@sjcrh/proteinpaint-client 2.211.0 → 2.212.0

package/dist/mds.fimo-KJ4HPMZP.js

@@ -1,513 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  font,
-  gmlst2loci,
-  keyupEnter,
-  make_table_2col
-} from "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import {
-  Menu
-} from "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch
-} from "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import {
-  axisTop
-} from "./chunk-Z2ZITHT4.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/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-KJ4HPMZP.js.map