@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/block.mds.geneboxplot-VJTIMZ6H.js

@@ -0,0 +1,828 @@
+import {
+  ase_color,
+  init_config,
+  measure,
+  showsingleitem_table
+} from "./chunk-AOVDTRFY.js";
+import {
+  appear2 as appear,
+  axisstyle,
+  disappear2 as disappear,
+  font,
+  make_table_2col,
+  newpane,
+  sayerror,
+  to_svg
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import {
+  dofetch2
+} from "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import {
+  axisTop
+} from "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import {
+  linear,
+  log
+} from "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// src/block.mds.geneboxplot.js
+var label_cnvgain = "CNV gain";
+var label_cnvloss = "CNV loss";
+var label_sv = "SV";
+var label_ase = "Allele-specific expression";
+var label_outlier = "Outlier expression";
+async function init(p) {
+  if (!p.genome) return alert("cannot initiate plot: genome missing");
+  const plot = p;
+  plot.tip = new Menu({ padding: "0px" });
+  if (plot.file || plot.url) {
+    plot.gecfg = {};
+  } else {
+    if (!plot.dslabel) return alert("dslabel missing");
+    if (!plot.querykey) return alert("querykey missing");
+    const d = plot.genome.datasets[plot.dslabel];
+    if (!d) return alert("invalid dataset label: " + plot.dslabel);
+    plot.gecfg = d.queries[plot.querykey];
+    if (!plot.gecfg) return alert("invalid query key: " + plot.querykey);
+  }
+  init_config(plot.gecfg);
+  if (p.block && p.block.debugmode) {
+    window.plot = plot;
+  }
+  plot.errdiv = plot.holder.append("div").style("margin", "10px");
+  const buttonrow = plot.holder.append("div").style("margin", "10px");
+  plot.buttonrow = buttonrow;
+  mayaddgrouperselect(plot);
+  const configdiv = plot.holder.append("div").style("margin", "10px").style("border", "solid 1px #ededed").style("padding", "10px").style("display", "none");
+  plot.table_boxplotstats = plot.holder.append("table").style("margin", "10px").style("border-spacing", "4px").style("border-collapse", "separate");
+  buttonrow.append("button").text("Log10").on("click", (event) => {
+    plot.uselog = !plot.uselog;
+    event.target.innerHTML = plot.uselog ? "Linear" : "Log10";
+    plot.place();
+  });
+  if (plot.sample) {
+    plot.sample.shown = true;
+    buttonrow.append("button").text(plot.sample.name + " toggle").on("click", () => {
+      plot.sample.shown = !plot.sample.shown;
+      plot.sample.line.attr("stroke-opacity", plot.sample.shown ? 1 : 0);
+      plot.sample.svgtext.attr("fill-opacity", plot.sample.shown ? 1 : 0);
+    });
+  }
+  if (plot.svcnv) {
+    buttonrow.append("button").text("SV/CNV options").on("click", () => {
+      if (configdiv.style("display") == "none") appear(configdiv);
+      else disappear(configdiv);
+    });
+    plot.svcnv.useloss = true;
+    plot.svcnv.usegain = true;
+    plot.cnvconfig = {};
+    plot.svconfig = {};
+    {
+      const row = configdiv.append("div");
+      const id = Math.random().toString();
+      row.append("input").attr("type", "checkbox").property("checked", true).attr("id", id).on("change", (event) => {
+        plot.svcnv.usegain = event.target.checked;
+        plot.cnvconfig.div.style("display", plot.svcnv.usegain || plot.svcnv.useloss ? "block" : "none");
+        loadplot(plot);
+      });
+      row.append("label").attr("for", id).attr("class", "sja_clbtext").html(" Add boxplot for samples with copy number gain over " + plot.gene).style("color", plot.color.cnvgain);
+    }
+    {
+      const row = configdiv.append("div");
+      const id = Math.random().toString();
+      row.append("input").attr("type", "checkbox").property("checked", true).attr("id", id).on("change", (event) => {
+        plot.svcnv.useloss = event.target.checked;
+        plot.cnvconfig.div.style("display", plot.svcnv.usegain || plot.svcnv.useloss ? "block" : "none");
+        loadplot(plot);
+      });
+      row.append("label").attr("for", id).attr("class", "sja_clbtext").html(" Add boxplot for samples with copy number loss over " + plot.gene).style("color", plot.color.cnvloss);
+    }
+    {
+      const d = configdiv.append("div");
+      plot.cnvconfig.div = d;
+      const d2 = d.append("div").style("display", "inline-block").style("margin", "5px 10px 10px 30px").style("border", "solid 1px #ededed").style("padding", "10px");
+      {
+        const row = d2.append("div").style("margin-bottom", "15px");
+        row.append("span").html("CNV log2(ratio) cutoff ");
+        row.append("input").property("value", plot.svcnv.valueCutoff || 0).attr("type", "number").style("width", "50px").on("keyup", (event) => {
+          if (event.code != "Enter" && event.code != "NumpadEnter") return;
+          let v = Number.parseFloat(event.target.value);
+          if (!v || v < 0) {
+            v = 0;
+          }
+          if (v == 0) {
+            if (plot.svcnv.valueCutoff) {
+              plot.svcnv.valueCutoff = 0;
+              loadplot(plot);
+            } else {
+            }
+            return;
+          }
+          if (plot.svcnv.valueCutoff) {
+            if (plot.svcnv.valueCutoff == v) {
+            } else {
+              plot.svcnv.valueCutoff = v;
+              loadplot(plot);
+            }
+          } else {
+            plot.svcnv.valueCutoff = v;
+            loadplot(plot);
+          }
+        });
+        row.append("div").style("font-size", ".7em").style("color", "#858585").html("CNV with absolute log2(ratio) lower than cutoff will not be considered. Set to 0 to cancel.");
+      }
+      {
+        const row = d2.append("div");
+        row.append("span").html("CNV segment size limit&nbsp;");
+        row.append("input").property("value", plot.svcnv.bplengthUpperLimit || 0).attr("type", "number").style("width", "80px").on("keyup", (event) => {
+          if (event.code != "Enter" && event.code != "NumpadEnter") return;
+          let v = Number.parseInt(event.target.value);
+          if (!v || v < 0) {
+            v = 0;
+          }
+          if (v == 0) {
+            if (plot.svcnv.bplengthUpperLimit) {
+              plot.svcnv.bplengthUpperLimit = 0;
+              loadplot(plot);
+            } else {
+            }
+            return;
+          }
+          if (plot.svcnv.bplengthUpperLimit) {
+            if (plot.svcnv.bplengthUpperLimit == v) {
+            } else {
+              plot.svcnv.bplengthUpperLimit = v;
+              loadplot(plot);
+            }
+          } else {
+            plot.svcnv.bplengthUpperLimit = v;
+            loadplot(plot);
+          }
+        });
+        row.append("span").html("&nbsp;bp");
+        row.append("div").style("font-size", ".7em").style("color", "#858585").html("CNV segment longer than cutoff will not be considered. Set to 0 to cancel.");
+      }
+    }
+    {
+      const row = configdiv.append("div");
+      const id = Math.random().toString();
+      row.append("input").attr("type", "checkbox").property("checked", false).attr("id", id).on("change", (event) => {
+        plot.svcnv.usesv = event.target.checked;
+        plot.svconfig.div.style("display", plot.svcnv.usesv ? "block" : "none");
+        loadplot(plot);
+      });
+      row.append("label").attr("for", id).attr("class", "sja_clbtext").html("&nbsp;Add boxplot for samples with structural variation over " + plot.gene).style("color", plot.color.sv);
+    }
+    {
+      const d = configdiv.append("div").style("display", "none");
+      plot.svconfig.div = d;
+      const d2 = d.append("div").style("display", "inline-block").style("margin", "5px 10px 10px 30px").style("border", "solid 1px #ededed").style("padding", "10px");
+      {
+        const row = d2.append("div");
+        row.append("span").html("Include SV from flanking region of length:&nbsp;");
+        row.append("input").property("value", 0).attr("type", "number").style("width", "80px").on("keyup", (event) => {
+          if (event.code != "Enter" && event.code != "NumpadEnter") return;
+          let v = Number.parseInt(event.target.value);
+          if (!v || v < 0) {
+            v = 0;
+          }
+          if (v == 0) {
+            if (plot.svcnv.svflank) {
+              plot.svcnv.svflank = 0;
+              loadplot(plot);
+            } else {
+            }
+            return;
+          }
+          if (plot.svcnv.svflank) {
+            if (plot.svcnv.svflank == v) {
+            } else {
+              plot.svcnv.svflank = v;
+              loadplot(plot);
+            }
+          } else {
+            plot.svcnv.svflank = v;
+            loadplot(plot);
+          }
+        });
+        row.append("span").html("&nbsp;bp");
+        row.append("div").style("font-size", ".7em").style("color", "#858585").html("Set to 0 to cancel.");
+      }
+    }
+  }
+  plot.buttonholder_boxplot = buttonrow.append("span");
+  plot.buttonholder_sampleexpdata = buttonrow.append("span");
+  buttonrow.append("button").text("SVG").on("click", () => {
+    to_svg(plot.svg.node(), "Expression");
+  });
+  plot.svg = plot.holder.append("svg");
+  const axisg = plot.svg.append("g");
+  plot.g0 = plot.svg.append("g");
+  const axisheight = 50;
+  const lablspace = 10;
+  const axisw = 500;
+  const rowheight = 16;
+  const rowspace = 10;
+  const _rowspace = 2;
+  const axispad2 = 30;
+  const fontsize = 14;
+  const circleyshift = 2;
+  plot.place = () => {
+    plot.axislabel.attr("x", axisw / 2);
+    let labwidth = 0;
+    let rightwidth = 0;
+    const scale0 = (plot.uselog ? log() : linear()).domain([plot.data.min == 0 ? 1e-3 : plot.data.min, plot.data.max]).range([0, axisw]);
+    const scale = (v) => {
+      if (plot.uselog) {
+        if (v == 0) return 0;
+      }
+      return scale0(v);
+    };
+    axisstyle({
+      axis: axisg.transition().call(axisTop().scale(scale0)),
+      showline: 1
+    });
+    let y = rowspace;
+    if (plot.data.lst) {
+      labwidth = 20;
+      rightwidth = 20;
+      for (const d of plot.data.lst) {
+        d.circle.transition().attr("cx", scale(d.value)).attr("cy", y).attr("r", rowheight / 2);
+        y += circleyshift;
+      }
+    } else {
+      for (const g of plot.data.groups) {
+        g.g.attr("transform", "translate(0," + y + ")");
+        const _rowheight = rowheight * (g.boxplots.length > 1 ? 0.8 : 1);
+        let _y = 0;
+        for (const bp of g.boxplots) {
+          if (bp.label) {
+            bp.label.attr("font-size", _rowheight).attr("x", axisw + 5).attr("y", _y + _rowheight / 2).each(function() {
+              rightwidth = Math.max(rightwidth, this.getBBox().width);
+            });
+          }
+          if (bp.hline) {
+            const w1 = scale(bp.w1);
+            const w2 = scale(bp.w2);
+            const p25 = scale(bp.p25);
+            const p50 = scale(bp.p50);
+            const p75 = scale(bp.p75);
+            bp.hline.transition().attr("x1", w1).attr("x2", w2).attr("y1", _y + _rowheight / 2).attr("y2", _y + _rowheight / 2);
+            bp.linew1.transition().attr("x1", w1).attr("x2", w1).attr("y1", _y).attr("y2", _y + _rowheight);
+            bp.linew2.transition().attr("x1", w2).attr("x2", w2).attr("y1", _y).attr("y2", _y + _rowheight);
+            bp.box.transition().attr("x", p25).attr("y", _y).attr("width", p75 - p25).attr("height", _rowheight);
+            bp.linep50.transition().attr("x1", p50).attr("x2", p50).attr("y1", _y).attr("y2", _y + _rowheight);
+          }
+          for (const d of bp.out) {
+            d.circle.transition().attr("cx", scale(d.value)).attr("cy", _y + _rowheight / 2).attr("r", _rowheight / 3);
+          }
+          _y += _rowheight + _rowspace;
+        }
+        const h = (_rowheight + _rowspace) * g.boxplots.length - _rowspace;
+        g.label.attr("x", -lablspace).attr("y", h / 2).attr("font-size", fontsize).each(function() {
+          labwidth = Math.max(labwidth, this.getBBox().width);
+        });
+        if (g.bg)
+          g.bg.attr("y", -rowspace / 2).attr("width", axisw).attr("height", h + rowspace);
+        y += h + rowspace;
+      }
+    }
+    plot.g0.attr("transform", "translate(" + (labwidth + lablspace) + "," + axisheight + ")");
+    axisg.attr("transform", "translate(" + (labwidth + lablspace) + "," + axisheight + ")");
+    if (plot.sample) {
+      plot.sample.g.transition().attr("transform", "translate(" + scale(plot.sample.value) + "," + y + ")");
+      plot.sample.line.attr("y1", -y);
+    }
+    plot.svg.attr("width", labwidth + lablspace + axisw + axispad2 + rightwidth).attr("height", axisheight + y + 30);
+  };
+  try {
+    await loadplot(plot);
+  } catch (e) {
+    sayerror(plot.errdiv, "Error: " + (e.message || e));
+    if (e.stack) console.log(e.stack);
+  }
+}
+async function loadplot(plot) {
+  const arg = {
+    genome: plot.genome.name,
+    gene: plot.gene,
+    chr: plot.chr,
+    start: plot.start,
+    stop: plot.stop,
+    svcnv: plot.svcnv,
+    index_boxplotgroupers: plot.index_boxplotgroupers,
+    sampleset: plot.sampleset
+  };
+  if (plot.dslabel) {
+    arg.dslabel = plot.dslabel;
+    arg.querykey = plot.querykey;
+  } else {
+    arg.iscustom = 1;
+    arg.file = plot.file;
+    arg.url = plot.url;
+    arg.indexURL = plot.indexURL;
+  }
+  plot.g0.append("text").text("Loading ...").attr("font-size", 20).attr("text-anchor", "center").attr("dominant-baseline", "central").attr("x", plot.svg.attr("width") / 2).attr("y", plot.svg.attr("height") / 2);
+  const data = await dofetch2("mdsgeneboxplot", { method: "POST", body: JSON.stringify(arg) });
+  if (data.error) throw data.error;
+  plot.g0.selectAll("*").remove();
+  plot.axislabel = plot.g0.append("text").attr("font-size", 14).attr("font-family", font).attr("text-anchor", "middle").attr("y", -25).text(plot.gene + " " + plot.gecfg.datatype);
+  plot.data = data;
+  const color0 = "green";
+  if (data.lst) {
+    addbutton_showdata_fromlst(plot);
+    for (const d of data.lst) {
+      d.circle = plot.g0.append("circle").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", color0).attr("stroke-opacity", 0.8).on("mouseover", (event) => {
+        plot.tip.clear().d.append("div").style("margin", "10px").html(d.sample + "<br>" + d.value);
+        plot.tip.show(event.clientX, event.clientY);
+      }).on("mouseout", () => plot.tip.hide());
+      if (plot.clicksample) {
+        d.circle.on("click", () => {
+          plot.clicksample(d, null, plot);
+        });
+      }
+    }
+  } else {
+    addbutton_boxplotstats(plot);
+    addbutton_showdata_newquery(plot);
+    for (const [i, g] of data.groups.entries()) {
+      g.g = plot.g0.append("g");
+      if (i % 2 == 0) {
+        g.bg = g.g.append("rect").attr("fill", "#f5f5f5");
+      }
+      g.label = g.g.append("text").attr("font-family", font).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("class", "sja_clbtext").text(g.name).on("click", (event) => {
+        init2(Math.max(100, event.clientX - 100), Math.max(100, event.clientY - 100), plot, g);
+      });
+      if (g.attributes) {
+        g.label.on("mouseover", (event) => {
+          plot.tip.clear().show(event.clientX, event.clientY);
+          const d = plot.tip.d.append("div").style("margin", "10px");
+          for (const a of g.attributes) {
+            d.append("div").html(
+              a.kvalue + (a.fullvalue ? ' <span style="opacity:.5;font-size:.8em;">' + a.fullvalue + "</span>" : "")
+            );
+          }
+        }).on("mouseout", () => {
+          plot.tip.hide();
+        });
+      }
+      for (const bp of g.boxplots) {
+        let color;
+        if (bp.iscnvgain) {
+          color = plot.color.cnvgain;
+          bp.label = g.g.append("text").text("CNV gain (" + bp.samplecount + ")");
+        } else if (bp.iscnvloss) {
+          color = plot.color.cnvloss;
+          bp.label = g.g.append("text").text("CNV loss (" + bp.samplecount + ")");
+        } else if (bp.issv) {
+          color = "black";
+          bp.label = g.g.append("text").text("SV (" + bp.samplecount + ")");
+        } else {
+          color = color0;
+        }
+        if (bp.label) {
+          bp.label.attr("fill", color).attr("font-family", font).attr("dominant-baseline", "central");
+        }
+        if (bp.w1 != void 0) {
+          bp.hline = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
+          bp.linew1 = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
+          bp.linew2 = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
+          bp.box = g.g.append("rect").attr("fill", "white").attr("stroke", color).attr("shape-rendering", "crispEdges");
+          bp.linep50 = g.g.append("line").attr("stroke", color).attr("shape-rendering", "crispEdges");
+        }
+        for (const d of bp.out) {
+          d.circle = g.g.append("circle").attr("stroke", color).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event) => {
+            plot.tip.clear().d.append("div").style("margin", "10px").html(d.sample + "<br>" + d.value);
+            plot.tip.show(event.clientX, event.clientY);
+          }).on("mouseout", () => {
+            plot.tip.hide();
+          });
+          if (plot.clicksample) {
+            d.circle.on("click", () => {
+              plot.clicksample(d, g, plot);
+            });
+          }
+        }
+      }
+    }
+  }
+  if (plot.sample) {
+    plot.sample.g = plot.g0.append("g");
+    plot.sample.svgtext = plot.sample.g.append("text").text(plot.sample.name).attr("font-family", font).attr("font-size", 12).attr("text-anchor", "middle").attr("dominant-baseline", "hanging").attr("fill", "blue");
+    plot.sample.line = plot.sample.g.append("line").attr("shape-rendering", "crispEdges").attr("stroke", "blue");
+  }
+  plot.place();
+}
+function addbutton_boxplotstats(plot) {
+  plot.buttonholder_boxplot.selectAll("*").remove();
+  plot.buttonholder_boxplot.append("button").text("Boxplots").on("click", () => {
+    if (plot.table_boxplotstats.style("display") == "block") {
+      disappear(plot.table_boxplotstats);
+      return;
+    }
+    plot.table_boxplotstats.selectAll("*").remove();
+    const tr = plot.table_boxplotstats.append("tr");
+    tr.append("td").text("Group").style("font-size", ".8em").style("opacity", 0.5);
+    tr.append("td").text("1st quartile").style("font-size", ".8em").style("opacity", 0.5);
+    tr.append("td").text("Median").style("font-size", ".8em").style("opacity", 0.5);
+    tr.append("td").text("3rd quartile").style("font-size", ".8em").style("opacity", 0.5);
+    for (const [i, g] of plot.data.groups.entries()) {
+      const tr2 = plot.table_boxplotstats.append("tr").style("background", i % 2 ? "" : "#f1f1f1");
+      tr2.append("td").text(g.name);
+      const boxplot = g.boxplots ? g.boxplots[0] : null;
+      tr2.append("td").text(boxplot ? boxplot.p25 : "");
+      tr2.append("td").text(boxplot ? boxplot.p50 : "");
+      tr2.append("td").text(boxplot ? boxplot.p75 : "");
+    }
+    appear(plot.table_boxplotstats);
+  });
+}
+function addbutton_showdata_fromlst(plot) {
+  plot.buttonrow.append("button").text(plot.gecfg.datatype).on("click", () => {
+    const pane = newpane({ x: 100, y: 100 });
+    pane.header.text(plot.gene + " " + plot.gecfg.datatype);
+    const table = pane.body.append("table").style("border-spacing", "4px").style("border-collapse", "separate");
+    const tr = table.append("tr");
+    tr.append("td").text("Sample").style("font-size", ".8em").style("opacity", 0.5);
+    tr.append("td").text(plot.gecfg.datatype).style("font-size", ".8em").style("opacity", 0.5);
+    for (const i of plot.data.lst) {
+      const tr2 = table.append("tr");
+      tr2.append("td").text(i.sample);
+      tr2.append("td").text(i.value);
+    }
+  });
+}
+function addbutton_showdata_newquery(plot) {
+  plot.buttonholder_sampleexpdata.selectAll("*").remove();
+  plot.buttonholder_sampleexpdata.append("button").text(plot.gecfg.datatype).on("click", async () => {
+    const pane = newpane({ x: 100, y: 100 });
+    pane.header.text(plot.gene + " " + plot.gecfg.datatype);
+    const wait = pane.body.append("div").style("margin", "30px").text("Loading...");
+    const arg = {
+      genome: plot.genome.name,
+      gene: plot.gene,
+      chr: plot.chr,
+      start: plot.start,
+      stop: plot.stop,
+      getalllst: 1
+    };
+    if (plot.dslabel) {
+      arg.dslabel = plot.dslabel;
+      arg.querykey = plot.querykey;
+    } else {
+      arg.iscustom = 1;
+      arg.file = plot.file;
+      arg.url = plot.url;
+      arg.indexURL = plot.indexURL;
+    }
+    try {
+      const data = await dofetch2("mdsgeneboxplot", { method: "POST", body: JSON.stringify(arg) });
+      if (data.error) throw data.error;
+      wait.remove();
+      const table = pane.body.append("table").style("border-spacing", "4px").style("border-collapse", "separate");
+      const tr = table.append("tr");
+      tr.append("td").text("Sample").style("font-size", ".8em").style("opacity", 0.5);
+      tr.append("td").text(plot.gecfg.datatype).style("font-size", ".8em").style("opacity", 0.5);
+      for (const i of data.lst) {
+        const tr2 = table.append("tr");
+        tr2.append("td").text(i.sample);
+        tr2.append("td").text(i.value);
+      }
+    } catch (e) {
+      wait.text("Error: " + (e.message || e));
+      if (e.stack) console.log(e.stack);
+    }
+  });
+}
+function init2(x, y, plot, group) {
+  const pane = newpane({ x, y });
+  pane.header.text(plot.gene + " " + plot.gecfg.datatype + " in " + group.name);
+  const pp = {
+    _plot: plot,
+    holder: pane.body,
+    uselog: plot.uselog
+  };
+  if (group.attributes) {
+    pp.getgroup = group.attributes;
+  } else {
+    pp.getgroup = 1;
+    pp.getgroup_unannotated = 1;
+  }
+  pp.errdiv = pp.holder.append("div").style("margin", "10px");
+  const buttonrow = pp.holder.append("div").style("margin", "10px");
+  const configdiv = pp.holder.append("div").style("margin", "10px").style("border", "solid 1px #ededed").style("padding", "10px").style("display", "none");
+  buttonrow.append("button").text("Log10").on("click", (event) => {
+    pp.uselog = !pp.uselog;
+    event.target.innerHTML = pp.uselog ? "Linear" : "Log10";
+    pp.place();
+  });
+  buttonrow.append("button").text("Data").on("click", () => {
+    const pane2 = newpane({ x: 200, y: 200 });
+    pane2.header.text(pane.header.node().innerHTML);
+    const table = pane2.body.append("table").style("border-spacing", "2px").style("border-collapse", "separate");
+    const tr = table.append("tr");
+    tr.append("td").text("Sample").style("font-size", ".8em").style("opacity", 0.5);
+    tr.append("td").text(plot.gecfg.datatype).style("font-size", ".8em").style("opacity", 0.5);
+    for (const [i, d] of pp.data.lst.entries()) {
+      const tr2 = table.append("tr");
+      const td = tr2.append("td").text(d.sample);
+      if (plot.clicksample) {
+        td.attr("class", "sja_clbtext").on("click", () => {
+          plot.clicksample(d, group, plot);
+        });
+      }
+      tr2.append("td").text(d.value);
+    }
+  });
+  pp.svg = pp.holder.append("svg");
+  pp.g0 = pp.svg.append("g");
+  const axisg = pp.svg.append("g");
+  const axiswidth = 400;
+  const circleradius = 6;
+  const axisticksize = 6;
+  const axislabelfontsize = 14;
+  const axispad = 10;
+  const statuscolpad = 5;
+  const circleyshift = 2;
+  pp.place = () => {
+    for (const col of pp.statuscolumns) {
+      col.width = 20;
+      for (const d of pp.data.lst) {
+        if (!d.status2cell) continue;
+        const cell = d.status2cell.get(col.name);
+        if (!cell) continue;
+        if (cell.label) {
+          cell.label.attr("font-size", circleradius * 2 - 2).each(function() {
+            col.width = Math.max(col.width, this.getBBox().width + 2);
+          });
+        }
+      }
+    }
+    let samplenamewidth = 0;
+    for (const d of pp.data.lst) {
+      if (d.samplelabel) {
+        d.samplelabel.attr("font-size", circleradius * 2 - 1).attr("x", -statuscolpad).attr("y", circleradius).each(function() {
+          samplenamewidth = Math.max(samplenamewidth, this.getBBox().width);
+        });
+      }
+    }
+    let statuslabelheight = 0;
+    let statustotalwidth = 0;
+    for (const col of pp.statuscolumns) {
+      if (!col.g) {
+        col.g = pp.g0.append("g");
+        col.namelabel = col.g.append("text").attr("font-family", font).attr("dominant-baseline", "central").attr("transform", "rotate(-90)").text(col.name);
+      }
+      col.g.attr("transform", "translate(" + (statustotalwidth + col.width / 2) + ",0)");
+      col.namelabel.attr("font-size", Math.min(15, col.width)).each(function() {
+        statuslabelheight = Math.max(statuslabelheight, this.getBBox().width);
+      });
+      statustotalwidth += col.width + statuscolpad;
+    }
+    statustotalwidth += circleradius;
+    const topheight = Math.max(statuslabelheight, axisticksize + axislabelfontsize + 20);
+    pp.g0.attr("transform", "translate(" + (samplenamewidth + statuscolpad) + "," + topheight + ")");
+    pp.axislabel.attr("x", statustotalwidth + axiswidth / 2);
+    axisg.attr("transform", "translate(" + (samplenamewidth + statuscolpad + statustotalwidth) + "," + topheight + ")");
+    const scale0 = (pp.uselog ? log() : linear()).domain([pp.data.min == 0 ? 1e-3 : pp.data.min, pp.data.max]).range([0, axiswidth]);
+    const scale = (v) => {
+      if (pp.uselog) {
+        if (v == 0) return 0;
+      }
+      return scale0(v);
+    };
+    axisstyle({
+      axis: axisg.transition().call(
+        axisTop().scale(scale0).tickSize(axisticksize)
+      ),
+      showline: 1
+    });
+    let y2 = axispad;
+    for (const [idx, d] of pp.data.lst.entries()) {
+      d.rowg.attr("transform", "translate(0," + y2 + ")");
+      if (d.rowbg) {
+        d.rowbg.attr("width", statustotalwidth + axiswidth).attr("height", circleradius * 2);
+      }
+      d.circle.transition().attr("r", circleradius).attr("cx", statustotalwidth + scale(d.value)).attr("cy", circleradius);
+      if (d.samplelabel) {
+        if (idx > 0 && !pp.data.lst[idx - 1].samplelabel) {
+          y2 += circleradius * 2 - circleyshift;
+          d.rowg.attr("transform", "translate(0," + y2 + ")");
+        }
+        if (d.status2cell) {
+          let x2 = 0;
+          for (const col of pp.statuscolumns) {
+            const cell = d.status2cell.get(col.name);
+            if (cell) {
+              cell.g.attr("transform", "translate(" + (x2 + col.width / 2) + "," + circleradius + ")");
+              cell.rect.attr("x", -col.width / 2).attr("y", -circleradius).attr("width", col.width).attr("height", circleradius * 2);
+            }
+            x2 += col.width + statuscolpad;
+          }
+        }
+        y2 += circleradius * 2;
+      } else {
+        y2 += circleyshift;
+      }
+    }
+    pp.svg.attr("width", samplenamewidth + statuscolpad + statustotalwidth + axiswidth + circleradius).attr("height", topheight + axispad + y2 + circleradius * 2);
+  };
+  pp.makegraph = () => {
+    const _p = pp._plot;
+    pp.axislabel = pp.g0.append("text").attr("font-size", 14).attr("font-family", font).attr("text-anchor", "middle").attr("y", -25).text(_p.gene + " " + _p.gecfg.datatype);
+    for (const d of pp.data.lst) {
+      measure(d, _p.gecfg);
+    }
+    let hasgain = false, hasloss = false, hassv = false, hasase = false, hasoutlier = false;
+    for (const d of pp.data.lst) {
+      if (d.gain) hasgain = true;
+      if (d.loss) hasloss = true;
+      if (d.sv) hassv = true;
+      if (d.estat.ase_monoallelic || d.estat.ase_uncertain || d.estat.ase_biallelic) hasase = true;
+      if (d.estat.outlier || d.estat.outlier_asehigh) hasoutlier = true;
+    }
+    pp.statuscolumns = [];
+    if (hasgain) {
+      pp.statuscolumns.push({
+        name: label_cnvgain
+        //width:20,
+      });
+    }
+    if (hasloss) {
+      pp.statuscolumns.push({
+        name: label_cnvloss
+        //width:20,
+      });
+    }
+    if (hassv) {
+      pp.statuscolumns.push({
+        name: label_sv,
+        width: 20
+      });
+    }
+    if (hasase) {
+      pp.statuscolumns.push({
+        name: label_ase,
+        width: 20
+      });
+    }
+    if (hasoutlier) {
+      pp.statuscolumns.push({
+        name: label_outlier,
+        width: 20
+      });
+    }
+    for (const d of pp.data.lst) {
+      d.rowg = pp.g0.append("g");
+      if (d.gain || d.loss || d.sv || d.estat.ase_monoallelic || d.estat.ase_biallelic || d.estat.ase_uncertain) {
+        d.rowbg = d.rowg.append("rect").attr("class", "sja_bgbox");
+      }
+      d.circle = d.rowg.append("circle").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", "#858585").on("mouseover", (event) => {
+        tooltip_pp(d, _p.tip.clear().d, pp);
+        _p.tip.show(event.clientX, event.clientY);
+      }).on("mouseout", () => {
+        _p.tip.hide();
+      });
+      if (_p.clicksample) {
+        d.circle.on("click", () => {
+          _p.clicksample(d, group, _p);
+        });
+      }
+      const status2cell = /* @__PURE__ */ new Map();
+      if (d.gain) {
+        const cell = { g: d.rowg.append("g") };
+        cell.rect = cell.g.append("rect").attr("fill", _p.color.cnvgain);
+        status2cell.set(label_cnvgain, cell);
+      }
+      if (d.loss) {
+        const cell = { g: d.rowg.append("g") };
+        cell.rect = cell.g.append("rect").attr("fill", _p.color.cnvloss);
+        status2cell.set(label_cnvloss, cell);
+      }
+      if (d.sv) {
+        const cell = { g: d.rowg.append("g") };
+        cell.rect = cell.g.append("rect").attr("fill", _p.color.sv);
+        status2cell.set(label_sv, cell);
+      }
+      if (d.estat.ase_monoallelic || d.estat.ase_biallelic || d.estat.ase_uncertain) {
+        const cell = { g: d.rowg.append("g") };
+        cell.rect = cell.g.append("rect").attr("fill", ase_color(d, _p.gecfg)), cell.label = cell.g.append("text").text(d.estat.ase_monoallelic ? "Mono" : d.estat.ase_biallelic ? "Bi" : "?").attr("font-family", font).attr("dominant-baseline", "central").attr("text-anchor", "middle").attr("fill", "white");
+        status2cell.set(label_ase, cell);
+      }
+      if (d.estat.outlier) {
+        const cell = { g: d.rowg.append("g") };
+        cell.rect = cell.g.append("rect").attr("fill", _p.gecfg.outlier.color_outlier);
+        status2cell.set(label_outlier, cell);
+      } else if (d.estat.outlier_asehigh) {
+        const cell = { g: d.rowg.append("g") };
+        cell.rect = cell.g.append("rect").attr("fill", _p.gecfg.outlier.color_outlier_asehigh);
+        status2cell.set(label_outlier, cell);
+      }
+      if (status2cell.size) {
+        d.status2cell = status2cell;
+        d.samplelabel = d.rowg.append("text").attr("font-family", font).attr("text-anchor", "end").attr("dominant-baseline", "central").text(d.sample);
+      }
+    }
+    pp.place();
+  };
+  loadplot2(pp);
+}
+async function loadplot2(pp) {
+  const _p = pp._plot;
+  const arg = {
+    genome: _p.genome.name,
+    gene: _p.gene,
+    chr: _p.chr,
+    start: _p.start,
+    stop: _p.stop,
+    getgroup: pp.getgroup,
+    getgroup_unannotated: pp.getgroup_unannotated,
+    svcnv: _p.svcnv,
+    sampleset: _p.sampleset
+  };
+  if (_p.dslabel) {
+    arg.dslabel = _p.dslabel;
+    arg.querykey = _p.querykey;
+  } else {
+    arg.iscustom = 1;
+    arg.file = _p.file;
+    arg.url = _p.url;
+    arg.indexURL = _p.indexURL;
+  }
+  pp.g0.append("text").text("Loading ...").attr("font-size", 20).attr("text-anchor", "center").attr("dominant-baseline", "central").attr("x", pp.svg.attr("width") / 2).attr("y", pp.svg.attr("height") / 2);
+  try {
+    const data = await dofetch2("mdsgeneboxplot", { method: "POST", body: JSON.stringify(arg) });
+    if (data.error) throw data.error;
+    pp.g0.selectAll("*").remove();
+    pp.data = data;
+    pp.makegraph();
+  } catch (e) {
+    sayerror(pp.errdiv, "Error: " + (e.message || e));
+    if (e.stack) console.log(e.stack);
+  }
+}
+function tooltip_pp(d, holder, pp) {
+  const lst = [{ k: "sample", v: d.sample }, { k: pp._plot.gecfg.datatype, v: d.value }];
+  if (d.gain || d.loss || d.sv) {
+    const l2 = [];
+    if (d.gain) {
+      l2.push(
+        '<span style="padding:0px 5px;color:white;background:' + pp._plot.color.cnvgain + '">Copy number gain</span>'
+      );
+    }
+    if (d.loss) {
+      l2.push(
+        '<span style="padding:0px 5px;color:white;background:' + pp._plot.color.cnvloss + '">Copy number loss</span>'
+      );
+    }
+    if (d.sv) {
+      l2.push('<span style="padding:0px 5px;color:white;background:' + pp._plot.color.sv + '">SV</span>');
+    }
+    lst.push({ k: "Overlap", v: l2.join(" ") });
+  }
+  const table = make_table_2col(holder, lst);
+  showsingleitem_table(d, pp._plot.gecfg, table);
+}
+function mayaddgrouperselect(plot) {
+  if (!plot.boxplotgroupers) return;
+  const select = plot.buttonrow.append("select").on("change", (event) => {
+    plot.index_boxplotgroupers = event.target.selectedIndex;
+    loadplot(plot);
+  });
+  for (const [idx, name] of plot.boxplotgroupers.entries()) {
+    select.append("option").text(name);
+  }
+}
+export {
+  init
+};
+//# sourceMappingURL=block.mds.geneboxplot-VJTIMZ6H.js.map