@sjcrh/proteinpaint-client 2.196.0 → 2.197.0

package/dist/mavb-ARUWOZES.js

@@ -0,0 +1,732 @@
+import {
+  blocklazyload
+} from "./chunk-NZCX4A7X.js";
+import {
+  d3lasso
+} from "./chunk-K5XPMCKP.js";
+import {
+  axisstyle,
+  first_genetrack_tolist,
+  font,
+  make_table_2col,
+  newpane,
+  newpane3,
+  renderSandboxFormDiv,
+  sayerror,
+  to_svg
+} from "./chunk-JHZK6IDA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-FYY3T565.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-7Z6E3NA5.js";
+import "./chunk-V2ET64EJ.js";
+import "./chunk-5ERYRSVV.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-23AEAG37.js";
+import "./chunk-M2PPUO4E.js";
+import "./chunk-ZRSJVACE.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import {
+  axisBottom,
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import {
+  linear
+} from "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// src/mavb.js
+var hlcolor = "#ffa200";
+var tip = new Menu();
+function mavbparseinput(mavb, sayerror2, holder, jwt) {
+  if (!mavb.dataname) {
+    mavb.dataname = "Differential expression";
+  }
+  if (mavb.input) {
+    const textinput = mavb.input;
+    delete mavb.input;
+    const err = parseRaw(
+      {
+        genome: mavb.genome,
+        filename: mavb.dataname,
+        holder,
+        tracks: mavb.tracks,
+        hostURL: mavb.hostURL,
+        jwt
+      },
+      textinput.trim().split("\n")
+    );
+    if (err) {
+      sayerror2("Error with diferential gene expressionn data: " + err);
+    }
+    return;
+  }
+  let request;
+  if (mavb.url) {
+    request = new Request(mavb.hostURL + "/urltextfile", {
+      method: "POST",
+      body: JSON.stringify({ url: mavb.url, jwt })
+    });
+    delete mavb.url;
+  } else if (mavb.file) {
+    request = new Request(mavb.hostURL + "/textfile", {
+      method: "POST",
+      body: JSON.stringify({ file: mavb.file, jwt })
+    });
+    delete mavb.file;
+  } else {
+    sayerror2("neither .input nor .url given for MA-Volcano plot");
+    return;
+  }
+  const wait = holder.append("div").style("margin", "20px").style("color", "#aaa").style("font-size", "1.5em").text("Loading differential gene expression data ...");
+  fetch(request).then((data) => {
+    return data.json();
+  }).then((data) => {
+    if (data.error) throw { message: data.error };
+    if (!data.text) throw { message: "no data loaded" };
+    const err = parseRaw(
+      {
+        genome: mavb.genome,
+        filename: mavb.dataname,
+        holder,
+        tracks: mavb.tracks,
+        hostURL: mavb.hostURL,
+        jwt
+      },
+      data.text.trim().split("\n")
+    );
+    if (err) throw { message: "Error with differential gene expression data: " + err };
+  }).catch((err) => {
+    sayerror2(err.message);
+    if (err.stack) console.log(err.stack);
+  }).then(() => {
+    wait.remove();
+  });
+}
+function mavbui(genomes, hostURL, jwt, holder, sandbox_header) {
+  let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
+  if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
+  else {
+    ;
+    [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
+    pane.header.text("Differential gene expression viewer");
+    pane.body.style("margin", "10px");
+  }
+  inputdiv.append("div").style("margin-top", "30px").style("color", "#858585").html(`
+		<p>Interactive MA and Volcano plot for exploring differentially expressed genes.</p>
+		<a href=https://docs.google.com/document/d/1gEhywyMzMQRM10NFvsObw1yDSWxVY7pxYjsQ2-nd6x4/edit?usp=sharing target=_blank>File format</a>
+		`);
+  function cmt(t, red) {
+    saydiv.style("color", red ? "red" : "black").text(t);
+  }
+  const fileui = () => {
+    filediv.selectAll("*").remove();
+    const input = filediv.append("input").attr("type", "file").on("change", (event2) => {
+      const file = event2.target.files[0];
+      if (!file) {
+        fileui();
+        return;
+      }
+      if (!file.size) {
+        cmt("Invalid file " + file.name);
+        fileui();
+        return;
+      }
+      const reader = new FileReader();
+      reader.onload = (event3) => {
+        const usegenome = gselect.options[gselect.selectedIndex].innerHTML;
+        const err = parseRaw(
+          {
+            genome: genomes[usegenome],
+            filename: file.name,
+            hostURL,
+            jwt,
+            holder,
+            sandbox_header
+          },
+          event3.target.result.trim().split("\n")
+        );
+        if (err) {
+          cmt(err, 1);
+          fileui();
+          return;
+        }
+        if (pane) pane.pane.remove();
+      };
+      reader.onerror = function() {
+        cmt("Error reading file " + file.name, 1);
+        fileui();
+        return;
+      };
+      reader.readAsText(file, "utf8");
+    });
+    setTimeout(() => input.node().focus(), 1100);
+  };
+  fileui();
+}
+function parseRaw(mavb, lines) {
+  if (mavb.tracks) {
+    for (const t of mavb.tracks) {
+      t.iscustom = true;
+    }
+  }
+  const [err, header] = parseHeader(lines[0].trim());
+  if (err) {
+    return err;
+  }
+  mavb.hastvalue = header.includes("tvalue");
+  const data = [];
+  let errpvalue = 0;
+  let errpvalueadj = 0;
+  let errlogfc = 0;
+  for (let i = 1; i < lines.length; i++) {
+    const line = lines[i];
+    if (line == "") continue;
+    if (line[0] == "#") continue;
+    const lst = line.trim().split("	");
+    const m = {};
+    for (let j = 0; j < header.length; j++) {
+      m[header[j]] = lst[j];
+    }
+    if (!m.gene) {
+      return "(line " + (i + 1) + ") missing gene";
+    }
+    m.gene = m.gene.replace(/"/g, "");
+    if (!m.logfoldchange) {
+      return "(line " + (i + 1) + ") missing log fold change";
+    }
+    {
+      const v = Number.parseFloat(m.logfoldchange);
+      if (Number.isNaN(v)) {
+        errlogfc++;
+        continue;
+      }
+      m.logfoldchange = v;
+    }
+    if (!m.averagevalue) {
+      return "(line " + (i + 1) + ") missing average value";
+    }
+    {
+      const v = Number.parseFloat(m.averagevalue);
+      if (Number.isNaN(v)) {
+        return "(line " + (i + 1) + ") invalid value for average value: " + m.averagevalue;
+      }
+      m.averagevalue = v;
+    }
+    if (!m.pvalue) {
+      errpvalue++;
+      continue;
+    } else {
+      const v = Number.parseFloat(m.pvalue);
+      if (Number.isNaN(v)) {
+        errpvalue++;
+        continue;
+      }
+      m.pvalue = v;
+    }
+    if (m.pvalueadj) {
+      const v = Number.parseFloat(m.pvalueadj);
+      if (Number.isNaN(v)) {
+        errpvalueadj++;
+        continue;
+      }
+      m.pvalueadj = v;
+    }
+    if (mavb.hastvalue) {
+      if (!m.tvalue) {
+        return "(line " + (i + 1) + ") missing T value";
+      }
+      {
+        const v = Number.parseFloat(m.tvalue);
+        if (Number.isNaN(v)) {
+          return "(line " + (i + 1) + ") invalid value for T value: " + m.tvalue;
+        }
+        m.tvalue = v;
+      }
+    }
+    data.push(m);
+  }
+  if (data.length == 0) {
+    return "No valid data";
+  }
+  if (mavb.holder == void 0) {
+    const pane = newpane({ x: 100, y: 100 });
+    pane.header.text(mavb.filename);
+    mavb.holder = pane.body;
+  } else {
+    mavb.holder.selectAll("*").remove();
+    if (mavb.sandbox_header !== void 0)
+      mavb.holder.append("div").html('<span style="opacity:.5;font-size:.7em">FILE: </span> ' + mavb.filename);
+  }
+  mavb.data = data;
+  if (errlogfc + errpvalue + errpvalueadj > 0) {
+    const div = mavb.holder.append("div").style("width", "800px");
+    if (errlogfc) {
+      sayerror(div, errlogfc + " lines dropped for invalid log fold change value");
+    }
+    if (errpvalue) {
+      sayerror(div, errpvalue + " lines dropped for invalid P value");
+    }
+    if (errpvalueadj) {
+      sayerror(div, errpvalueadj + " lines dropped for invalid adjusted P value");
+    }
+  }
+  render(mavb);
+  return null;
+}
+function parseHeader(line) {
+  const lower = line.toLowerCase().split("	");
+  const header = line.split("	");
+  if (header.length <= 1) {
+    return ["invalid file header"];
+  }
+  const htry = (...lst) => {
+    for (const i2 of lst) {
+      const j = lower.indexOf(i2);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene");
+  if (i == -1) return ["gene missing from header"];
+  header[i] = "gene";
+  i = htry("logfc", "log.foldchange");
+  if (i == -1) return ["log.foldchange missing from header"];
+  header[i] = "logfoldchange";
+  i = htry("aveexpr", "average.value");
+  if (i == -1) return ["average.value missing from header"];
+  header[i] = "averagevalue";
+  i = htry("t", "t.value");
+  if (i != -1) {
+    header[i] = "tvalue";
+  }
+  i = htry("p.value");
+  if (i == -1) return ["p.value missing from header"];
+  header[i] = "pvalue";
+  i = htry("p.value.adjusted", "adj.p.val", "adjustedp-value(fdr)");
+  if (i != -1) {
+    header[i] = "pvalueadj";
+  }
+  return [null, header];
+}
+function render(mavb) {
+  if (mavb.hastvalue) {
+    let tmin = Math.abs(mavb.data[0].tvalue);
+    let tmax = 0;
+    for (const d of mavb.data) {
+      const v = Math.abs(d.tvalue);
+      tmin = Math.min(tmin, v);
+      tmax = Math.max(tmax, v);
+    }
+    mavb.tvaluemin = tmin;
+    mavb.tvaluemax = tmax;
+  }
+  const maplotdiv = mavb.holder.append("div").style("display", "inline-block").style("vertical-align", "top").style("margin", "20px");
+  const ma_svg = render_ma(maplotdiv, mavb);
+  const voplotdiv = mavb.holder.append("div").style("display", "inline-block").style("vertical-align", "top").style("margin", "20px");
+  const vo_svg = render_volcano(voplotdiv, mavb);
+  const div3 = mavb.holder.append("div").style("margin", "20px");
+  const textarea = div3.append("textarea").style("display", "inline-block").attr("rows", 5).attr("cols", 10).style("resize", "both").attr("placeholder", "Enter genes, separate by space or newline");
+  const div31 = div3.append("div").style("display", "inline-block").style("margin-left", "10px").style("vertical-align", "top");
+  div31.append("button").style("display", "block").text("Show gene labels").on("click", (event2) => {
+    const str = textarea.property("value").trim();
+    if (str == "") return;
+    const genes = /* @__PURE__ */ new Set();
+    for (const n of str.split(/[\s\n\t]+/)) {
+      genes.add(n.toUpperCase());
+    }
+    if (genes.size == 0) return;
+    for (const d of mavb.data) {
+      if (!d.ma_label && genes.has(d.gene.toUpperCase())) {
+        hltoggle(d, mavb);
+      }
+    }
+  });
+  div31.append("button").style("display", "block").text("Remove all labels").on("click", (event2) => {
+    for (const d of mavb.data) {
+      if (d.ma_label) {
+        hltoggle(d, mavb);
+      }
+    }
+  });
+  div31.append("div").style("margin-top", "10px").style("color", "#858585").style("font-size", ".8em").html(
+    '<span style="font-size:1.3em">TIP:</span> click circles to toggle highlight on genes;<br>drag to move a gene label around.'
+  );
+  const div32 = div3.append("div").style("display", "inline-block").style("margin-left", "30px").style("vertical-align", "top");
+  div32.append("button").text("Get MA plot").style("display", "block").on("click", (event2) => {
+    to_svg(ma_svg.node(), "MAplot");
+  });
+  div32.append("button").text("Get volcano plot").style("display", "block").on("click", (event2) => {
+    to_svg(vo_svg.node(), "Volcano");
+  });
+}
+function render_ma(holder, mavb) {
+  const avlst = [];
+  let minlogfc = 0, maxlogfc = 0;
+  for (const d of mavb.data) {
+    minlogfc = Math.min(minlogfc, d.logfoldchange);
+    maxlogfc = Math.max(maxlogfc, d.logfoldchange);
+    avlst.push(d.averagevalue);
+  }
+  avlst.sort((a, b) => a - b);
+  const minav = avlst[0];
+  const maxav = avlst[avlst.length - 1];
+  let yaxisw, xaxish, width, height, xpad, ypad, boxh, toppad = 50, rightpad = 50, radius;
+  const svg = holder.append("svg");
+  const yaxisg = svg.append("g");
+  const xaxisg = svg.append("g");
+  const xlab = svg.append("text").text("Average expression value").attr("fill", "black").attr("text-anchor", "middle");
+  const ylab = svg.append("text").text("log2(fold change)").attr("fill", "black").attr("text-anchor", "middle");
+  mavb.ma_dotarea = svg.append("g");
+  const box = mavb.ma_dotarea.append("rect").attr("stroke", "#ededed").attr("fill", "none").attr("shape-rendering", "crispEdges");
+  const xscale = linear().domain([minav, maxav]);
+  const yscale = linear().domain([minlogfc, maxlogfc]);
+  let radiusscale;
+  if (mavb.hastvalue) {
+    radiusscale = linear().domain([mavb.tvaluemin, mavb.tvaluemax]);
+  }
+  const dotg = mavb.ma_dotarea.selectAll().data(mavb.data).enter().append("g").each(function(d) {
+    d.ma_g = this;
+  });
+  const circle = dotg.append("circle").attr("stroke", "black").attr("stroke-opacity", 0.2).attr("stroke-width", 1).attr("fill", hlcolor).attr("fill-opacity", 0).each(function(d) {
+    d.ma_circle = this;
+  }).on("mouseover", circlemouseover).on("mouseout", circlemouseout).on("click", (event2, d) => {
+    circleclick(d, mavb, event2.clientX, event2.clientY);
+  });
+  const logfc0line = mavb.ma_dotarea.append("line").attr("stroke", "#ccc").attr("shape-rendering", "crispEdges");
+  const bpg = svg.append("g");
+  const bpthroughline = bpg.append("line").attr("stroke", hlcolor).attr("shape-rendering", "crispEdges");
+  const percentile05line = bpg.append("line").attr("stroke", hlcolor).attr("shape-rendering", "crispEdges");
+  const percentile95line = bpg.append("line").attr("stroke", hlcolor).attr("shape-rendering", "crispEdges");
+  const bpbox = bpg.append("rect").attr("fill", "white").attr("stroke", hlcolor).attr("shape-rendering", "crispEdges");
+  const bpmedianline = bpg.append("line").attr("stroke", hlcolor).attr("shape-rendering", "crispEdges");
+  const avpercentile05 = avlst[Math.ceil(avlst.length * 0.05)];
+  const avpercentile95 = avlst[Math.ceil(avlst.length * 0.95)];
+  const avpercentile25 = avlst[Math.ceil(avlst.length * 0.25)];
+  const avpercentile75 = avlst[Math.ceil(avlst.length * 0.75)];
+  const avmedian = avlst[Math.ceil(avlst.length / 2)];
+  function resize(w, h) {
+    width = w;
+    height = h;
+    yaxisw = Math.max(50, width / 8);
+    xaxish = Math.max(50, height / 8);
+    radius = Math.max(width, height) / 80;
+    const maxradius = radius * 3;
+    xscale.range([0, width]);
+    yscale.range([height, 0]);
+    if (radiusscale) radiusscale.range([radius, maxradius]);
+    circle.each((d) => {
+      d.ma_radius = radiusscale ? radiusscale(Math.abs(d.tvalue)) : radius;
+    });
+    boxh = radius * 3;
+    xpad = Math.max(maxradius, width / 50);
+    ypad = Math.max(maxradius, height / 50);
+    yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
+    xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad + boxh + ypad) + ")");
+    xlab.attr("x", yaxisw + xpad + width / 2).attr("y", toppad + height + ypad + boxh + ypad + xaxish - 5);
+    ylab.attr("transform", "translate(15," + (toppad + height / 2) + ") rotate(-90)");
+    mavb.ma_dotarea.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
+    box.attr("width", width).attr("height", height);
+    dotg.attr("transform", (d) => {
+      return "translate(" + xscale(d.averagevalue) + "," + yscale(d.logfoldchange) + ")";
+    });
+    circle.attr("r", (d) => {
+      return d.ma_radius;
+    });
+    logfc0line.attr("x2", width).attr("y1", yscale(0)).attr("y2", yscale(0));
+    bpg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
+    const p05 = xscale(avpercentile05), p25 = xscale(avpercentile25), p50 = xscale(avmedian), p75 = xscale(avpercentile75), p95 = xscale(avpercentile95);
+    percentile05line.attr("x1", p05).attr("x2", p05).attr("y2", boxh);
+    percentile95line.attr("x1", p95).attr("x2", p95).attr("y2", boxh);
+    bpmedianline.attr("x1", p50).attr("x2", p50).attr("y2", boxh);
+    bpbox.attr("x", p25).attr("width", p75 - p25).attr("height", boxh);
+    bpthroughline.attr("x1", p05).attr("x2", p95).attr("y1", boxh / 2).attr("y2", boxh / 2);
+    svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + boxh + ypad + xaxish);
+    axisstyle({
+      axis: yaxisg.call(axisLeft().scale(yscale)),
+      color: "black",
+      showline: true
+    });
+    axisstyle({
+      axis: xaxisg.call(axisBottom().scale(xscale)),
+      color: "black",
+      showline: true
+    });
+  }
+  resize(400, 400);
+  add_lasso(dotg.selectAll("circle"), svg, "vo_circle");
+  return svg;
+}
+function render_volcano(holder, mavb) {
+  let minlogfc = 0, maxlogfc = 0, minlogpv = 0, maxlogpv = 0;
+  for (const d of mavb.data) {
+    minlogfc = Math.min(minlogfc, d.logfoldchange);
+    maxlogfc = Math.max(maxlogfc, d.logfoldchange);
+    if (d.pvalue == 0) {
+      continue;
+    } else {
+      const v = -Math.log(d.pvalue, 10);
+      minlogpv = Math.min(minlogpv, v);
+      maxlogpv = Math.max(maxlogpv, v);
+    }
+  }
+  let yaxisw, xaxish, width, height, xpad, ypad, toppad = 50, rightpad = 50, radius;
+  const svg = holder.append("svg");
+  const yaxisg = svg.append("g");
+  const xaxisg = svg.append("g");
+  const xlab = svg.append("text").text("log2(fold change)").attr("fill", "black").attr("text-anchor", "middle");
+  const ylab = svg.append("text").text("-log(P value)").attr("fill", "black").attr("text-anchor", "middle");
+  mavb.vo_dotarea = svg.append("g");
+  const box = mavb.vo_dotarea.append("rect").attr("stroke", "#ededed").attr("fill", "none").attr("shape-rendering", "crispEdges");
+  const xscale = linear().domain([minlogfc, maxlogfc]);
+  const yscale = linear().domain([minlogpv, maxlogpv]);
+  let radiusscale;
+  if (mavb.hastvalue) radiusscale = linear().domain([mavb.tvaluemin, mavb.tvaluemax]);
+  const dotg = mavb.vo_dotarea.selectAll().data(mavb.data).enter().append("g").each(function(d) {
+    d.vo_g = this;
+  });
+  const circle = dotg.append("circle").attr("stroke", "black").attr("stroke-opacity", 0.2).attr("stroke-width", 1).attr("fill", hlcolor).attr("fill-opacity", 0).each(function(d) {
+    d.vo_circle = this;
+  }).on("mouseover", circlemouseover).on("mouseout", circlemouseout).on("click", (event2, d) => {
+    circleclick(d, mavb, event2.clientX, event2.clientY);
+  });
+  const logfc0line = mavb.vo_dotarea.append("line").attr("stroke", "#ccc").attr("shape-rendering", "crispEdges");
+  function resize(w, h) {
+    width = w;
+    height = h;
+    yaxisw = Math.max(50, width / 8);
+    xaxish = Math.max(50, height / 8);
+    radius = Math.max(width, height) / 80;
+    const maxradius = radius * 3;
+    if (radiusscale) radiusscale.range([radius, maxradius]);
+    circle.each((d) => {
+      d.vo_radius = radiusscale ? radiusscale(Math.abs(d.tvalue)) : radius;
+    });
+    xpad = Math.max(maxradius, width / 50);
+    ypad = Math.max(maxradius, height / 50);
+    yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
+    xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
+    xlab.attr("x", yaxisw + xpad + width / 2).attr("y", toppad + height + ypad + xaxish - 5);
+    ylab.attr("transform", "translate(15," + (toppad + height / 2) + ") rotate(-90)");
+    mavb.vo_dotarea.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
+    box.attr("width", width).attr("height", height);
+    xscale.range([0, width]);
+    yscale.range([height, 0]);
+    dotg.attr("transform", (d) => {
+      return "translate(" + xscale(d.logfoldchange) + "," + yscale(d.pvalue == 0 ? maxlogpv : -Math.log(d.pvalue, 10)) + ")";
+    });
+    circle.attr("r", (d) => {
+      return d.vo_radius;
+    });
+    logfc0line.attr("x1", xscale(0)).attr("x2", xscale(0)).attr("y2", height);
+    svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
+    axisstyle({
+      axis: yaxisg.call(axisLeft().scale(yscale)),
+      color: "black",
+      showline: true
+    });
+    axisstyle({
+      axis: xaxisg.call(axisBottom().scale(xscale)),
+      color: "black",
+      showline: true
+    });
+  }
+  resize(400, 400);
+  if (mavb.data[0].pvalueadj != void 0) {
+    const row = holder.append("div").style("margin", "20px");
+    row.append("span").text("Select P value for Volcano plot:");
+    const select = row.append("select").style("margin-left", "5px").on("change", (event2) => {
+      minlogpv = 0;
+      maxlogpv = 0;
+      const useun = select.node().selectedIndex == 0;
+      for (const d of mavb.data) {
+        const pv = useun ? d.pvalue : d.pvalueadj;
+        if (pv == 0) continue;
+        const v = -Math.log(pv, 10);
+        minlogpv = Math.min(minlogpv, v);
+        maxlogpv = Math.max(maxlogpv, v);
+      }
+      yscale.domain([minlogpv, maxlogpv]);
+      axisstyle({
+        axis: yaxisg.call(axisLeft().scale(yscale)),
+        color: "black",
+        showline: true
+      });
+      dotg.attr("transform", (d) => {
+        const pv = useun ? d.pvalue : d.pvalueadj;
+        return "translate(" + xscale(d.logfoldchange) + "," + yscale(pv == 0 ? maxlogpv : -Math.log(pv, 10)) + ")";
+      });
+      ylab.text(useun ? "-log(P value)" : "-log(adjusted P value)");
+    });
+    select.append("option").text("Unadjusted P value");
+    select.append("option").text("Adjusted P value");
+  }
+  add_lasso(dotg.selectAll("circle"), svg, "ma_circle");
+  return svg;
+}
+function add_lasso(selectable_items, svg, other_svg_item_key) {
+  const lasso = d3lasso().items(selectable_items).targetArea(svg);
+  function mavb_lasso_start() {
+    svg.selectAll(".possible").style("fill-opacity", 0).classed("not_possible", true).classed("selected", false).each((d) => {
+      select_default(d[other_svg_item_key]).attr("fill-opacity", 0);
+    });
+  }
+  function mavb_lasso_draw() {
+    lasso.possibleItems().style("fill-opacity", 0.9).classed("not_possible", false).classed("possible", true).each((d) => {
+      select_default(d[other_svg_item_key]).attr("fill-opacity", 0.9);
+    });
+  }
+  function mavb_lasso_end() {
+  }
+  lasso.on("start", mavb_lasso_start).on("draw", mavb_lasso_draw).on("end", mavb_lasso_end);
+  svg.call(lasso);
+}
+function circlemouseover(event2, d) {
+  tip.clear().show(event2.clientX, event2.clientY);
+  const lst = [
+    { k: "gene", v: d.gene },
+    { k: "average value", v: d.averagevalue },
+    { k: "log fold change", v: d.logfoldchange },
+    { k: "P value", v: d.pvalue }
+  ];
+  if (d.pvalueadj != void 0) {
+    lst.push({ k: "adjusted P value", v: d.pvalueadj });
+  }
+  if (d.tvalue != void 0) {
+    lst.push({ k: "T value", v: d.tvalue });
+  }
+  for (const k in d) {
+    if (k == "gene" || k == "averagevalue" || k == "logfoldchange" || k == "pvalue" || k == "pvalueadj" || k == "tvalue") {
+      continue;
+    }
+    const v = d[k];
+    if (typeof v != "string") {
+      continue;
+    }
+    lst.push({ k, v });
+  }
+  make_table_2col(tip.d, lst);
+  if (!d.ma_label) {
+    select_default(d.ma_circle).attr("fill-opacity", 0.9);
+    select_default(d.vo_circle).attr("fill-opacity", 0.9);
+  }
+}
+function circlemouseout(event2, d) {
+  tip.hide();
+  if (!d.ma_label) {
+    select_default(d.ma_circle).attr("fill-opacity", 0);
+    select_default(d.vo_circle).attr("fill-opacity", 0);
+  }
+}
+function hltoggle(d, mavb) {
+  if (d.ma_label) {
+    d.ma_label.remove();
+    d.ma_labelbg.remove();
+    d.ma_label = null;
+    d.vo_label.remove();
+    d.vo_labelbg.remove();
+    d.vo_label = null;
+    select_default(d.ma_circle).attr("fill-opacity", 0);
+    select_default(d.vo_circle).attr("fill-opacity", 0);
+    return;
+  }
+  mavb.ma_dotarea.node().appendChild(d.ma_g);
+  d.ma_labelbg = select_default(d.ma_g).append("text").text(d.gene).attr("x", d.ma_radius + 5).attr("y", 0).attr("dominant-baseline", "central").attr("font-size", 14).attr("font-family", font).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 3);
+  d.ma_label = select_default(d.ma_g).append("text").text(d.gene).attr("x", d.ma_radius + 5).attr("y", 0).attr("dominant-baseline", "central").attr("font-size", 14).attr("fill", "black").attr("font-family", font).on("mousedown", (event2, d2) => {
+    labelmousedown(d2.ma_label, d2.ma_labelbg, event2);
+  });
+  mavb.vo_dotarea.node().appendChild(d.vo_g);
+  d.vo_labelbg = select_default(d.vo_g).append("text").text(d.gene).attr("x", d.vo_radius + 5).attr("y", 0).attr("dominant-baseline", "central").attr("font-size", 14).attr("font-family", font).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 3);
+  d.vo_label = select_default(d.vo_g).append("text").text(d.gene).attr("x", d.vo_radius + 5).attr("y", 0).attr("dominant-baseline", "central").attr("font-size", 14).attr("fill", "black").attr("font-family", font).on("mousedown", (event2, d2) => {
+    labelmousedown(d2.vo_label, d2.vo_labelbg, event2);
+  });
+  select_default(d.ma_circle).attr("fill-opacity", 0.8);
+  select_default(d.vo_circle).attr("fill-opacity", 0.8);
+}
+function labelmousedown(label, labelbg, evt) {
+  event.preventDefault();
+  const labx = Number.parseFloat(label.attr("x"));
+  const laby = Number.parseFloat(label.attr("y"));
+  const x0 = evt.clientX;
+  const y0 = evt.clientY;
+  const body = select_default(document.body);
+  body.on("mousemove", (event2) => {
+    label.attr("x", labx + event2.clientX - x0).attr("y", laby + event2.clientY - y0);
+    labelbg.attr("x", labx + event2.clientX - x0).attr("y", laby + event2.clientY - y0);
+  }).on("mouseup", (event2) => {
+    body.on("mousemove", null).on("mouseup", null);
+  });
+}
+function circleclick(d, mavb, mousex, mousey) {
+  if (mavb.tracks) {
+    if (!d.ma_label) {
+      const pane = newpane({ x: mousex + 20, y: mousey - 50 });
+      pane.header.text(d.gene);
+      showTracks(mavb, d.gene, pane.body);
+    }
+  }
+  hltoggle(d, mavb);
+}
+function showTracks(mavb, gene, holder) {
+  fetch(
+    new Request(mavb.hostURL + "/genelookup", {
+      method: "POST",
+      body: JSON.stringify({ deep: 1, input: gene, genome: mavb.genome.name, jwt: mavb.jwt })
+    })
+  ).then((data) => {
+    return data.json();
+  }).then((data) => {
+    if (data.error) throw { message: data.error };
+    if (!data.gmlst || data.gmlst.length == 0) throw { message: "No genes can be found for " + gene };
+    const chr2pos = /* @__PURE__ */ new Map();
+    for (const m of data.gmlst) {
+      if (!chr2pos.has(m.chr)) {
+        chr2pos.set(m.chr, { chr: m.chr, start: m.start, stop: m.stop });
+      }
+      chr2pos.get(m.chr).start = Math.min(m.start, chr2pos.get(m.chr).start);
+      chr2pos.get(m.chr).stop = Math.max(m.stop, chr2pos.get(m.chr).stop);
+    }
+    const coord = [...chr2pos][0][1];
+    const tklst = [...mavb.tracks];
+    first_genetrack_tolist(mavb.genome, tklst);
+    blocklazyload({
+      holder,
+      hostURL: mavb.hostURL,
+      jwt: mavb.jwt,
+      genome: mavb.genome,
+      chr: coord.chr,
+      start: coord.start,
+      stop: coord.stop,
+      tklst,
+      nobox: true
+    });
+  }).catch((err) => {
+    sayerror(holder, err.message);
+    if (err.stack) console.log(err.stack);
+  });
+}
+export {
+  mavbparseinput,
+  mavbui
+};
+//# sourceMappingURL=mavb-ARUWOZES.js.map