@sjcrh/proteinpaint-client 2.219.1 → 2.221.0

package/dist/mavb-KIM63AC4.js

@@ -1,726 +0,0 @@
-import {
-  blocklazyload
-} from "./chunk-MP7BA3GK.js";
-import {
-  d3lasso
-} from "./chunk-JH73IL4C.js";
-import {
-  axisstyle,
-  first_genetrack_tolist,
-  font,
-  make_table_2col,
-  newpane,
-  newpane3,
-  renderSandboxFormDiv,
-  sayerror,
-  to_svg
-} from "./chunk-BKW35Z4U.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-ETXOEP4N.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-5NI77Z3O.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-CJHNPYFQ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-NR6WFCPF.js";
-import "./chunk-GN2A5NL5.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-ME3HB3V6.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.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",
-      headers: { "content-type": "application/json" },
-      body: JSON.stringify({ url: mavb.url, jwt })
-    });
-    delete mavb.url;
-  } else if (mavb.file) {
-    request = new Request(mavb.hostURL + "/textfile", {
-      method: "POST",
-      headers: { "content-type": "application/json" },
-      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",
-      headers: { "content-type": "application/json" },
-      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-KIM63AC4.js.map