr("stroke-opacity", 0.5);
+        box.attr("fill-opacity", 0.3);
+        tooltip_genefpkm(gene, tk);
+      }).on("mouseout", (event2) => {
+        line.attr("stroke-opacity", 0.4);
+        box.attr("fill-opacity", 0.2);
+        tk.tktip.hide();
+      });
+    }
+  }
+}
+function tooltip_genefpkm(gene, tk) {
+  tk.tktip.clear().show(event.clientX, event.clientY);
+  const lst = [
+    {
+      k: gene.gene + " " + tk.gecfg.datatype,
+      v: gene.fpkm
+    }
+  ];
+  const table = make_table_2col(tk.tktip.d, lst);
+  showsingleitem_table(gene, tk.gecfg, table);
+}
+function makeTk(tk, block) {
+  delete tk.uninitialized;
+  if (!tk.barypad) tk.barypad = 0;
+  if (!tk.rna) tk.rna = {};
+  tk.rna.coverageaxisg = tk.gleft.append("g");
+  tk.rna.coveragelabel = block.maketklefthandle(tk).attr("class", null).attr("dominant-baseline", "hanging").text("RNA coverage");
+  tk.rna.coverageauto = true;
+  if (!tk.rna.coveragebarh) tk.rna.coveragebarh = 50;
+  if (!tk.dna) tk.dna = {};
+  tk.dna.coverageaxisg = tk.gleft.append("g");
+  tk.dna.coveragelabel = block.maketklefthandle(tk).attr("class", null).text("DNA coverage");
+  tk.dna.coveragemax = 0;
+  if (!tk.dna.coveragebarh) tk.dna.coveragebarh = 50;
+  if (!tk.dna.refcolor) tk.dna.refcolor = "#188FF5";
+  if (!tk.dna.altcolor) tk.dna.altcolor = "#F51818";
+  if (!tk.yspace1) tk.yspace1 = 15;
+  tk.gecfg = { datatype: "FPKM" };
+  init_config(tk.gecfg);
+  if (!tk.fpkm) tk.fpkm = {};
+  tk.fpkm.axisg = tk.gleft.append("g");
+  tk.fpkm.label = block.maketklefthandle(tk).attr("class", null).text("Gene " + tk.gecfg.datatype);
+  if (!tk.fpkm.barh) tk.fpkm.barh = 50;
+  tk.config_handle = block.maketkconfighandle(tk).attr("y", 10 + block.labelfontsize).on("click", (event2) => {
+    configPanel(tk, block);
+  });
+  if (!tk.checkrnabam) tk.checkrnabam = {};
+  rnabamtk_initparam(tk.checkrnabam);
+}
+function configPanel(tk, block) {
+  tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+  const d = tk.tkconfigtip.d.append("div");
+  d.append("div").text("RNA-seq coverage is shown at all covered bases.").style("font-size", ".8em").style("opacity", 0.5);
+  {
+    const row = d.append("div").style("margin", "5px 0px");
+    row.append("span").html("Bar height&nbsp;");
+    row.append("input").attr("type", "numeric").property("value", tk.rna.coveragebarh).style("width", "80px").on("keyup", (event2) => {
+      if (!keyupEnter(event2)) return;
+      const v = Number.parseInt(event2.target.value);
+      if (v <= 20) return;
+      if (v == tk.rna.coveragebarh) return;
+      tk.rna.coveragebarh = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin", "5px 0px");
+    const id = Math.random();
+    row.append("input").attr("type", "checkbox").attr("id", id).property("checked", tk.rna.coverageauto).on("change", (event2) => {
+      tk.rna.coverageauto = event2.target.checked;
+      fixed.style("display", tk.rna.coverageauto ? "none" : "inline");
+      loadTk(tk, block);
+    });
+    row.append("label").html("&nbsp;automatic scale").attr("for", id);
+    const fixed = row.append("div").style("display", tk.rna.coverageauto ? "none" : "inline").style("margin-left", "20px");
+    fixed.append("span").html("Fixed max&nbsp");
+    fixed.append("input").attr("value", "numeric").property("value", tk.rna.coveragemax).style("width", "50px").on("keyup", (event2) => {
+      if (!keyupEnter(event2)) return;
+      const v = Number.parseInt(event2.target.value);
+      if (v <= 0) return;
+      if (v == tk.rna.coveragemax) return;
+      tk.rna.coveragemax = v;
+      loadTk(tk, block);
+    });
+  }
+  d.append("div").text("SNPs are only shown for those heterozygous in DNA.").style("font-size", ".8em").style("opacity", 0.5).style("margin-top", "25px");
+  {
+    const row = d.append("div").style("margin", "5px 0px");
+    row.append("span").html("Bar height&nbsp;");
+    row.append("input").attr("type", "numeric").property("value", tk.dna.coveragebarh).style("width", "80px").on("keyup", (event2) => {
+      if (!keyupEnter(event2)) return;
+      const v = Number.parseInt(event2.target.value);
+      if (v <= 20) return;
+      if (v == tk.dna.coveragebarh) return;
+      tk.dna.coveragebarh = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin", "5px 0px 25px 0px");
+    row.append("span").html("Allele color&nbsp;&nbsp;Ref:&nbsp;");
+    row.append("input").attr("type", "color").property("value", tk.dna.refcolor).on("change", (event2) => {
+      tk.dna.refcolor = event2.target.value;
+      loadTk(tk, block);
+    });
+    row.append("span").html("&nbsp;Alt:&nbsp;");
+    row.append("input").attr("type", "color").property("value", tk.dna.altcolor).on("change", (event2) => {
+      tk.dna.altcolor = event2.target.value;
+      loadTk(tk, block);
+    });
+  }
+  configPanel_rnabam(tk, block, loadTk);
+}
+export {
+  loadTk
+};
+//# sourceMappingURL=block.tk.ase-V3AJRYT6.js.map