@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/mds.survivalplot-KTTMHHII.js

@@ -1,483 +0,0 @@
-import {
-  axisstyle,
-  sayerror,
-  to_svg
-} from "./chunk-TKW5TW4Z.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-3SHZTAGF.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-6QCYT6G2.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-OTTMHVYH.js";
-import "./chunk-GNS6CQMA.js";
-import {
-  dofetch
-} from "./chunk-JVPWIVDT.js";
-import "./chunk-4WF3XDQP.js";
-import "./chunk-7JRDJNLR.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-MPSLUEI4.js";
-import {
-  bplen
-} from "./chunk-6PNPHACF.js";
-import "./chunk-WPHUM5S5.js";
-import "./chunk-JNITUVXP.js";
-import {
-  category10_default
-} from "./chunk-2KXLYFAO.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import {
-  linear,
-  ordinal
-} from "./chunk-UJELJXJG.js";
-import "./chunk-BZTWTH4Y.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// src/mds.survivalplot.js
-async function init(obj, holder, debugmode) {
-  if (debugmode) {
-    window.obj = obj;
-  }
-  obj.plots = [];
-  obj.menu = new Menu({ padding: "5px" });
-  obj.tip = new Menu({ padding: "5px" });
-  obj.errordiv = holder.append("div").style("margin", "10px");
-  obj.sayerror = (e) => {
-    sayerror(obj.errordiv, typeof e == "string" ? e : e.message);
-    if (e.stack) console.log(e.stack);
-  };
-  obj.uidiv = holder.append("div").style("margin", "20px");
-  obj.plotdiv = holder.append("div").style("margin", "20px");
-  obj.legendtable = holder.append("table").style("border-spacing", "5px");
-  holder.append("button").text("SVG").on("click", () => {
-    to_svg(obj.plotlist[0].svg.node(), "Survival");
-  });
-  try {
-    await init_dataset_config(obj);
-    if (!obj.plotlist) {
-      obj.plotlist = [];
-    }
-    if (!Array.isArray(obj.plotlist)) throw ".plotlist should be array";
-    if (obj.plotlist.length == 0) {
-      const p = {
-        type: obj.plottypes[0].key
-      };
-      obj.plotlist.push(p);
-    }
-    for (const p of obj.plotlist) {
-      init_a_plot(p, obj);
-    }
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    obj.sayerror("Cannot make plot: " + (e.message || e));
-  }
-}
-function init_dataset_config(obj) {
-  const par = {
-    genome: obj.genome.name,
-    dslabel: obj.mds.label,
-    init: 1
-  };
-  return dofetch("mdssurvivalplot", par).then((data) => {
-    if (data.error) throw data.error;
-    if (!data.plottypes) throw "plottypes[] missing";
-    obj.plottypes = data.plottypes;
-    obj.samplegroupings = data.samplegroupings;
-  });
-}
-function init_a_plot(p, obj) {
-  init_a_plot_filldefault(p, obj);
-  const div = obj.uidiv.append("div").style("margin", "20px");
-  if (obj.plottypes.length > 1) {
-    const s = div.append("div").style("margin-bottom", "10px").append("select").on("change", (event) => {
-      p.type = event.target.options[event.target.selectedIndex].value;
-    });
-    for (const [i, t] of obj.plottypes.entries()) {
-      s.append("option").text(t.name).property("value", t.key);
-      if (t.key == p.type) {
-        s.node().selectedIndex = i;
-      }
-    }
-  }
-  if (obj.samplegroupings && !p.samplerule.full.immutable) {
-    const row = div.append("div").style("margin-bottom", "20px");
-    const custom_input_row = div.append("div").style("display", "none");
-    row.append("span").html("Choose samples from ").style("opacity", 0.5);
-    const attr2select = {};
-    const s = row.append("select").style("margin-right", "5px").on("change", (event) => {
-      for (const k in attr2select) {
-        attr2select[k].style("display", "none");
-      }
-      const o = event.target.options[event.target.selectedIndex];
-      custom_input_row.style("display", o.usesampleset ? "block" : "none");
-      if (o.useall) {
-        p.samplerule.full.useall = 1;
-        delete p.samplerule.full.byattr;
-        return;
-      }
-      if (o.usesampleset) {
-        delete p.samplerule.full.byattr;
-        delete p.samplerule.full.useall;
-        p.samplerule.full.usesampleset = 1;
-        show_sampleinput(p, custom_input_row);
-        return;
-      }
-      delete p.samplerule.full.useall;
-      p.samplerule.full.byattr = 1;
-      p.samplerule.key = o.key;
-      const s3 = attr2select[o.key];
-      s3.style("display", "inline");
-      p.samplerule.full.value = s3.node().options[s3.node().selectedIndex].value;
-    });
-    for (const [i, attr] of obj.samplegroupings.entries()) {
-      s.append("option").text(attr.label).property("key", attr.key);
-      const usingthisattr = p.samplerule.full.byattr && p.samplerule.full.key == attr.key;
-      if (usingthisattr) {
-        s.node().selectedIndex = i;
-      }
-      const s2 = row.append("select").on("change", (event) => {
-        p.samplerule.full.value = event.target.options[event.target.selectedIndex].value;
-      });
-      attr2select[attr.key] = s2;
-      s2.style("display", usingthisattr ? "inline" : "none");
-      for (const [j, v] of attr.values.entries()) {
-        s2.append("option").text(v.value + " (n=" + v.count + ")").property("value", v.value);
-        if (usingthisattr && v.value == p.samplerule.full.value) {
-          s2.node().selectedIndex = j;
-        }
-      }
-    }
-    s.append("option").text("all samples").property("useall", 1);
-    if (p.samplerule.full.useall) {
-      s.node().selectedIndex = obj.samplegroupings.length;
-    }
-    s.append("option").text("custom sampleset").property("usesampleset", 1);
-  }
-  show_dividerules(p, div);
-  p.button = div.append("button").text("Make plot").on("click", () => {
-    loadPlot(p, obj);
-  });
-  p.d = obj.plotdiv.append("div").style("margin", "20px"), p.legend = {
-    d_pvalue: p.d.append("div").style("margin", "10px"),
-    d_samplefull: p.d.append("div").style("margin", "10px"),
-    d_curves: p.d.append("div").style("margin", "10px")
-  };
-  p.svg = p.d.append("svg");
-  p.resize_handle = p.d.append("div").append("div").attr("class", "sja_clbtext").text("drag to resize").style("float", "right");
-  if (p.renderplot) {
-    loadPlot(p, obj);
-  }
-}
-function init_a_plot_filldefault(p, obj) {
-  if (!p.type) {
-    p.type = obj.plottypes[0].key;
-  }
-  if (!p.samplerule) {
-    p.samplerule = {};
-  }
-  if (!p.samplerule.full) {
-    p.samplerule.full = {};
-  }
-  if (obj.samplegroupings) {
-    if (!p.samplerule.full.useall) {
-      p.samplerule.full.byattr = 1;
-      if (!p.samplerule.full.key) {
-        p.samplerule.full.key = obj.samplegroupings[0].key;
-        p.samplerule.full.value = obj.samplegroupings[0].values[0].value;
-      }
-    }
-  } else {
-    p.samplerule.full.useall = 1;
-  }
-  if (p.samplerule.set) {
-    const st = p.samplerule.set;
-    if (st.geneexpression) {
-      if (!st.bymedian && !st.byquartile) {
-        st.bymedian = 1;
-      }
-    }
-  }
-  if (!p.width) p.width = 500;
-  if (!p.height) p.height = 500;
-  if (!p.toppad) p.toppad = 10;
-  if (!p.rightpad) p.rightpad = 10;
-  if (!p.xaxispad) p.xaxispad = 10;
-  if (!p.yaxispad) p.yaxispad = 10;
-  if (!p.xaxish) p.xaxish = 40;
-  if (!p.yaxisw) p.yaxisw = 65;
-  if (!p.censorticksize) p.censorticksize = 6;
-  if (!p.tickfontsize) p.tickfontsize = 14;
-  if (!p.labfontsize) p.labfontsize = 15;
-}
-function doPlot(plot, obj) {
-  const colorfunc = ordinal(category10_default);
-  const minx = 0;
-  let maxx = 0;
-  for (const curve of plot.samplesets) {
-    curve.color = colorfunc(curve.name);
-    for (const s of curve.steps) {
-      maxx = Math.max(maxx, s.x);
-    }
-  }
-  plot.svg.selectAll("*").remove();
-  const curves_g = plot.svg.append("g");
-  for (const curve of plot.samplesets) {
-    curve.path = curves_g.append("path").attr("stroke", curve.color).attr("fill", "none");
-    curve.ticks = curves_g.append("path").attr("stroke", curve.color).attr("fill", "none");
-  }
-  const yaxis_g = plot.svg.append("g");
-  const yaxis_scale = linear().domain([0, 1]);
-  const yaxis_lab_g = plot.svg.append("g");
-  const yaxis_lab = yaxis_lab_g.append("text").text("Survival").attr("transform", "rotate(-90)");
-  const xaxis_g = plot.svg.append("g");
-  const xaxis_scale = linear().domain([minx, maxx]);
-  const xaxis_lab = plot.svg.append("text").attr("font-size", plot.labfontsize).text(obj.plottypes.find((i) => i.key == plot.type).timelabel).attr("x", plot.yaxisw + plot.yaxispad + plot.width / 2).attr("y", plot.toppad + plot.height + plot.xaxispad + plot.xaxish - 3);
-  function resize() {
-    curves_g.attr("transform", "translate(" + (plot.yaxisw + plot.yaxispad) + "," + plot.toppad + ")");
-    for (const curve of plot.samplesets) {
-      const ticks = [];
-      const pathd = ["M 0 0"];
-      for (const s of curve.steps) {
-        pathd.push("H " + plot.width * s.x / maxx);
-        const y = plot.height * (s.y + s.drop);
-        pathd.push("V " + y);
-        if (s.censored) {
-          const y2 = plot.height * s.y;
-          for (const c of s.censored) {
-            const x = plot.width * c / maxx;
-            ticks.push(
-              "M " + (x - plot.censorticksize / 2) + " " + (y2 - plot.censorticksize / 2) + " l " + plot.censorticksize + " " + plot.censorticksize + " M " + (x + plot.censorticksize / 2) + " " + (y2 - plot.censorticksize / 2) + " l -" + plot.censorticksize + " " + plot.censorticksize
-            );
-          }
-        }
-      }
-      curve.path.attr("d", pathd.join(" "));
-      if (ticks.length) {
-        curve.ticks.attr("d", ticks.join(" "));
-      }
-    }
-    yaxis_g.attr("transform", "translate(" + plot.yaxisw + "," + plot.toppad + ")");
-    axisstyle({
-      axis: yaxis_g.call(
-        axisLeft().scale(yaxis_scale.range([plot.height, 0])).ticks(Math.floor(plot.height / (plot.tickfontsize + 20)))
-      ),
-      showline: 1,
-      fontsize: plot.tickfontsize
-    });
-    yaxis_lab_g.attr("transform", "translate(" + plot.labfontsize + "," + (plot.toppad + plot.height / 2) + ")");
-    yaxis_lab.attr("font-size", plot.labfontsize);
-    xaxis_g.attr(
-      "transform",
-      "translate(" + (plot.yaxisw + plot.yaxispad) + "," + (plot.toppad + plot.height + plot.xaxispad) + ")"
-    );
-    let xticknumber;
-    xaxis_g.append("text").text(maxx).attr("font-size", plot.tickfontsize).each(function() {
-      xticknumber = Math.floor(plot.width / (this.getBBox().width + 30));
-    }).remove();
-    axisstyle({
-      axis: xaxis_g.call(
-        axisBottom().scale(xaxis_scale.range([0, plot.width])).ticks(xticknumber)
-      ),
-      showline: 1,
-      fontsize: plot.tickfontsize
-    });
-    xaxis_lab.attr("font-size", plot.labfontsize).attr("x", plot.yaxisw + plot.yaxispad + plot.width / 2).attr("y", plot.toppad + plot.height + plot.xaxispad + plot.xaxish - 3);
-    plot.svg.attr("width", plot.yaxisw + plot.yaxispad + plot.width + plot.rightpad).attr("height", plot.toppad + plot.height + plot.xaxispad + plot.xaxish);
-  }
-  resize();
-  plot.resize_handle.on("mousedown", (event) => {
-    event.preventDefault();
-    const b = select_default(document.body);
-    const x = event.clientX;
-    const y = event.clientY;
-    const w0 = plot.width;
-    const h0 = plot.height;
-    b.on("mousemove", () => {
-      plot.width = w0 + event.clientX - x;
-      plot.height = h0 + event.clientY - y;
-      resize();
-    });
-    b.on("mouseup", () => {
-      b.on("mousemove", null).on("mouseup", null);
-    });
-  });
-  if (Number.isFinite(plot.pvalue)) {
-    plot.legend.d_pvalue.style("display", "block").text("P-value: " + plot.pvalue);
-  } else {
-    plot.legend.d_pvalue.style("display", "none");
-  }
-  plot.legend.d_curves.selectAll("*").remove();
-  for (const c of plot.samplesets) {
-    plot.legend.d_curves.append("div").style("margin", "3px").html(
-      '<span style="background:' + c.color + '">&nbsp;&nbsp;</span> ' + c.name + (c.pvalue == void 0 ? "" : ", P-value: " + c.pvalue)
-    );
-  }
-}
-function loadPlot(plot, obj) {
-  plot.button.text("Loading...").attr("disabled", 1);
-  const par = {
-    genome: obj.genome.name,
-    dslabel: obj.mds.label,
-    type: plot.type,
-    samplerule: plot.samplerule
-  };
-  dofetch("mdssurvivalplot", par).then((data) => {
-    if (data.error) throw data.error;
-    if (!data.samplesets) throw "samplesets[] missing";
-    plot.samplesets = data.samplesets;
-    plot.pvalue = data.pvalue;
-    doPlot(plot, obj);
-    if (plot.samplerule.set && plot.samplerule.set.mutation) {
-      if (plot.mutation_count.cnv) plot.mutation_count.cnv.html("(n=" + data.count_cnv + ")&nbsp;");
-      if (plot.mutation_count.loh) plot.mutation_count.loh.html("(n=" + data.count_loh + ")&nbsp;");
-      if (plot.mutation_count.snvindel) plot.mutation_count.snvindel.html("(n=" + data.count_snvindel + ")&nbsp;");
-      if (plot.mutation_count.sv) plot.mutation_count.sv.html("(n=" + data.count_sv + ")&nbsp;");
-      if (plot.mutation_count.fusion) plot.mutation_count.fusion.html("(n=" + data.count_fusion + ")&nbsp;");
-      if (plot.mutation_count.itd) plot.mutation_count.itd.html("(n=" + data.count_itd + ")&nbsp;");
-    }
-  }).catch((e) => {
-    obj.sayerror(e);
-  }).then(() => {
-    plot.button.text("Update plot").attr("disabled", null);
-  });
-}
-function show_dividerules(p, div) {
-  if (!p.samplerule.set) return;
-  const st = p.samplerule.set;
-  if (st.geneexpression) {
-    if (!st.bymedian && !st.byquartile) {
-      st.bymedian = 1;
-    }
-    const row = div.append("div").style("margin-bottom", "10px");
-    row.append("span").style("opacity", 0.5).html("Divide samples by " + st.gene + " expression with&nbsp;");
-    const s = row.append("select").on("change", (event) => {
-      const o = event.target.options[event.target.selectedIndex];
-      if (o.median) {
-        p.samplerule.set.bymedian = 1;
-        delete p.samplerule.set.byquartile;
-        span_quartilecompare.style("display", "none");
-      } else if (o.quartile) {
-        p.samplerule.set.byquartile = 1;
-        delete p.samplerule.set.bymedian;
-        span_quartilecompare.style("display", "inline");
-      }
-    });
-    s.append("option").text("median (group=2)").property("median", 1);
-    s.append("option").text("quartile (group=4)").property("quartile", 1);
-    const span_quartilecompare = row.append("span").style("margin-left", "10px");
-    span_quartilecompare.append("span").html("Compare each quartile against&nbsp;").style("opacity", 0.5);
-    {
-      const s2 = span_quartilecompare.append("select").on("change", (event) => {
-        delete p.samplerule.set.against1st;
-        delete p.samplerule.set.against4th;
-        switch (event.target.selectedIndex) {
-          case 0:
-            break;
-          case 1:
-            p.samplerule.set.against1st = 1;
-            break;
-          case 2:
-            p.samplerule.set.against4th = 1;
-            break;
-        }
-      });
-      s2.append("option").text("none");
-      s2.append("option").text("first quartile");
-      s2.append("option").text("fourth quartile");
-      if (st.against1st) {
-        s2.node().selectedIndex = 1;
-      } else if (s2.against4th) {
-        s2.node().selectedIndex = 2;
-      }
-    }
-    if (st.bymedian) {
-      s.node().selectedIndex = 0;
-      span_quartilecompare.style("display", "none");
-    } else if (st.byquartile) {
-      s.node().selectedIndex = 1;
-      span_quartilecompare.style("display", "inline");
-    }
-  }
-  if (st.mutation) {
-    p.mutation_count = {};
-    if (st.snvindel) {
-      const row = div.append("div").style("margin-bottom", "20px");
-      p.mutation_count.snvindel = row.append("span");
-      if (st.snvindel.name) {
-        row.append("span").html("SNV/indel&nbsp;");
-        const s = row.append("select");
-        s.append("option").text(st.snvindel.name).property("named", 1);
-        s.append("option").text("any mutation at " + st.chr + ":" + st.start);
-      } else {
-        row.append("span").text("SNV/indel at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop));
-      }
-    }
-    if (st.cnv) {
-      const row = div.append("div").style("margin-bottom", "20px");
-      p.mutation_count.cnv = row.append("span");
-      row.append("span").html(
-        "Copy number variation over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span>&nbsp;"
-      );
-    }
-    if (st.loh) {
-      const row = div.append("div").style("margin-bottom", "20px");
-      p.mutation_count.loh = row.append("span");
-      row.append("span").html(
-        "LOH over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span>&nbsp;"
-      );
-    }
-    if (st.sv) {
-      const row = div.append("div").style("margin-bottom", "20px");
-      p.mutation_count.sv = row.append("span");
-      row.append("span").html("SV at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop) + "&nbsp;");
-    }
-    if (st.fusion) {
-      const row = div.append("div").style("margin-bottom", "20px");
-      p.mutation_count.fusion = row.append("span");
-      row.append("span").html("Fusion at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop) + "&nbsp;");
-    }
-    if (st.itd) {
-      const row = div.append("div").style("margin-bottom", "20px");
-      p.mutation_count.itd = row.append("span");
-      row.append("span").html(
-        "ITD over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span>&nbsp;"
-      );
-    }
-  }
-}
-function show_sampleinput(p, div) {
-  let rendered_flag = div.selectAll("div").size();
-  if (rendered_flag) return;
-  const row = div.append("div").style("margin-bottom", "10px");
-  const samplelist_div = row.append("div").style("margin-left", "20px");
-  samplelist_div.append("div").style("vertical-align", "top").style("display", "inline-block").style("opacity", 0.5).html("Enter sample names<br>(one sample per line) &nbsp;");
-  const sample_input = samplelist_div.append("textarea").style("display", "inline-block").attr("cols", "20").attr("rows", "10").on("change", () => {
-    let sampleset = p.samplerule.full.sampleset = [];
-    const str = sample_input.property("value").trim();
-    if (!str) return;
-    for (const sample of str.split("\n")) {
-      sampleset.push(sample);
-    }
-  });
-}
-export {
-  init
-};
-//# sourceMappingURL=mds.survivalplot-KTTMHHII.js.map

package/dist/numericDictTermCluster-H4JSPW22.js

@@ -1,65 +0,0 @@
-import {
-  NumericModes
-} from "./chunk-7JRDJNLR.js";
-import "./chunk-6PNPHACF.js";
-import "./chunk-2KXLYFAO.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-UJELJXJG.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/numericDictTermCluster.ts
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const menuDiv = holder.append("div");
-  const numericDictTermCluster = chartsInstance.state.termdbConfig.numericDictTermCluster;
-  if (numericDictTermCluster?.plots) {
-    for (const plot of numericDictTermCluster.plots) {
-      menuDiv.append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "inline-block").text(plot.name).on("click", async () => {
-        chartsInstance.dom.tip.hide();
-        const config = await chartsInstance.app.vocabApi.getNumericDictTermClusterByName(plot.name);
-        config.preBuiltPlotTitle = plot.name;
-        chartsInstance.app.dispatch({
-          type: "plot_create",
-          config
-        });
-      });
-    }
-  }
-  const chart = {
-    //use the app name defined in dataset file
-    label: numericDictTermCluster?.appName || "Numeric Dictionary Term cluster",
-    chartType: "numericDictTermCluster",
-    clickTo: chartsInstance.showTree_selectlst,
-    minTermsToSubmit: 3,
-    usecase: {
-      target: "numericDictTermCluster",
-      detail: { exclude: numericDictTermCluster?.exclude }
-    },
-    updateActionBySelectedTerms: (action, termlst) => {
-      if (!termlst?.length) throw "cannot launch clustering: no terms selected";
-      const twlst = termlst.map((term) => ({
-        term: structuredClone(term),
-        q: { mode: NumericModes.continuous }
-      }));
-      action.config.chartType = "hierCluster";
-      action.config.dataType = twlst[0].term.type || "float";
-      if (numericDictTermCluster?.appName) action.config.appName = numericDictTermCluster.appName;
-      action.config.termgroups = [
-        {
-          name: numericDictTermCluster?.settings?.termGroupName || "Numeric Dictionary Term Cluster",
-          lst: twlst,
-          type: "hierCluster"
-        }
-      ];
-    }
-  };
-  chartsInstance.showTree_selectlst(chart);
-}
-export {
-  makeChartBtnMenu
-};
-//# sourceMappingURL=numericDictTermCluster-H4JSPW22.js.map