@sjcrh/proteinpaint-client 2.222.0 → 2.223.0

package/dist/mds.fimo-7WH5GVFZ.js

@@ -1,509 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  font,
-  gmlst2loci,
-  keyupEnter,
-  make_table_2col
-} from "./chunk-4ASBDE27.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-OF6FDDKV.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch
-} from "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import {
-  axisTop
-} from "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/mds.fimo.js
-var headerheight = 80;
-var headerunderpad = 5;
-async function init(obj) {
-  window.obj = obj;
-  obj.errdiv = obj.div.append("div");
-  try {
-    init_ui(obj);
-    await do_query(obj);
-  } catch (e) {
-    obj.errdiv.text(e.message || e);
-    if (e.stack) console.log(e.stack);
-  }
-}
-function init_ui(obj) {
-  obj.motifrowheight = 16;
-  obj.gaincolor = "red";
-  obj.losscolor = "blue";
-  obj.flankspan = 15;
-  if (!obj.fimo_thresh) obj.fimo_thresh = 1e-3;
-  if (!obj.minabslogp) obj.minabslogp = 1;
-  obj.tip = new Menu();
-  const table = obj.div.append("table").style("border-spacing", "3px").style("border-collapse", "separate").style("margin", "10px");
-  {
-    const tr = table.append("tr");
-    tr.append("td").text("Flanking sequence (#nt)");
-    const td = tr.append("td");
-    td.append("input").attr("type", "number").style("margin", "0px 10px").style("width", "100px").property("value", obj.flankspan).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      const v = Number.parseInt(event.target.value);
-      if (v < 10) {
-        window.alert("Enter integer above 10");
-        return;
-      }
-      if (v == obj.flankspan) return;
-      obj.flankspan = v;
-      do_query(obj);
-    });
-    td.append("span").style("font-size", "0.7em").style("opacity", 0.5).text("Press ENTER to update");
-  }
-  {
-    const tr = table.append("tr");
-    tr.append("td").text("P-value cutoff");
-    const td = tr.append("td");
-    td.append("input").attr("type", "number").style("margin", "0px 10px").style("width", "100px").property("value", obj.fimo_thresh).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      const v = Number.parseFloat(event.target.value);
-      if (v <= 0) {
-        window.alert("Enter a p value between 0 to 1");
-        return;
-      }
-      if (v == obj.fimo_thresh) return;
-      obj.fimo_thresh = v;
-      do_query(obj);
-    });
-    td.append("span").style("font-size", "0.7em").style("opacity", 0.5).text("Press ENTER to update");
-  }
-  {
-    const tr = table.append("tr");
-    tr.append("td").text("Minimum log10 p-value difference");
-    const td = tr.append("td");
-    td.append("input").attr("type", "number").style("margin", "0px 10px").style("width", "100px").property("value", obj.minabslogp).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      const v = Number.parseFloat(event.target.value);
-      if (v <= 0) {
-        window.alert("Enter a number above 0");
-        return;
-      }
-      if (v == obj.minabslogp) return;
-      obj.minabslogp = v;
-      do_query(obj);
-    });
-    td.append("span").style("font-size", "0.7em").style("opacity", 0.5).text("Press ENTER to update");
-  }
-  obj.wait = obj.div.append("div");
-  obj.svg = obj.div.append("svg");
-  obj.dynamic_g = obj.svg.append("g");
-  obj.legend = {};
-  obj.legend.logpvaluediv = obj.div.append("div");
-  may_init_factorprofiles(obj);
-}
-function may_init_factorprofiles(obj) {
-  if (!obj.factor_profiles) return;
-  if (!Array.isArray(obj.factor_profiles)) throw "factor_profiles is not array";
-  for (const profile of obj.factor_profiles) {
-    if (!profile.name) throw "name missing for a profile";
-    if (!profile.leftpad) profile.leftpad = 20;
-    if (!profile.width) profile.width = 300;
-    profile.headerg = obj.svg.append("g");
-    profile.textlabel = profile.headerg.append("text").text(profile.name).attr("x", profile.width / 2).attr("text-anchor", "middle").attr("y", -30);
-    if (profile.isgenevalue) {
-      profile.color = "green";
-      profile.axisg = profile.headerg.append("g");
-      continue;
-    }
-    if (profile.isgenevalueonesample) {
-      if (!profile.samplename) throw "samplename missing for isgenevalueonesample";
-      profile.barcolor = "#62945B";
-      profile.axisg = profile.headerg.append("g");
-      continue;
-    }
-    throw "unknown profile type";
-  }
-}
-function do_query(obj) {
-  appear(obj.wait.text("Loading..."));
-  obj.dynamic_g.selectAll("*").remove();
-  const arg = {
-    genome: obj.genome.name,
-    m: obj.m,
-    fimo_thresh: obj.fimo_thresh,
-    flankspan: obj.flankspan,
-    minabslogp: obj.minabslogp
-  };
-  return dofetch("fimo", arg).then((data) => {
-    if (data.error) throw "Error: cannot do motif finding: " + data.error;
-    if (obj.callback_once) {
-      obj.callback_once();
-      delete obj.callback_once;
-    }
-    if (!data.items || data.items.length == 0) throw "Found no motif change due to this mutation";
-    obj.wait.style("display", "none");
-    for (const m of data.items) {
-      if (m.attr) {
-        m.gene = m.attr["Transcription factor"];
-      } else {
-        m.gene = m.name;
-      }
-    }
-    return show_result(data, obj);
-  }).catch((e) => {
-    obj.wait.style("display", "block").text(e.message || e);
-    if (e.stack) console.log(e.stack);
-  });
-}
-async function show_result(data, obj) {
-  draw_motif_simplified(data, obj);
-  if (obj.factor_profiles) {
-    await get_gene_position(data, obj);
-    let width = Number.parseInt(obj.svg.attr("width"));
-    for (const profile of obj.factor_profiles) {
-      profile.headerg.attr("transform", "translate(" + (width + profile.leftpad) + "," + headerheight + ")");
-      profile.motifs = [];
-      for (const motif of data.items) {
-        const pg = motif.layer1_g.append("g").attr("transform", "translate(" + (width + profile.leftpad) + ",0)");
-        profile.motifs.push({
-          motif,
-          g: pg,
-          message: pg.append("text").text("Loading...").attr("dominant-baseline", "central").attr("fill", "#ccc")
-        });
-      }
-      width += profile.leftpad + profile.width;
-      obj.svg.attr("width", width + 5);
-      await load_factorprofile(obj, profile);
-      for (const m of data.items) {
-        m.bgbox.attr("width", width);
-        m.coverbox.attr("width", width);
-      }
-    }
-  }
-}
-function draw_motif_simplified(data, obj) {
-  const ntwidth = 14;
-  const motifgraphwidth = ntwidth * data.refseq.length;
-  const ntfontsize = 16;
-  const rulerheight = 30;
-  {
-    const x = (obj.m.pos - data.refstart + 0.5) * ntwidth;
-    const g2 = obj.dynamic_g.append("g").attr("transform", "translate(" + x + "," + headerheight + ")");
-    g2.append("rect").attr("x", -ntwidth / 2).attr("y", -10).attr("width", ntwidth).attr("height", 10).attr("fill", "#666");
-    g2.append("text").attr("y", -15).attr("text-anchor", "middle").text(obj.m.chr + ":" + obj.m.pos + " " + obj.m.ref + ">" + obj.m.alt);
-  }
-  let svgheight = headerheight + headerunderpad;
-  const rowspace = 1;
-  const g = obj.dynamic_g.append("g").attr("transform", "translate(0," + svgheight + ")");
-  for (const [i, motif] of data.items.entries()) {
-    motif.g = g.append("g").attr("transform", "translate(0," + (obj.motifrowheight * (i + 0.5) + rowspace * i) + ")");
-    motif.layer1_g = motif.g.append("g");
-    motif.layer2_g = motif.g.append("g");
-    motif.bgbox = motif.layer1_g.append("rect").attr("y", -obj.motifrowheight / 2).attr("width", motifgraphwidth).attr("height", obj.motifrowheight).attr("fill", "white");
-    const x = (motif.start - data.refstart) * ntwidth;
-    const w = (Math.min(motif.stop, data.refstop) - motif.start) * ntwidth;
-    motif.layer1_g.append("rect").attr("x", x).attr("y", -obj.motifrowheight / 2).attr("width", w).attr("height", obj.motifrowheight).attr("fill", motif.gain ? obj.gaincolor : obj.losscolor).attr("fill-opacity", motif.logpvaluediff / (motif.gain ? data.valuemax : data.valuemin));
-    let str;
-    if (motif.strand == "+") {
-      str = ">  " + motif.name + "  >";
-    } else {
-      str = "<  " + motif.name + "  <";
-    }
-    motif.layer1_g.append("text").text(str).attr("x", x + w / 2).attr("dominant-baseline", "central").attr("text-anchor", "middle").attr("stroke", "white").attr("stroke-width", 3).attr("font-size", obj.motifrowheight - 3).attr("font-family", font).style("white-space", "pre");
-    motif.layer1_g.append("text").text(str).attr("x", x + w / 2).attr("dominant-baseline", "central").attr("text-anchor", "middle").attr("font-size", obj.motifrowheight - 3).attr("font-family", font).style("white-space", "pre");
-    motif.coverbox = motif.layer2_g.append("rect").attr("y", -obj.motifrowheight / 2).attr("width", motifgraphwidth).attr("height", obj.motifrowheight).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event) => {
-      motif.bgbox.attr("fill", "#f9fabd");
-      motif_tooltip(motif, obj, event);
-    }).on("mouseout", () => {
-      motif.bgbox.attr("fill", "white");
-      obj.tip.hide();
-    });
-  }
-  svgheight += (rowspace + obj.motifrowheight) * data.items.length + 20;
-  make_legend(data, obj);
-  obj.svg.attr("width", motifgraphwidth).attr("height", svgheight);
-}
-function motif_tooltip(motif, obj, event) {
-  obj.tip.clear();
-  if (motif.attr) {
-    obj.tip.d.append("div").text("MOTIF").style("font-weight", "bold");
-    const lst1 = [
-      { k: "P-values", v: htmlpvalue(motif, obj) },
-      { k: "Strand", v: motif.strand }
-    ];
-    make_table_2col(obj.tip.d, lst1);
-    obj.tip.d.append("div").text("FACTOR").style("font-weight", "bold");
-    const lst2 = [];
-    for (const k in motif.attr) {
-      lst2.push({ k, v: motif.attr[k] });
-    }
-    make_table_2col(obj.tip.d, lst2);
-  } else {
-    const lst = [
-      { k: "TF", v: motif.name },
-      { k: "P-values", v: htmlpvalue(motif, obj) },
-      { k: "Strand", v: motif.strand }
-    ];
-    make_table_2col(obj.tip.d, lst);
-  }
-  obj.tip.show(event.clientX, event.clientY);
-}
-function htmlpvalue(m, obj) {
-  return (m.pvalue_ref == void 0 ? '<span style="opacity:.5;padding:2px"><span style="font-size:.7em">REF</span> not found</span>' : '<span style="background-color:' + obj.losscolor + ';padding:2px;color:white;"><span style="font-size:.7em">REF</span> ' + m.pvalue_ref + "</span>") + "<br>" + (m.pvalue_alt == void 0 ? '<span style="opacity:.5;padding:2px"><span style="font-size:.7em">ALT</span> not found</span>' : '<span style="background-color:' + obj.gaincolor + ';padding:2px;color:white;"><span style="font-size:.7em">ALT</span> ' + m.pvalue_alt + "</span>");
-}
-function make_legend(data, obj) {
-  obj.legend.logpvaluediv.selectAll("*").remove();
-  const leftpad = 50, axistickh = 4, fontsize = 12, barw = 55, barh = 20;
-  obj.legend.logpvaluediv.append("span").text("Log10 p-value difference");
-  const svg = obj.legend.logpvaluediv.append("svg").attr("width", (leftpad + barw) * 2).attr("height", fontsize + axistickh + barh);
-  const axisg = svg.append("g").attr("transform", "translate(" + leftpad + "," + (fontsize + axistickh) + ")");
-  axisstyle({
-    axis: axisg.call(
-      axisTop().scale(
-        linear().domain([data.valuemin, 0, data.valuemax]).range([0, barw, barw * 2])
-      ).tickValues([data.valuemin, 0, data.valuemax]).tickSize(axistickh)
-    )
-  });
-  const gain_id = Math.random().toString();
-  const loss_id = Math.random().toString();
-  const defs = svg.append("defs");
-  {
-    const grad = defs.append("linearGradient").attr("id", loss_id);
-    grad.append("stop").attr("offset", "0%").attr("stop-color", obj.losscolor);
-    grad.append("stop").attr("offset", "100%").attr("stop-color", "white");
-  }
-  {
-    const grad = defs.append("linearGradient").attr("id", gain_id);
-    grad.append("stop").attr("offset", "0%").attr("stop-color", "white");
-    grad.append("stop").attr("offset", "100%").attr("stop-color", obj.gaincolor);
-  }
-  svg.append("rect").attr("x", leftpad).attr("y", fontsize + axistickh).attr("width", barw).attr("height", barh).attr("fill", "url(#" + loss_id + ")");
-  svg.append("rect").attr("x", leftpad + barw).attr("y", fontsize + axistickh).attr("width", barw).attr("height", barh).attr("fill", "url(#" + gain_id + ")");
-  svg.append("text").attr("x", leftpad - 5).attr("y", fontsize + axistickh + barh / 2).attr("font-family", font).attr("font-size", fontsize).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("fill", "black").text("Loss");
-  svg.append("text").attr("x", leftpad + barw * 2 + 5).attr("y", fontsize + axistickh + barh / 2).attr("font-family", font).attr("font-size", fontsize).attr("dominant-baseline", "central").attr("fill", "black").text("Gain");
-}
-async function get_gene_position(data, obj) {
-  obj.gene2position = {};
-  const factornames = /* @__PURE__ */ new Set();
-  for (const m of data.items) {
-    factornames.add(m.gene);
-  }
-  for (const genename of factornames) {
-    const pos = await get_one_gene_position(genename, obj);
-    if (pos) {
-      obj.gene2position[genename] = pos;
-    }
-  }
-}
-function get_one_gene_position(genename, obj) {
-  return dofetch("genelookup", { genome: obj.genome.name, input: genename, deep: 1 }).then((data) => {
-    if (!data.gmlst) return null;
-    const loci = gmlst2loci(data.gmlst);
-    return loci[0];
-  });
-}
-function load_factorprofile(obj, profile) {
-  if (profile.isgenevalue) {
-    return load_factorprofile_genevalue(obj, profile);
-  }
-  if (profile.isgenevalueonesample) {
-    return load_factorprofile_genevalueonesample(obj, profile);
-  }
-  throw "unknown profile type";
-}
-async function load_factorprofile_genevalueonesample(obj, profile) {
-  const arg = {
-    genome: obj.genome.name,
-    genes: [],
-    sample: profile.samplename
-  };
-  if (profile.mdslabel) {
-    arg.dslabel = profile.mdslabel;
-    arg.querykey = profile.querykey;
-    if (profile.samplegroup_attrlst) {
-      arg.getgroup = profile.samplegroup_attrlst;
-    }
-  } else {
-    arg.iscustom = 1;
-    arg.file = profile.file;
-    arg.url = profile.url;
-    arg.indexURL = profile.indexURL;
-  }
-  for (const g in obj.gene2position) {
-    const r = obj.gene2position[g];
-    arg.genes.push({
-      gene: g,
-      chr: r.chr,
-      start: r.start,
-      stop: r.stop
-    });
-  }
-  return dofetch("mdsgenevalueonesample", arg).then((data) => {
-    if (data.error) throw data.error;
-    for (const m of profile.motifs) {
-      m.message.text("No data");
-    }
-    if (data.nodata) return;
-    if (!data.result) throw "error";
-    let min = 0, max = 0;
-    for (const g in data.result) {
-      min = Math.min(min, data.result[g]);
-      max = Math.max(max, data.result[g]);
-    }
-    const scale = linear().domain([min, max]).range([0, profile.width]);
-    axisstyle({
-      axis: profile.axisg.call(axisTop().scale(scale).ticks(4)),
-      showline: 1
-    });
-    for (const m of profile.motifs) {
-      const v = data.result[m.motif.gene];
-      if (Number.isFinite(v)) {
-        m.message.text("");
-        m.g.append("rect").attr("y", -obj.motifrowheight / 2).attr("width", Math.max(1, scale(v))).attr("height", obj.motifrowheight).attr("shape-rendering", "crispEdges").attr("fill", profile.barcolor);
-      }
-    }
-    profile.textlabel.attr("x", profile.width / 2).attr("text-anchor", "middle").attr("y", -30);
-  }).catch((e) => {
-    if (e.stack) console.log(e.stack);
-    appear(obj.wait.text(e.message || e));
-  });
-}
-async function load_factorprofile_genevalue(obj, profile) {
-  profile.gene2result = /* @__PURE__ */ new Map();
-  for (const gene in obj.gene2position) {
-    const data = await factorprofile_genevalue_onegene_loadboxplot(obj, profile, gene);
-    if (data) {
-      factorprofile_genevalue_onegene_makeboxplot(obj, profile, gene, data);
-      profile.gene2result.set(gene, data);
-      factorprofile_genevalue_updatescale(obj, profile);
-    }
-  }
-  factorprofile_genevalue_finish(obj, profile);
-}
-function factorprofile_genevalue_onegene_makeboxplot(obj, profile, gene, data) {
-  if (data.nodata) return;
-  for (const m of profile.motifs) {
-    if (m.motif.gene != gene) continue;
-    m.boxplot = {
-      out: []
-    };
-    if (data.w1 != void 0) {
-      m.boxplot.hline = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
-      m.boxplot.linew1 = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
-      m.boxplot.linew2 = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
-      m.boxplot.box = m.g.append("rect").attr("fill", "white").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
-      m.boxplot.linep50 = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
-    }
-    if (data.out) {
-      for (const d of data.out) {
-        const circle = m.g.append("circle").attr("stroke", profile.color).attr("fill", "white").attr("fill-opacity", 0);
-        m.boxplot.out.push({
-          value: d.value,
-          circle
-        });
-      }
-    }
-  }
-}
-function factorprofile_genevalue_updatescale(obj, profile) {
-  let min = 0, max = 0;
-  for (const g of profile.gene2result.values()) {
-    min = Math.min(min, g.min);
-    max = Math.max(max, g.max);
-  }
-  const scale = linear().domain([min, max]).range([0, profile.width]);
-  const h = obj.motifrowheight - 2;
-  for (const [g, r] of profile.gene2result) {
-    for (const m of profile.motifs) {
-      if (m.motif.gene != g) continue;
-      const bp = m.boxplot;
-      if (!bp) continue;
-      if (bp.hline) {
-        const w1 = scale(r.w1);
-        const w2 = scale(r.w2);
-        const p25 = scale(r.p25);
-        const p50 = scale(r.p50);
-        const p75 = scale(r.p75);
-        bp.hline.transition().attr("x1", w1).attr("x2", w2);
-        bp.linew1.transition().attr("x1", w1).attr("x2", w1).attr("y1", -h / 2).attr("y2", h / 2);
-        bp.linew2.transition().attr("x1", w2).attr("x2", w2).attr("y1", -h / 2).attr("y2", h / 2);
-        bp.box.transition().attr("x", p25).attr("y", -h / 2).attr("width", p75 - p25).attr("height", h);
-        bp.linep50.transition().attr("x1", p50).attr("x2", p50).attr("y1", -h / 2).attr("y2", h / 2);
-      }
-      for (const d of bp.out) {
-        d.circle.transition().attr("cx", scale(d.value)).attr("r", h / 3);
-      }
-    }
-  }
-  axisstyle({
-    axis: profile.axisg.transition().call(axisTop().scale(scale).ticks(4)),
-    showline: 1
-  });
-}
-function factorprofile_genevalue_onegene_loadboxplot(obj, profile, gene) {
-  const r = obj.gene2position[gene];
-  const arg = {
-    genome: obj.genome.name,
-    gene,
-    chr: r.chr,
-    start: r.start,
-    stop: r.stop,
-    getgroup2boxplot: 1
-  };
-  if (profile.mdslabel) {
-    arg.dslabel = profile.mdslabel;
-    arg.querykey = profile.querykey;
-    if (profile.samplegroup_attrlst) {
-      arg.getgroup = profile.samplegroup_attrlst;
-    }
-  } else {
-    arg.iscustom = 1;
-    arg.file = profile.file;
-    arg.url = profile.url;
-    arg.indexURL = profile.indexURL;
-  }
-  return dofetch("mdsgeneboxplot", arg).then((data) => {
-    if (data.error) throw "Error: " + data.error;
-    if (data.nodata) throw "No data";
-    for (const m of profile.motifs) {
-      if (m.motif.gene == gene) {
-        m.message.text("");
-      }
-    }
-    return data;
-  }).catch((e) => {
-    if (e.stack) console.log(e.stack);
-    for (const m of profile.motifs) {
-      if (m.motif.gene == gene) {
-        m.message.text(e.message || e);
-      }
-    }
-  });
-}
-function factorprofile_genevalue_finish(obj, profile) {
-  let n = 0;
-  for (const g of profile.gene2result.values()) {
-    n = Math.max(n, g.n);
-  }
-  profile.textlabel.text(profile.name + " (n=" + n + ")").attr("x", profile.width / 2).attr("text-anchor", "middle").attr("y", -30);
-}
-export {
-  init
-};
-//# sourceMappingURL=mds.fimo-7WH5GVFZ.js.map

package/dist/mds.fimo-7WH5GVFZ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/mds.fimo.js"],
-  "sourcesContent": ["import * as client from './client'\nimport { axisTop } from 'd3-axis'\nimport { scaleLinear } from 'd3-scale'\n\n/*\n\n\n\nobj{}:\n.genome {}\n.fimo_thresh\n.minabslogp    min abs log p\n.flankspan     bp\n.gain/losscolor\n.motifrowheight\n.m{}\n\t.chr\n\t.pos\n\t.ref\n\t.alt\n.div<>\n.svg<>\n.legend{}\n.callback_once()\n.gene2position{}     for current list of factors\n\n.factor_profiles[ {} ]\n\t.name\n\t.headerg<>\n\t.leftpad\n\t.width\n\t.motifs[ {} ]\n\t\t.motif    ---> one of data.items[]\n\t\t.g\n\t\t.boxplot{}\n\t\t\t.out[]\n\t=== PROFILE TYPE ===\n\t.isgenevalue\n\t\t.mdslabel\n\t\t.querykey\n\t\t.samplegroup_attrlst[{}]\n\t\t\t.k\n\t\t\t.kvalue\n\t\t.axisg<>\n\t\t.gene2result{}\n\t=== OTHER TYPE ===\n\n\n\ndata{} returned by /fimo\n.refseq   nt sequence\n.refstart\n.refstop\n.items[{}]\n\t.loss/gain   BOOL\n\t.pvalue\n\t.name           factor name\n\t.logpvaluediff\n\t.attr{}\n\t.gene   from .attr.gene\n\t.start\n\t.stop\n\t.strand +/-\n\t.g<>\n\t.layer1_g<>\n\t.layer2_g<>\n\t.bgbox<>\n\t.coverbox<>\n\n\n\n********************** EXPORTED\ninit()\n********************** INTERNAL\nshow_result()\ndraw_motif_simplified()\nload_factorprofile\nload_factorprofile_genevalue\nload_factorprofile_genevalueonesample\nfactorprofile_genevalue_onegene_loadboxplot\n*/\n\n// header height, for all panels\n// this may be dynamic as certain profile may increase it\nconst headerheight = 80\n\nconst headerunderpad = 5\n\nexport async function init(obj) {\n\t/*\n\t */\n\twindow.obj = obj\n\n\tobj.errdiv = obj.div.append('div')\n\n\ttry {\n\t\tinit_ui(obj)\n\t\tawait do_query(obj)\n\t} catch (e) {\n\t\tobj.errdiv.text(e.message || e)\n\t\tif (e.stack) console.log(e.stack)\n\t}\n}\n\nfunction init_ui(obj) {\n\t// set attr\n\tobj.motifrowheight = 16\n\tobj.gaincolor = 'red'\n\tobj.losscolor = 'blue'\n\tobj.flankspan = 15\n\tif (!obj.fimo_thresh) obj.fimo_thresh = 1e-3\n\tif (!obj.minabslogp) obj.minabslogp = 1\n\n\tobj.tip = new client.Menu()\n\n\tconst table = obj.div\n\t\t.append('table')\n\t\t.style('border-spacing', '3px')\n\t\t.style('border-collapse', 'separate')\n\t\t.style('margin', '10px')\n\n\t// flank bp len\n\t{\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td').text('Flanking sequence (#nt)')\n\t\tconst td = tr.append('td')\n\t\ttd.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.style('margin', '0px 10px')\n\t\t\t.style('width', '100px')\n\t\t\t.property('value', obj.flankspan)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (!client.keyupEnter(event)) return\n\t\t\t\tconst v = Number.parseInt(event.target.value)\n\t\t\t\tif (v < 10) {\n\t\t\t\t\twindow.alert('Enter integer above 10')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (v == obj.flankspan) return\n\t\t\t\tobj.flankspan = v\n\t\t\t\tdo_query(obj)\n\t\t\t})\n\t\ttd.append('span').style('font-size', '0.7em').style('opacity', 0.5).text('Press ENTER to update')\n\t}\n\t// p thresh\n\t{\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td').text('P-value cutoff')\n\t\tconst td = tr.append('td')\n\t\ttd.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.style('margin', '0px 10px')\n\t\t\t.style('width', '100px')\n\t\t\t.property('value', obj.fimo_thresh)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (!client.keyupEnter(event)) return\n\t\t\t\tconst v = Number.parseFloat(event.target.value)\n\t\t\t\tif (v <= 0) {\n\t\t\t\t\twindow.alert('Enter a p value between 0 to 1')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (v == obj.fimo_thresh) return\n\t\t\t\tobj.fimo_thresh = v\n\t\t\t\tdo_query(obj)\n\t\t\t})\n\t\ttd.append('span').style('font-size', '0.7em').style('opacity', 0.5).text('Press ENTER to update')\n\t}\n\n\t// minimum logp for display\n\t{\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td').text('Minimum log10 p-value difference')\n\t\tconst td = tr.append('td')\n\t\ttd.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.style('margin', '0px 10px')\n\t\t\t.style('width', '100px')\n\t\t\t.property('value', obj.minabslogp)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (!client.keyupEnter(event)) return\n\t\t\t\tconst v = Number.parseFloat(event.target.value)\n\t\t\t\tif (v <= 0) {\n\t\t\t\t\twindow.alert('Enter a number above 0')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (v == obj.minabslogp) return\n\t\t\t\tobj.minabslogp = v\n\t\t\t\tdo_query(obj)\n\t\t\t})\n\t\ttd.append('span').style('font-size', '0.7em').style('opacity', 0.5).text('Press ENTER to update')\n\t}\n\n\t// dom\n\tobj.wait = obj.div.append('div')\n\tobj.svg = obj.div.append('svg')\n\tobj.dynamic_g = obj.svg.append('g') // all dynamic components rendered after loading data\n\tobj.legend = {}\n\tobj.legend.logpvaluediv = obj.div.append('div')\n\n\tmay_init_factorprofiles(obj)\n}\n\nfunction may_init_factorprofiles(obj) {\n\tif (!obj.factor_profiles) return\n\tif (!Array.isArray(obj.factor_profiles)) throw 'factor_profiles is not array'\n\tfor (const profile of obj.factor_profiles) {\n\t\tif (!profile.name) throw 'name missing for a profile'\n\t\tif (!profile.leftpad) profile.leftpad = 20\n\t\tif (!profile.width) profile.width = 300\n\n\t\tprofile.headerg = obj.svg.append('g')\n\t\tprofile.textlabel = profile.headerg\n\t\t\t.append('text')\n\t\t\t.text(profile.name)\n\t\t\t.attr('x', profile.width / 2)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('y', -30)\n\n\t\tif (profile.isgenevalue) {\n\t\t\tprofile.color = 'green'\n\t\t\tprofile.axisg = profile.headerg.append('g')\n\t\t\tcontinue\n\t\t}\n\t\tif (profile.isgenevalueonesample) {\n\t\t\tif (!profile.samplename) throw 'samplename missing for isgenevalueonesample'\n\t\t\tprofile.barcolor = '#62945B'\n\t\t\tprofile.axisg = profile.headerg.append('g')\n\t\t\tcontinue\n\t\t}\n\t\tthrow 'unknown profile type'\n\t}\n}\n\nfunction do_query(obj) {\n\tclient.appear(obj.wait.text('Loading...'))\n\tobj.dynamic_g.selectAll('*').remove()\n\n\tconst arg = {\n\t\tgenome: obj.genome.name,\n\t\tm: obj.m,\n\t\tfimo_thresh: obj.fimo_thresh,\n\t\tflankspan: obj.flankspan,\n\t\tminabslogp: obj.minabslogp\n\t}\n\n\treturn client\n\t\t.dofetch('fimo', arg)\n\t\t.then(data => {\n\t\t\tif (data.error) throw 'Error: cannot do motif finding: ' + data.error\n\n\t\t\tif (obj.callback_once) {\n\t\t\t\tobj.callback_once()\n\t\t\t\tdelete obj.callback_once\n\t\t\t}\n\n\t\t\tif (!data.items || data.items.length == 0) throw 'Found no motif change due to this mutation'\n\n\t\t\tobj.wait.style('display', 'none')\n\n\t\t\t// get gene name\n\t\t\tfor (const m of data.items) {\n\t\t\t\tif (m.attr) {\n\t\t\t\t\tm.gene = m.attr['Transcription factor']\n\t\t\t\t} else {\n\t\t\t\t\tm.gene = m.name\n\t\t\t\t}\n\t\t\t}\n\n\t\t\treturn show_result(data, obj)\n\t\t})\n\t\t.catch(e => {\n\t\t\tobj.wait.style('display', 'block').text(e.message || e)\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t})\n}\n\nasync function show_result(data, obj) {\n\t/*\ndraw motif line up against ref sequence\nif expression is available, draw placeholder for each factor and query\n*/\n\n\tdraw_motif_simplified(data, obj)\n\n\t// update factor profile when motifs are added/removed\n\tif (obj.factor_profiles) {\n\t\tawait get_gene_position(data, obj)\n\n\t\t// expand svg width\n\t\tlet width = Number.parseInt(obj.svg.attr('width'))\n\n\t\tfor (const profile of obj.factor_profiles) {\n\t\t\tprofile.headerg.attr('transform', 'translate(' + (width + profile.leftpad) + ',' + headerheight + ')')\n\n\t\t\t// for this profile, every motif gets a holder\n\t\t\t// even if two motifs are of same factor\n\t\t\tprofile.motifs = []\n\t\t\tfor (const motif of data.items) {\n\t\t\t\tconst pg = motif.layer1_g.append('g').attr('transform', 'translate(' + (width + profile.leftpad) + ',0)')\n\t\t\t\tprofile.motifs.push({\n\t\t\t\t\tmotif: motif,\n\t\t\t\t\tg: pg,\n\t\t\t\t\tmessage: pg.append('text').text('Loading...').attr('dominant-baseline', 'central').attr('fill', '#ccc')\n\t\t\t\t})\n\t\t\t}\n\n\t\t\twidth += profile.leftpad + profile.width\n\n\t\t\tobj.svg.attr('width', width + 5)\n\n\t\t\tawait load_factorprofile(obj, profile)\n\n\t\t\t// extend row bg/cover box width\n\t\t\tfor (const m of data.items) {\n\t\t\t\tm.bgbox.attr('width', width)\n\t\t\t\tm.coverbox.attr('width', width)\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction draw_motif_simplified(data, obj) {\n\t/*\n\t */\n\n\tconst ntwidth = 14 // basepair width\n\tconst motifgraphwidth = ntwidth * data.refseq.length\n\tconst ntfontsize = 16\n\tconst rulerheight = 30\n\n\t/*\n\t// plot ruler\n\t{\n\t\tconst g = obj.svg.append('g')\n\t\t\t.attr('transform','translate('+(ntwidth/2)+','+rulerheight+')')\n\t\tconst fontsize = 14 // axis lab\n\t\tlet w\n\t\tg.append('text')\n\t\t\t.text(data.refstart)\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.each(function(){\n\t\t\t\tw = this.getBBox().width\n\t\t\t})\n\t\t\t.remove()\n\t\tclient.axisstyle({\n\t\t\taxis: g.call(\n\t\t\t\taxisTop().scale(\n\t\t\t\t\tscaleLinear().domain([data.refstart, data.refstop]).range([ 0, motifgraphwidth - ntwidth ])\n\t\t\t\t)\n\t\t\t\t.ticks( Math.floor( motifgraphwidth / (w+30) ) )\n\t\t\t),\n\t\t\tshowline: 1,\n\t\t\tfontsize: fontsize\n\t\t})\n\t}\n\n\t// plot nt\n\t{\n\t\tconst g = obj.svg.append('g')\n\t\t\t.attr('transform','translate(0,'+(rulerheight+ntfontsize)+')')\n\t\tfor(let i=0; i<data.refseq.length; i++) {\n\t\t\tg.append('text')\n\t\t\t\t.text(data.refseq[i])\n\t\t\t\t.attr('font-size',ntfontsize)\n\t\t\t\t.attr('x', ntwidth*(i+.5) )\n\t\t\t\t.attr('text-anchor','middle')\n\t\t}\n\t}\n\t*/\n\n\t// instead of ruler, plot mutation\n\t{\n\t\tconst x = (obj.m.pos - data.refstart + 0.5) * ntwidth\n\t\tconst g = obj.dynamic_g.append('g').attr('transform', 'translate(' + x + ',' + headerheight + ')')\n\t\tg.append('rect')\n\t\t\t.attr('x', -ntwidth / 2)\n\t\t\t.attr('y', -10)\n\t\t\t.attr('width', ntwidth)\n\t\t\t.attr('height', 10)\n\t\t\t.attr('fill', '#666')\n\t\tg.append('text')\n\t\t\t.attr('y', -15)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.text(obj.m.chr + ':' + obj.m.pos + ' ' + obj.m.ref + '>' + obj.m.alt)\n\t}\n\n\t// cumulative height\n\tlet svgheight = headerheight + headerunderpad\n\n\tconst rowspace = 1\n\n\tconst g = obj.dynamic_g.append('g').attr('transform', 'translate(0,' + svgheight + ')')\n\n\t// each motif\n\tfor (const [i, motif] of data.items.entries()) {\n\t\t// at vertical center\n\t\tmotif.g = g.append('g').attr('transform', 'translate(0,' + (obj.motifrowheight * (i + 0.5) + rowspace * i) + ')')\n\n\t\t// layer 1: row background, motif bar, factor profiles\n\t\tmotif.layer1_g = motif.g.append('g')\n\n\t\t// layer 2: mouse over\n\t\tmotif.layer2_g = motif.g.append('g')\n\n\t\t// bg box to flicker by mouse over and stretch across all profile panels\n\t\tmotif.bgbox = motif.layer1_g\n\t\t\t.append('rect')\n\t\t\t.attr('y', -obj.motifrowheight / 2)\n\t\t\t.attr('width', motifgraphwidth)\n\t\t\t.attr('height', obj.motifrowheight)\n\t\t\t.attr('fill', 'white')\n\n\t\tconst x = (motif.start - data.refstart) * ntwidth\n\t\tconst w = (Math.min(motif.stop, data.refstop) - motif.start) * ntwidth\n\n\t\t// motif color by change\n\n\t\t// motif box\n\t\tmotif.layer1_g\n\t\t\t.append('rect')\n\t\t\t.attr('x', x)\n\t\t\t.attr('y', -obj.motifrowheight / 2)\n\t\t\t.attr('width', w)\n\t\t\t.attr('height', obj.motifrowheight)\n\t\t\t.attr('fill', motif.gain ? obj.gaincolor : obj.losscolor)\n\t\t\t.attr('fill-opacity', motif.logpvaluediff / (motif.gain ? data.valuemax : data.valuemin))\n\n\t\t// tf name\n\t\tlet str\n\t\tif (motif.strand == '+') {\n\t\t\tstr = '>  ' + motif.name + '  >'\n\t\t} else {\n\t\t\tstr = '<  ' + motif.name + '  <'\n\t\t}\n\t\tmotif.layer1_g\n\t\t\t.append('text')\n\t\t\t.text(str)\n\t\t\t.attr('x', x + w / 2)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('stroke', 'white')\n\t\t\t.attr('stroke-width', 3)\n\t\t\t.attr('font-size', obj.motifrowheight - 3)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.style('white-space', 'pre')\n\t\tmotif.layer1_g\n\t\t\t.append('text')\n\t\t\t.text(str)\n\t\t\t.attr('x', x + w / 2)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('font-size', obj.motifrowheight - 3)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.style('white-space', 'pre')\n\n\t\tmotif.coverbox = motif.layer2_g\n\t\t\t.append('rect')\n\t\t\t.attr('y', -obj.motifrowheight / 2)\n\t\t\t.attr('width', motifgraphwidth)\n\t\t\t.attr('height', obj.motifrowheight)\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.on('mouseover', event => {\n\t\t\t\tmotif.bgbox.attr('fill', '#f9fabd')\n\t\t\t\tmotif_tooltip(motif, obj, event)\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tmotif.bgbox.attr('fill', 'white')\n\t\t\t\tobj.tip.hide()\n\t\t\t})\n\t}\n\n\tsvgheight += (rowspace + obj.motifrowheight) * data.items.length + 20\n\n\tmake_legend(data, obj)\n\n\tobj.svg.attr('width', motifgraphwidth).attr('height', svgheight)\n}\n\nfunction motif_tooltip(motif, obj, event) {\n\tobj.tip.clear()\n\tif (motif.attr) {\n\t\tobj.tip.d.append('div').text('MOTIF').style('font-weight', 'bold')\n\t\tconst lst1 = [\n\t\t\t{ k: 'P-values', v: htmlpvalue(motif, obj) },\n\t\t\t{ k: 'Strand', v: motif.strand }\n\t\t]\n\t\tclient.make_table_2col(obj.tip.d, lst1)\n\n\t\tobj.tip.d.append('div').text('FACTOR').style('font-weight', 'bold')\n\t\tconst lst2 = []\n\t\tfor (const k in motif.attr) {\n\t\t\tlst2.push({ k: k, v: motif.attr[k] })\n\t\t}\n\t\tclient.make_table_2col(obj.tip.d, lst2)\n\t} else {\n\t\tconst lst = [\n\t\t\t{ k: 'TF', v: motif.name },\n\t\t\t{ k: 'P-values', v: htmlpvalue(motif, obj) },\n\t\t\t{ k: 'Strand', v: motif.strand }\n\t\t]\n\t\tclient.make_table_2col(obj.tip.d, lst)\n\t}\n\tobj.tip.show(event.clientX, event.clientY)\n}\n\nfunction htmlpvalue(m, obj) {\n\treturn (\n\t\t(m.pvalue_ref == undefined\n\t\t\t? '<span style=\"opacity:.5;padding:2px\"><span style=\"font-size:.7em\">REF</span> not found</span>'\n\t\t\t: '<span style=\"background-color:' +\n\t\t\t  obj.losscolor +\n\t\t\t  ';padding:2px;color:white;\"><span style=\"font-size:.7em\">REF</span> ' +\n\t\t\t  m.pvalue_ref +\n\t\t\t  '</span>') +\n\t\t'<br>' +\n\t\t(m.pvalue_alt == undefined\n\t\t\t? '<span style=\"opacity:.5;padding:2px\"><span style=\"font-size:.7em\">ALT</span> not found</span>'\n\t\t\t: '<span style=\"background-color:' +\n\t\t\t  obj.gaincolor +\n\t\t\t  ';padding:2px;color:white;\"><span style=\"font-size:.7em\">ALT</span> ' +\n\t\t\t  m.pvalue_alt +\n\t\t\t  '</span>')\n\t)\n}\n\nfunction make_legend(data, obj) {\n\tobj.legend.logpvaluediv.selectAll('*').remove()\n\n\tconst leftpad = 50,\n\t\taxistickh = 4,\n\t\tfontsize = 12,\n\t\tbarw = 55,\n\t\tbarh = 20\n\n\tobj.legend.logpvaluediv.append('span').text('Log10 p-value difference')\n\n\tconst svg = obj.legend.logpvaluediv\n\t\t.append('svg')\n\t\t.attr('width', (leftpad + barw) * 2)\n\t\t.attr('height', fontsize + axistickh + barh)\n\n\t// axis\n\tconst axisg = svg.append('g').attr('transform', 'translate(' + leftpad + ',' + (fontsize + axistickh) + ')')\n\tclient.axisstyle({\n\t\taxis: axisg.call(\n\t\t\taxisTop()\n\t\t\t\t.scale(\n\t\t\t\t\tscaleLinear()\n\t\t\t\t\t\t.domain([data.valuemin, 0, data.valuemax])\n\t\t\t\t\t\t.range([0, barw, barw * 2])\n\t\t\t\t)\n\t\t\t\t.tickValues([data.valuemin, 0, data.valuemax])\n\t\t\t\t.tickSize(axistickh)\n\t\t)\n\t})\n\n\tconst gain_id = Math.random().toString()\n\tconst loss_id = Math.random().toString()\n\n\tconst defs = svg.append('defs')\n\t{\n\t\t// loss\n\t\tconst grad = defs.append('linearGradient').attr('id', loss_id)\n\t\tgrad.append('stop').attr('offset', '0%').attr('stop-color', obj.losscolor)\n\t\tgrad.append('stop').attr('offset', '100%').attr('stop-color', 'white')\n\t}\n\t{\n\t\t// gain\n\t\tconst grad = defs.append('linearGradient').attr('id', gain_id)\n\t\tgrad.append('stop').attr('offset', '0%').attr('stop-color', 'white')\n\t\tgrad.append('stop').attr('offset', '100%').attr('stop-color', obj.gaincolor)\n\t}\n\n\tsvg\n\t\t.append('rect')\n\t\t.attr('x', leftpad)\n\t\t.attr('y', fontsize + axistickh)\n\t\t.attr('width', barw)\n\t\t.attr('height', barh)\n\t\t.attr('fill', 'url(#' + loss_id + ')')\n\n\tsvg\n\t\t.append('rect')\n\t\t.attr('x', leftpad + barw)\n\t\t.attr('y', fontsize + axistickh)\n\t\t.attr('width', barw)\n\t\t.attr('height', barh)\n\t\t.attr('fill', 'url(#' + gain_id + ')')\n\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', leftpad - 5)\n\t\t.attr('y', fontsize + axistickh + barh / 2)\n\t\t.attr('font-family', client.font)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('text-anchor', 'end')\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('fill', 'black')\n\t\t.text('Loss')\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', leftpad + barw * 2 + 5)\n\t\t.attr('y', fontsize + axistickh + barh / 2)\n\t\t.attr('font-family', client.font)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('fill', 'black')\n\t\t.text('Gain')\n}\n\nasync function get_gene_position(data, obj) {\n\tobj.gene2position = {}\n\tconst factornames = new Set()\n\tfor (const m of data.items) {\n\t\tfactornames.add(m.gene)\n\t}\n\tfor (const genename of factornames) {\n\t\tconst pos = await get_one_gene_position(genename, obj)\n\t\tif (pos) {\n\t\t\tobj.gene2position[genename] = pos\n\t\t}\n\t}\n}\n\nfunction get_one_gene_position(genename, obj) {\n\treturn client.dofetch('genelookup', { genome: obj.genome.name, input: genename, deep: 1 }).then(data => {\n\t\tif (!data.gmlst) return null\n\t\tconst loci = client.gmlst2loci(data.gmlst)\n\t\treturn loci[0]\n\t\t// ignore multiple loci\n\t})\n}\n\nfunction load_factorprofile(obj, profile) {\n\tif (profile.isgenevalue) {\n\t\treturn load_factorprofile_genevalue(obj, profile)\n\t}\n\tif (profile.isgenevalueonesample) {\n\t\treturn load_factorprofile_genevalueonesample(obj, profile)\n\t}\n\tthrow 'unknown profile type'\n}\n\nasync function load_factorprofile_genevalueonesample(obj, profile) {\n\t// get value for each gene for a sample\n\n\tconst arg = {\n\t\tgenome: obj.genome.name,\n\t\tgenes: [],\n\t\tsample: profile.samplename\n\t}\n\tif (profile.mdslabel) {\n\t\targ.dslabel = profile.mdslabel\n\t\targ.querykey = profile.querykey\n\t\tif (profile.samplegroup_attrlst) {\n\t\t\targ.getgroup = profile.samplegroup_attrlst\n\t\t}\n\t} else {\n\t\targ.iscustom = 1\n\t\targ.file = profile.file\n\t\targ.url = profile.url\n\t\targ.indexURL = profile.indexURL\n\t}\n\tfor (const g in obj.gene2position) {\n\t\tconst r = obj.gene2position[g]\n\t\targ.genes.push({\n\t\t\tgene: g,\n\t\t\tchr: r.chr,\n\t\t\tstart: r.start,\n\t\t\tstop: r.stop\n\t\t})\n\t}\n\treturn client\n\t\t.dofetch('mdsgenevalueonesample', arg)\n\t\t.then(data => {\n\t\t\tif (data.error) throw data.error\n\t\t\t// defaults message of all genes to no data\n\t\t\t// for any gene with data, will remove message\n\t\t\tfor (const m of profile.motifs) {\n\t\t\t\tm.message.text('No data')\n\t\t\t}\n\t\t\tif (data.nodata) return\n\t\t\tif (!data.result) throw 'error'\n\t\t\t// bar plot\n\t\t\tlet min = 0,\n\t\t\t\tmax = 0\n\t\t\tfor (const g in data.result) {\n\t\t\t\tmin = Math.min(min, data.result[g])\n\t\t\t\tmax = Math.max(max, data.result[g])\n\t\t\t}\n\t\t\tconst scale = scaleLinear().domain([min, max]).range([0, profile.width])\n\n\t\t\tclient.axisstyle({\n\t\t\t\taxis: profile.axisg.call(axisTop().scale(scale).ticks(4)),\n\t\t\t\tshowline: 1\n\t\t\t})\n\n\t\t\tfor (const m of profile.motifs) {\n\t\t\t\tconst v = data.result[m.motif.gene]\n\t\t\t\tif (Number.isFinite(v)) {\n\t\t\t\t\t// this gene has valid value\n\t\t\t\t\tm.message.text('')\n\t\t\t\t\tm.g\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('y', -obj.motifrowheight / 2)\n\t\t\t\t\t\t.attr('width', Math.max(1, scale(v)))\n\t\t\t\t\t\t.attr('height', obj.motifrowheight)\n\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t\t.attr('fill', profile.barcolor)\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tprofile.textlabel\n\t\t\t\t.attr('x', profile.width / 2)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('y', -30)\n\t\t})\n\t\t.catch(e => {\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t\tclient.appear(obj.wait.text(e.message || e))\n\t\t})\n}\n\nasync function load_factorprofile_genevalue(obj, profile) {\n\t// get data for each uniq factor\n\n\tprofile.gene2result = new Map()\n\t// k: gene name\n\t// v: boxplot data\n\n\tfor (const gene in obj.gene2position) {\n\t\tconst data = await factorprofile_genevalue_onegene_loadboxplot(obj, profile, gene)\n\n\t\tif (data) {\n\t\t\t// has valid data for this factor\n\t\t\tfactorprofile_genevalue_onegene_makeboxplot(obj, profile, gene, data)\n\n\t\t\t// collect data so far\n\t\t\tprofile.gene2result.set(gene, data)\n\n\t\t\t// update scale based on collected data\n\t\t\tfactorprofile_genevalue_updatescale(obj, profile)\n\t\t}\n\t}\n\n\tfactorprofile_genevalue_finish(obj, profile)\n}\n\nfunction factorprofile_genevalue_onegene_makeboxplot(obj, profile, gene, data) {\n\t// plot boxplot for all motifs of this gene\n\n\tif (data.nodata) return\n\n\tfor (const m of profile.motifs) {\n\t\tif (m.motif.gene != gene) continue\n\t\tm.boxplot = {\n\t\t\tout: []\n\t\t}\n\n\t\tif (data.w1 != undefined) {\n\t\t\t// has valid values for boxplot, could be missing\n\t\t\tm.boxplot.hline = m.g.append('line').attr('stroke', profile.color).attr('shape-rendering', 'crispEdges')\n\t\t\tm.boxplot.linew1 = m.g.append('line').attr('stroke', profile.color).attr('shape-rendering', 'crispEdges')\n\t\t\tm.boxplot.linew2 = m.g.append('line').attr('stroke', profile.color).attr('shape-rendering', 'crispEdges')\n\t\t\tm.boxplot.box = m.g\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('fill', 'white')\n\t\t\t\t.attr('stroke', profile.color)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\tm.boxplot.linep50 = m.g.append('line').attr('stroke', profile.color).attr('shape-rendering', 'crispEdges')\n\t\t}\n\t\t// outliers\n\t\tif (data.out) {\n\t\t\tfor (const d of data.out) {\n\t\t\t\tconst circle = m.g.append('circle').attr('stroke', profile.color).attr('fill', 'white').attr('fill-opacity', 0)\n\t\t\t\tm.boxplot.out.push({\n\t\t\t\t\tvalue: d.value,\n\t\t\t\t\tcircle: circle\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction factorprofile_genevalue_updatescale(obj, profile) {\n\t// calls every time boxplot data is loaded for a gene\n\tlet min = 0,\n\t\tmax = 0\n\tfor (const g of profile.gene2result.values()) {\n\t\tmin = Math.min(min, g.min)\n\t\tmax = Math.max(max, g.max)\n\t}\n\n\tconst scale = scaleLinear().domain([min, max]).range([0, profile.width])\n\n\tconst h = obj.motifrowheight - 2\n\n\tfor (const [g, r] of profile.gene2result) {\n\t\tfor (const m of profile.motifs) {\n\t\t\tif (m.motif.gene != g) continue\n\n\t\t\tconst bp = m.boxplot\n\t\t\tif (!bp) continue\n\n\t\t\tif (bp.hline) {\n\t\t\t\tconst w1 = scale(r.w1)\n\t\t\t\tconst w2 = scale(r.w2)\n\t\t\t\tconst p25 = scale(r.p25)\n\t\t\t\tconst p50 = scale(r.p50)\n\t\t\t\tconst p75 = scale(r.p75)\n\t\t\t\tbp.hline.transition().attr('x1', w1).attr('x2', w2)\n\t\t\t\tbp.linew1\n\t\t\t\t\t.transition()\n\t\t\t\t\t.attr('x1', w1)\n\t\t\t\t\t.attr('x2', w1)\n\t\t\t\t\t.attr('y1', -h / 2)\n\t\t\t\t\t.attr('y2', h / 2)\n\t\t\t\tbp.linew2\n\t\t\t\t\t.transition()\n\t\t\t\t\t.attr('x1', w2)\n\t\t\t\t\t.attr('x2', w2)\n\t\t\t\t\t.attr('y1', -h / 2)\n\t\t\t\t\t.attr('y2', h / 2)\n\t\t\t\tbp.box\n\t\t\t\t\t.transition()\n\t\t\t\t\t.attr('x', p25)\n\t\t\t\t\t.attr('y', -h / 2)\n\t\t\t\t\t.attr('width', p75 - p25)\n\t\t\t\t\t.attr('height', h)\n\t\t\t\tbp.linep50\n\t\t\t\t\t.transition()\n\t\t\t\t\t.attr('x1', p50)\n\t\t\t\t\t.attr('x2', p50)\n\t\t\t\t\t.attr('y1', -h / 2)\n\t\t\t\t\t.attr('y2', h / 2)\n\t\t\t}\n\t\t\tfor (const d of bp.out) {\n\t\t\t\td.circle\n\t\t\t\t\t.transition()\n\t\t\t\t\t.attr('cx', scale(d.value))\n\t\t\t\t\t.attr('r', h / 3)\n\t\t\t}\n\t\t}\n\t}\n\n\tclient.axisstyle({\n\t\taxis: profile.axisg.transition().call(axisTop().scale(scale).ticks(4)),\n\t\tshowline: 1\n\t})\n}\n\nfunction factorprofile_genevalue_onegene_loadboxplot(obj, profile, gene) {\n\tconst r = obj.gene2position[gene]\n\tconst arg = {\n\t\tgenome: obj.genome.name,\n\t\tgene: gene,\n\t\tchr: r.chr,\n\t\tstart: r.start,\n\t\tstop: r.stop,\n\t\tgetgroup2boxplot: 1\n\t}\n\tif (profile.mdslabel) {\n\t\targ.dslabel = profile.mdslabel\n\t\targ.querykey = profile.querykey\n\t\tif (profile.samplegroup_attrlst) {\n\t\t\targ.getgroup = profile.samplegroup_attrlst\n\t\t}\n\t} else {\n\t\targ.iscustom = 1\n\t\targ.file = profile.file\n\t\targ.url = profile.url\n\t\targ.indexURL = profile.indexURL\n\t}\n\treturn client\n\t\t.dofetch('mdsgeneboxplot', arg)\n\t\t.then(data => {\n\t\t\tif (data.error) throw 'Error: ' + data.error\n\t\t\tif (data.nodata) throw 'No data'\n\t\t\t// hide message for motifs of this gene\n\t\t\tfor (const m of profile.motifs) {\n\t\t\t\tif (m.motif.gene == gene) {\n\t\t\t\t\tm.message.text('')\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn data\n\t\t})\n\t\t.catch(e => {\n\t\t\t// update message for motifs of this gene\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t\tfor (const m of profile.motifs) {\n\t\t\t\tif (m.motif.gene == gene) {\n\t\t\t\t\tm.message.text(e.message || e)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n}\n\nfunction factorprofile_genevalue_finish(obj, profile) {\n\t// update sample size\n\tlet n = 0\n\tfor (const g of profile.gene2result.values()) {\n\t\tn = Math.max(n, g.n)\n\t}\n\tprofile.textlabel\n\t\t.text(profile.name + ' (n=' + n + ')') // update name showing n\n\t\t.attr('x', profile.width / 2)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('y', -30)\n}\n"],
-  "mappings": 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