@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/spliceevent.exonskip.diagram-XZHXB77R.js

@@ -0,0 +1,283 @@
+import {
+  spliceevent_phrase_default
+} from "./chunk-E55LLYRX.js";
+import {
+  font
+} from "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-Z5U6HOE4.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import "./chunk-I6WR4CG7.js";
+import {
+  IN_frame,
+  exoncolor
+} from "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// src/spliceevent.exonskip.diagram.js
+function spliceevent_exonskip_diagram_default(arg) {
+  const evt = arg.event;
+  const holder = arg.holder.append("div").style("vertical-align", "top");
+  if (!evt.isaltexon && !evt.isskipexon) {
+    holder.append("div").text(".isskipexon or .isaltexon is not set for event");
+    return;
+  }
+  if (!arg.nophrase) {
+    holder.append("div").html(spliceevent_phrase_default(evt));
+  }
+  const diagram = arg.holder.append("svg").style("display", "inline-block");
+  const canonicaljunctionreadcounttext = /* @__PURE__ */ new Map();
+  const canonicaljlst = [];
+  const exonwidth = 40;
+  const exonheight = 20;
+  const junctionheight = 20;
+  const intronwidth = 20;
+  const xpad = 20;
+  const ypad = 20;
+  const fontsize = 14;
+  const diagramg = diagram.append("g").attr("transform", "translate(" + xpad + "," + ypad + ")");
+  const skipexonidxbegin = evt.skippedexon[0];
+  const skipexonidxend = evt.skippedexon[evt.skippedexon.length - 1];
+  let showup1exon = false;
+  let showdown1exon = false;
+  if (evt.isskipexon) {
+    if (skipexonidxbegin > 1) {
+      showup1exon = true;
+    }
+    if (evt.down1junction) {
+      showdown1exon = true;
+    }
+  }
+  diagram.attr(
+    "width",
+    xpad + (showup1exon ? exonwidth + intronwidth : 0) + exonwidth + intronwidth + (exonwidth + intronwidth) * evt.skippedexon.length + exonwidth + (showdown1exon ? exonwidth + intronwidth : 0) + xpad
+  ).attr("height", ypad + fontsize + junctionheight + exonheight + junctionheight + fontsize + ypad);
+  const exony = fontsize + junctionheight;
+  const sample2jrc = /* @__PURE__ */ new Map();
+  let xoff = 0;
+  if (showup1exon) {
+    diagramg.append("rect").attr("x", xoff).attr("y", exony).attr("width", exonwidth).attr("height", exonheight).attr("fill", exoncolor);
+    diagramg.append("text").text("e" + (skipexonidxbegin - 1)).attr("x", xoff + exonwidth / 2).attr("y", exony + exonheight / 2).attr("text-anchor", "middle").attr("dominant-baseline", "central").attr("fill", "white").attr("font-size", fontsize);
+    xoff += exonwidth + intronwidth;
+    let nojunction = true;
+    let readcount = "?";
+    if (evt.up1junction) {
+      if (evt.junctionB.data) {
+        if (evt.junctionB.data.length == 1) {
+          const sampleid = evt.junctionB.data[0].tkid;
+          if (evt.up1junction.data) {
+            for (const sampledata of evt.up1junction.data) {
+              if (sampledata.tkid == sampleid) {
+                nojunction = false;
+                readcount = sampledata.v;
+                break;
+              }
+            }
+          }
+        } else if (evt.junctionB.data.length > 1) {
+          let readcountsum = 0;
+          let samplecount = 0;
+          for (const sample1 of evt.junctionB.data) {
+            for (const sample2 of evt.up1junction.data) {
+              if (sample1.tkid == sample2.tkid) {
+                readcountsum += sample2.v;
+                samplecount++;
+                break;
+              }
+            }
+          }
+          if (samplecount > 0) {
+            nojunction = false;
+            readcount = Math.ceil(readcountsum / samplecount);
+          }
+        }
+      } else {
+        nojunction = false;
+        readcount = evt.up1junction.v;
+      }
+    }
+    diagramg.append("path").attr(
+      "d",
+      "M" + (xoff - intronwidth) + "," + (exony + exonheight) + "L" + (xoff - intronwidth / 2) + "," + (exony + exonheight + junctionheight) + "L" + xoff + "," + (exony + exonheight)
+    ).attr("stroke", exoncolor).attr("stroke-dasharray", nojunction ? "2,2" : "none").attr("fill", "none");
+    if (!nojunction) {
+      const text = diagramg.append("text").text(readcount).attr("x", xoff - intronwidth / 2).attr("y", exony + exonheight + junctionheight + 2).attr("font-size", fontsize).attr("fill", "black").attr("font-family", font).attr("text-anchor", "middle").attr("dominant-baseline", "hanging");
+      canonicaljunctionreadcounttext.set(
+        evt.up1junction.start + "." + evt.up1junction.stop + "." + evt.up1junction.strand,
+        text
+      );
+      canonicaljlst.push([evt.up1junction.start, evt.up1junction.stop, evt.up1junction.strand]);
+    }
+  }
+  diagramg.append("rect").attr("x", xoff).attr("y", exony).attr("width", exonwidth).attr("height", exonheight).attr("fill", exoncolor);
+  diagramg.append("text").text("e" + skipexonidxbegin).attr("x", xoff + exonwidth / 2).attr("y", exony + exonheight / 2).attr("text-anchor", "middle").attr("dominant-baseline", "central").attr("fill", "white").attr("font-size", fontsize);
+  xoff += exonwidth + intronwidth;
+  for (let exonidx = skipexonidxbegin; exonidx <= skipexonidxend + 1; exonidx++) {
+    const islastone = exonidx == skipexonidxend + 1;
+    diagramg.append("rect").attr("x", xoff).attr("y", exony).attr("width", exonwidth).attr("height", exonheight).attr("fill", islastone ? exoncolor : "none").attr("stroke", islastone ? "none" : exoncolor).attr("shape-rendering", "crispEdges");
+    diagramg.append("text").text("e" + (exonidx + 1)).attr("x", xoff + exonwidth / 2).attr("y", exony + exonheight / 2).attr("text-anchor", "middle").attr("dominant-baseline", "central").attr("fill", islastone ? "white" : exoncolor).attr("font-size", fontsize);
+    const thisjunction = evt.junctionAlst[exonidx - skipexonidxbegin];
+    diagramg.append("path").attr(
+      "d",
+      "M" + (xoff - intronwidth) + "," + (exony + exonheight) + "L" + (xoff - intronwidth / 2) + "," + (exony + exonheight + junctionheight) + "L" + xoff + "," + (exony + exonheight)
+    ).attr("stroke", exoncolor).attr("stroke-dasharray", thisjunction ? "none" : "2,2").attr("fill", "none");
+    if (thisjunction) {
+      let readcount = "?";
+      if (evt.junctionB.data) {
+        if (evt.junctionB.data.length == 1) {
+          if (!thisjunction.data) {
+            console.error(".data missing from junctionA");
+          } else {
+            for (const sampledata of thisjunction.data) {
+              if (sampledata.tkid == evt.junctionB.data[0].tkid) {
+                readcount = sampledata.v;
+                break;
+              }
+            }
+          }
+        } else if (evt.junctionB.data.length > 1) {
+          readcount = "e" + exonidx + "-" + (exonidx + 1);
+          for (const thissample of evt.junctionB.data) {
+            if (!sample2jrc.has(thissample.tkid)) {
+              sample2jrc.set(thissample.tkid, {
+                sampleobj: thissample,
+                readcountlst: []
+              });
+            }
+            let thissamplereadcount = 0;
+            for (const sampledata of thisjunction.data) {
+              if (sampledata.tkid == thissample.tkid) {
+                thissamplereadcount = sampledata.v;
+                break;
+              }
+            }
+            sample2jrc.get(thissample.tkid).readcountlst.push(thissamplereadcount);
+          }
+        }
+      } else {
+        readcount = thisjunction.v;
+      }
+      const text = diagramg.append("text").text(readcount).attr("x", xoff - intronwidth / 2).attr("y", exony + exonheight + junctionheight + 2).attr("font-size", fontsize).attr("fill", "black").attr("font-family", font).attr("text-anchor", "middle").attr("dominant-baseline", "hanging");
+      canonicaljunctionreadcounttext.set(thisjunction.start + "." + thisjunction.stop + "." + thisjunction.strand, text);
+      canonicaljlst.push([thisjunction.start, thisjunction.stop, thisjunction.strand]);
+    }
+    xoff += exonwidth + intronwidth;
+  }
+  {
+    const midx = xoff - exonwidth - intronwidth - ((exonwidth + intronwidth) * evt.skippedexon.length + intronwidth) / 2;
+    diagramg.append("path").attr(
+      "d",
+      "M" + ((showup1exon ? exonwidth + intronwidth : 0) + exonwidth) + "," + exony + "L" + midx + "," + (exony - junctionheight) + "L" + (xoff - exonwidth - intronwidth) + "," + exony
+    ).attr("fill", "none").attr("stroke", evt.color);
+    let jBreadcount = "?";
+    if (evt.junctionB.data) {
+      if (evt.junctionB.data.length == 1) {
+        jBreadcount = evt.junctionB.data[0].v;
+      } else {
+        jBreadcount = "e" + skipexonidxbegin + "-" + (skipexonidxend + 2);
+        for (const thissample of evt.junctionB.data) {
+          if (!sample2jrc.has(thissample.tkid)) {
+            console.error("sample has junctionB but no junctionA! " + thissample.tkid);
+            continue;
+          }
+          let readcount = 0;
+          for (const sampledata of evt.junctionB.data) {
+            if (sampledata.tkid == thissample.tkid) {
+              readcount = sampledata.v;
+              break;
+            }
+          }
+          sample2jrc.get(thissample.tkid).readcountlst.unshift(readcount);
+        }
+      }
+    } else {
+      jBreadcount = evt.junctionB.v;
+    }
+    if (typeof evt.frame == "boolean") {
+      jBreadcount += ", " + (evt.frame == IN_frame ? "in frame" : "out of frame");
+    }
+    const bclab = diagramg.append("text").text(jBreadcount).attr("x", midx).attr("y", exony - junctionheight - 2).attr("font-size", fontsize).attr("fill", evt.color).attr("font-family", font).attr("text-anchor", "middle");
+  }
+  if (showdown1exon) {
+    diagramg.append("rect").attr("x", xoff).attr("y", exony).attr("width", exonwidth).attr("height", exonheight).attr("fill", exoncolor);
+    diagramg.append("text").text("e" + (skipexonidxend + 3)).attr("x", xoff + exonwidth / 2).attr("y", exony + exonheight / 2).attr("text-anchor", "middle").attr("dominant-baseline", "central").attr("fill", "white").attr("font-size", fontsize);
+    let nojunction = true;
+    let readcount = "?";
+    if (evt.down1junction) {
+      if (evt.junctionB.data) {
+        if (evt.junctionB.data.length == 1) {
+          const sampleid = evt.junctionB.data[0].tkid;
+          if (evt.down1junction.data) {
+            for (const sampledata of evt.down1junction.data) {
+              if (sampledata.tkid == sampleid) {
+                nojunction = false;
+                readcount = sampledata.v;
+                break;
+              }
+            }
+          }
+        } else if (evt.junctionB.data.length > 1) {
+          let readcountsum = 0;
+          let samplecount = 0;
+          for (const sample1 of evt.junctionB.data) {
+            for (const sample2 of evt.down1junction.data) {
+              if (sample1.tkid == sample2.tkid) {
+                readcountsum += sample2.v;
+                samplecount++;
+                break;
+              }
+            }
+          }
+          if (samplecount > 0) {
+            nojunction = false;
+            readcount = Math.ceil(readcountsum / samplecount);
+          }
+        }
+      } else {
+        nojunction = false;
+        readcount = evt.down1junction.v;
+      }
+    }
+    diagramg.append("path").attr(
+      "d",
+      "M" + (xoff - intronwidth) + "," + (exony + exonheight) + "L" + (xoff - intronwidth / 2) + "," + (exony + exonheight + junctionheight) + "L" + xoff + "," + (exony + exonheight)
+    ).attr("stroke", exoncolor).attr("stroke-dasharray", nojunction ? "2,2" : "none").attr("fill", "none");
+    if (!nojunction) {
+      const text = diagramg.append("text").text(readcount).attr("x", xoff - intronwidth / 2).attr("y", exony + exonheight + junctionheight + 2).attr("font-size", fontsize).attr("fill", "black").attr("font-family", font).attr("text-anchor", "middle").attr("dominant-baseline", "hanging");
+      canonicaljunctionreadcounttext.set(
+        evt.down1junction.start + "." + evt.down1junction.stop + "." + evt.down1junction.strand,
+        text
+      );
+      canonicaljlst.push([evt.down1junction.start, evt.down1junction.stop, evt.down1junction.strand]);
+    }
+  }
+  return [canonicaljunctionreadcounttext, canonicaljlst];
+}
+export {
+  spliceevent_exonskip_diagram_default as default
+};
+//# sourceMappingURL=spliceevent.exonskip.diagram-XZHXB77R.js.map

package/dist/spliceevent.exonskip.diagram-XZHXB77R.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../src/spliceevent.exonskip.diagram.js"],
+  "sourcesContent": ["import * as client from './client'\nimport { exoncolor, IN_frame, OUT_frame } from '#shared/common.js'\nimport spliceeventphrase from './spliceevent.phrase'\n\n/* no longer doing sample-junction read count line plots\nimport {axisLeft} from 'd3-axis'\nimport {scaleLinear,scaleOrdinal,schemeCategory20} from 'd3-scale'\n*/\n\n/*\ndraw diagram for exon-skipping or exon alt usage\n\nat tip of each junction, show read count value\n\nfor mds junction:\n\tonly median read count for junctionB is given\n\tjunctionAs do not have median read count over the same set of samples as junctionB, thus is waiting to be calculated\n\twhen rendering diagram, will create <text> as read count placeholder for each junction, and return the junction-<text> mapping for further median read count summary\n\n*/\n\nexport default function (arg) {\n\t/*\nsingle event, arg:\n\t.event\n\t\t.isaltexon\n\t\t.isskipexon\n\t.holder\n\t.nophrase\n*/\n\n\tconst evt = arg.event\n\n\tconst holder = arg.holder.append('div').style('vertical-align', 'top')\n\n\tif (!evt.isaltexon && !evt.isskipexon) {\n\t\tholder.append('div').text('.isskipexon or .isaltexon is not set for event')\n\t\treturn\n\t}\n\n\tif (!arg.nophrase) {\n\t\t// print phrase as summary\n\t\tholder.append('div').html(spliceeventphrase(evt))\n\t}\n\n\t// svg for drawing diagram\n\tconst diagram = arg.holder.append('svg').style('display', 'inline-block')\n\n\t// canonical junction read count\n\tconst canonicaljunctionreadcounttext = new Map()\n\t// k: start.stop\n\t// v: <text>\n\tconst canonicaljlst = [] // [start,stop] for each canonical junction\n\n\t/* svg for lineplot\nnot in use\n\nlet samplelineplot\nif(evt.junctionB.data) {\n\t// track is multi-sample\n\tif(evt.junctionB.data.length>1) {\n\t\t// multiple samples for this event\n\t\t// draw a line plot to show junction read counts in each sample\n\t\tsamplelineplot=arg.holder.append('svg')\n\t\t\t.style('display','inline-block')\n\t\t\t.style('margin-left','10px')\n\t} else {\n\t\t// single sample\n\t\t// no line plot\n\t}\n}\n*/\n\n\tconst exonwidth = 40\n\tconst exonheight = 20\n\tconst junctionheight = 20\n\tconst intronwidth = 20\n\tconst xpad = 20\n\tconst ypad = 20\n\tconst fontsize = 14\n\n\tconst diagramg = diagram.append('g').attr('transform', 'translate(' + xpad + ',' + ypad + ')')\n\n\t// array idx of skipped exon\n\tconst skipexonidxbegin = evt.skippedexon[0]\n\tconst skipexonidxend = evt.skippedexon[evt.skippedexon.length - 1]\n\n\t// whether to show up1/down1 exon\n\t// this affects graph width\n\tlet showup1exon = false\n\tlet showdown1exon = false\n\n\tif (evt.isskipexon) {\n\t\tif (skipexonidxbegin > 1) {\n\t\t\t// still show up1 exon no matter if up1junction exists\n\t\t\tshowup1exon = true\n\t\t}\n\t\tif (evt.down1junction) {\n\t\t\tshowdown1exon = true\n\t\t}\n\t}\n\n\tdiagram\n\t\t.attr(\n\t\t\t'width',\n\t\t\txpad +\n\t\t\t\t(showup1exon ? exonwidth + intronwidth : 0) +\n\t\t\t\texonwidth +\n\t\t\t\tintronwidth +\n\t\t\t\t(exonwidth + intronwidth) * evt.skippedexon.length +\n\t\t\t\texonwidth +\n\t\t\t\t(showdown1exon ? exonwidth + intronwidth : 0) +\n\t\t\t\txpad\n\t\t)\n\t\t.attr('height', ypad + fontsize + junctionheight + exonheight + junctionheight + fontsize + ypad)\n\n\tconst exony = fontsize + junctionheight\n\n\t// always show exons from 5' to 3'\n\n\t// when in multi-sample mode, for each sample, gather junction read count by the order of junction 5->3\n\tconst sample2jrc = new Map()\n\n\tlet xoff = 0\n\n\tif (showup1exon) {\n\t\t// up1 exon\n\t\tdiagramg\n\t\t\t.append('rect')\n\t\t\t.attr('x', xoff)\n\t\t\t.attr('y', exony)\n\t\t\t.attr('width', exonwidth)\n\t\t\t.attr('height', exonheight)\n\t\t\t.attr('fill', exoncolor)\n\t\tdiagramg\n\t\t\t.append('text')\n\t\t\t.text('e' + (skipexonidxbegin - 1))\n\t\t\t.attr('x', xoff + exonwidth / 2)\n\t\t\t.attr('y', exony + exonheight / 2)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('font-size', fontsize)\n\t\txoff += exonwidth + intronwidth\n\t\t// up1 junction\n\t\tlet nojunction = true\n\t\tlet readcount = '?'\n\t\t// in multi-sample mode, if there is no sample from junctionB has up1junction, treat this junction as not exist\n\t\tif (evt.up1junction) {\n\t\t\t// up1 read count\n\t\t\tif (evt.junctionB.data) {\n\t\t\t\tif (evt.junctionB.data.length == 1) {\n\t\t\t\t\tconst sampleid = evt.junctionB.data[0].tkid\n\t\t\t\t\tif (evt.up1junction.data) {\n\t\t\t\t\t\tfor (const sampledata of evt.up1junction.data) {\n\t\t\t\t\t\t\tif (sampledata.tkid == sampleid) {\n\t\t\t\t\t\t\t\tnojunction = false\n\t\t\t\t\t\t\t\treadcount = sampledata.v\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else if (evt.junctionB.data.length > 1) {\n\t\t\t\t\tlet readcountsum = 0\n\t\t\t\t\tlet samplecount = 0\n\t\t\t\t\tfor (const sample1 of evt.junctionB.data) {\n\t\t\t\t\t\tfor (const sample2 of evt.up1junction.data) {\n\t\t\t\t\t\t\tif (sample1.tkid == sample2.tkid) {\n\t\t\t\t\t\t\t\treadcountsum += sample2.v\n\t\t\t\t\t\t\t\tsamplecount++\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (samplecount > 0) {\n\t\t\t\t\t\tnojunction = false\n\t\t\t\t\t\treadcount = Math.ceil(readcountsum / samplecount)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tnojunction = false\n\t\t\t\treadcount = evt.up1junction.v\n\t\t\t}\n\t\t}\n\t\tdiagramg\n\t\t\t.append('path')\n\t\t\t.attr(\n\t\t\t\t'd',\n\t\t\t\t'M' +\n\t\t\t\t\t(xoff - intronwidth) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight) +\n\t\t\t\t\t'L' +\n\t\t\t\t\t(xoff - intronwidth / 2) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight + junctionheight) +\n\t\t\t\t\t'L' +\n\t\t\t\t\txoff +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight)\n\t\t\t)\n\t\t\t.attr('stroke', exoncolor)\n\t\t\t.attr('stroke-dasharray', nojunction ? '2,2' : 'none')\n\t\t\t.attr('fill', 'none')\n\t\tif (!nojunction) {\n\t\t\t// will print read count\n\t\t\tconst text = diagramg\n\t\t\t\t.append('text')\n\t\t\t\t.text(readcount)\n\t\t\t\t.attr('x', xoff - intronwidth / 2)\n\t\t\t\t.attr('y', exony + exonheight + junctionheight + 2)\n\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t.attr('fill', 'black')\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('dominant-baseline', 'hanging')\n\t\t\tcanonicaljunctionreadcounttext.set(\n\t\t\t\tevt.up1junction.start + '.' + evt.up1junction.stop + '.' + evt.up1junction.strand,\n\t\t\t\ttext\n\t\t\t)\n\t\t\tcanonicaljlst.push([evt.up1junction.start, evt.up1junction.stop, evt.up1junction.strand])\n\t\t}\n\t}\n\n\t// the exon upstream of first skipped exon\n\tdiagramg\n\t\t.append('rect')\n\t\t.attr('x', xoff)\n\t\t.attr('y', exony)\n\t\t.attr('width', exonwidth)\n\t\t.attr('height', exonheight)\n\t\t.attr('fill', exoncolor)\n\tdiagramg\n\t\t.append('text')\n\t\t.text('e' + skipexonidxbegin) // print id of this exon is skipexonidxbegin\n\t\t.attr('x', xoff + exonwidth / 2)\n\t\t.attr('y', exony + exonheight / 2)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('fill', 'white')\n\t\t.attr('font-size', fontsize)\n\txoff += exonwidth + intronwidth\n\n\t// for each skipped exon including the one immediately after it\n\tfor (let exonidx = skipexonidxbegin; exonidx <= skipexonidxend + 1; exonidx++) {\n\t\tconst islastone = exonidx == skipexonidxend + 1\n\n\t\t// draw this exon\n\t\tdiagramg\n\t\t\t.append('rect')\n\t\t\t.attr('x', xoff)\n\t\t\t.attr('y', exony)\n\t\t\t.attr('width', exonwidth)\n\t\t\t.attr('height', exonheight)\n\t\t\t.attr('fill', islastone ? exoncolor : 'none')\n\t\t\t.attr('stroke', islastone ? 'none' : exoncolor)\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\tdiagramg\n\t\t\t.append('text')\n\t\t\t.text('e' + (exonidx + 1)) // print id of this exon is skipexonidxbegin\n\t\t\t.attr('x', xoff + exonwidth / 2)\n\t\t\t.attr('y', exony + exonheight / 2)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('fill', islastone ? 'white' : exoncolor)\n\t\t\t.attr('font-size', fontsize)\n\n\t\tconst thisjunction = evt.junctionAlst[exonidx - skipexonidxbegin]\n\t\t// A (canonical) junctions are allowed to be missing\n\n\t\t// at bottom, draw canonical junction\n\t\t// from the end of previous exon to start of current exon\n\t\tdiagramg\n\t\t\t.append('path')\n\t\t\t.attr(\n\t\t\t\t'd',\n\t\t\t\t'M' +\n\t\t\t\t\t(xoff - intronwidth) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight) +\n\t\t\t\t\t'L' +\n\t\t\t\t\t(xoff - intronwidth / 2) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight + junctionheight) +\n\t\t\t\t\t'L' +\n\t\t\t\t\txoff +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight)\n\t\t\t)\n\t\t\t.attr('stroke', exoncolor)\n\t\t\t.attr('stroke-dasharray', thisjunction ? 'none' : '2,2')\n\t\t\t.attr('fill', 'none')\n\n\t\tif (thisjunction) {\n\t\t\t// this A junction exists, show read count\n\t\t\t// if multiple sample, show exon numbers instead\n\t\t\tlet readcount = '?'\n\t\t\tif (evt.junctionB.data) {\n\t\t\t\tif (evt.junctionB.data.length == 1) {\n\t\t\t\t\tif (!thisjunction.data) {\n\t\t\t\t\t\tconsole.error('.data missing from junctionA')\n\t\t\t\t\t} else {\n\t\t\t\t\t\tfor (const sampledata of thisjunction.data) {\n\t\t\t\t\t\t\tif (sampledata.tkid == evt.junctionB.data[0].tkid) {\n\t\t\t\t\t\t\t\treadcount = sampledata.v\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else if (evt.junctionB.data.length > 1) {\n\t\t\t\t\t// multiple samples have this junction\n\t\t\t\t\t// show from-to exon number\n\t\t\t\t\treadcount = 'e' + exonidx + '-' + (exonidx + 1)\n\t\t\t\t\t// collect read count for each sample for line plot\n\t\t\t\t\tfor (const thissample of evt.junctionB.data) {\n\t\t\t\t\t\tif (!sample2jrc.has(thissample.tkid)) {\n\t\t\t\t\t\t\tsample2jrc.set(thissample.tkid, {\n\t\t\t\t\t\t\t\tsampleobj: thissample,\n\t\t\t\t\t\t\t\treadcountlst: []\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t}\n\t\t\t\t\t\t// slot read count for this sample\n\t\t\t\t\t\tlet thissamplereadcount = 0\n\t\t\t\t\t\tfor (const sampledata of thisjunction.data) {\n\t\t\t\t\t\t\tif (sampledata.tkid == thissample.tkid) {\n\t\t\t\t\t\t\t\tthissamplereadcount = sampledata.v\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsample2jrc.get(thissample.tkid).readcountlst.push(thissamplereadcount)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\treadcount = thisjunction.v\n\t\t\t}\n\t\t\t// show read count for this junction\n\t\t\tconst text = diagramg\n\t\t\t\t.append('text')\n\t\t\t\t.text(readcount)\n\t\t\t\t.attr('x', xoff - intronwidth / 2)\n\t\t\t\t.attr('y', exony + exonheight + junctionheight + 2)\n\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t.attr('fill', 'black')\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('dominant-baseline', 'hanging')\n\t\t\tcanonicaljunctionreadcounttext.set(thisjunction.start + '.' + thisjunction.stop + '.' + thisjunction.strand, text)\n\t\t\tcanonicaljlst.push([thisjunction.start, thisjunction.stop, thisjunction.strand])\n\t\t}\n\t\txoff += exonwidth + intronwidth\n\t}\n\n\t// draw junction B\n\t{\n\t\tconst midx = xoff - exonwidth - intronwidth - ((exonwidth + intronwidth) * evt.skippedexon.length + intronwidth) / 2\n\n\t\tdiagramg\n\t\t\t.append('path')\n\t\t\t.attr(\n\t\t\t\t'd',\n\t\t\t\t'M' +\n\t\t\t\t\t((showup1exon ? exonwidth + intronwidth : 0) + exonwidth) +\n\t\t\t\t\t',' +\n\t\t\t\t\texony +\n\t\t\t\t\t'L' +\n\t\t\t\t\tmidx +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony - junctionheight) +\n\t\t\t\t\t'L' +\n\t\t\t\t\t(xoff - exonwidth - intronwidth) +\n\t\t\t\t\t',' +\n\t\t\t\t\texony\n\t\t\t)\n\t\t\t.attr('fill', 'none')\n\t\t\t.attr('stroke', evt.color)\n\n\t\t// get read count of junction B\n\t\tlet jBreadcount = '?'\n\t\tif (evt.junctionB.data) {\n\t\t\tif (evt.junctionB.data.length == 1) {\n\t\t\t\tjBreadcount = evt.junctionB.data[0].v\n\t\t\t} else {\n\t\t\t\t// multi-sample\n\t\t\t\t// show label instead of read count\n\t\t\t\tjBreadcount = 'e' + skipexonidxbegin + '-' + (skipexonidxend + 2)\n\t\t\t\t// for each sample, find jB read count and save it for line plot\n\t\t\t\tfor (const thissample of evt.junctionB.data) {\n\t\t\t\t\tif (!sample2jrc.has(thissample.tkid)) {\n\t\t\t\t\t\tconsole.error('sample has junctionB but no junctionA! ' + thissample.tkid)\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tlet readcount = 0\n\t\t\t\t\tfor (const sampledata of evt.junctionB.data) {\n\t\t\t\t\t\tif (sampledata.tkid == thissample.tkid) {\n\t\t\t\t\t\t\treadcount = sampledata.v\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tsample2jrc.get(thissample.tkid).readcountlst.unshift(readcount)\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\tjBreadcount = evt.junctionB.v\n\t\t}\n\n\t\tif (typeof evt.frame == 'boolean') {\n\t\t\tjBreadcount += ', ' + (evt.frame == IN_frame ? 'in frame' : 'out of frame')\n\t\t}\n\n\t\t// show junction B read count/label\n\t\tconst bclab = diagramg\n\t\t\t.append('text')\n\t\t\t.text(jBreadcount)\n\t\t\t.attr('x', midx)\n\t\t\t.attr('y', exony - junctionheight - 2)\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('fill', evt.color)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('text-anchor', 'middle')\n\t}\n\n\tif (showdown1exon) {\n\t\t// down1 exon\n\t\tdiagramg\n\t\t\t.append('rect')\n\t\t\t.attr('x', xoff)\n\t\t\t.attr('y', exony)\n\t\t\t.attr('width', exonwidth)\n\t\t\t.attr('height', exonheight)\n\t\t\t.attr('fill', exoncolor)\n\t\tdiagramg\n\t\t\t.append('text')\n\t\t\t.text('e' + (skipexonidxend + 3))\n\t\t\t.attr('x', xoff + exonwidth / 2)\n\t\t\t.attr('y', exony + exonheight / 2)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('font-size', fontsize)\n\n\t\tlet nojunction = true\n\t\tlet readcount = '?'\n\t\t// in multi-sample mode, if there is no sample from junctionB has down1junction, treat this junction as not exist\n\t\tif (evt.down1junction) {\n\t\t\t// up1 read count\n\t\t\tif (evt.junctionB.data) {\n\t\t\t\tif (evt.junctionB.data.length == 1) {\n\t\t\t\t\tconst sampleid = evt.junctionB.data[0].tkid\n\t\t\t\t\tif (evt.down1junction.data) {\n\t\t\t\t\t\tfor (const sampledata of evt.down1junction.data) {\n\t\t\t\t\t\t\tif (sampledata.tkid == sampleid) {\n\t\t\t\t\t\t\t\tnojunction = false\n\t\t\t\t\t\t\t\treadcount = sampledata.v\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else if (evt.junctionB.data.length > 1) {\n\t\t\t\t\tlet readcountsum = 0\n\t\t\t\t\tlet samplecount = 0\n\t\t\t\t\tfor (const sample1 of evt.junctionB.data) {\n\t\t\t\t\t\tfor (const sample2 of evt.down1junction.data) {\n\t\t\t\t\t\t\tif (sample1.tkid == sample2.tkid) {\n\t\t\t\t\t\t\t\treadcountsum += sample2.v\n\t\t\t\t\t\t\t\tsamplecount++\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (samplecount > 0) {\n\t\t\t\t\t\tnojunction = false\n\t\t\t\t\t\treadcount = Math.ceil(readcountsum / samplecount)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tnojunction = false\n\t\t\t\treadcount = evt.down1junction.v\n\t\t\t}\n\t\t}\n\t\tdiagramg\n\t\t\t.append('path')\n\t\t\t.attr(\n\t\t\t\t'd',\n\t\t\t\t'M' +\n\t\t\t\t\t(xoff - intronwidth) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight) +\n\t\t\t\t\t'L' +\n\t\t\t\t\t(xoff - intronwidth / 2) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight + junctionheight) +\n\t\t\t\t\t'L' +\n\t\t\t\t\txoff +\n\t\t\t\t\t',' +\n\t\t\t\t\t(exony + exonheight)\n\t\t\t)\n\t\t\t.attr('stroke', exoncolor)\n\t\t\t.attr('stroke-dasharray', nojunction ? 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