@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/spliceevent.exonskip.diagram-H54N7ZKY.js

@@ -0,0 +1,283 @@
+import {
+  spliceevent_phrase_default
+} from "./chunk-OOWXMY7U.js";
+import {
+  font
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import "./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 "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import {
+  IN_frame,
+  exoncolor
+} from "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.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/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-H54N7ZKY.js.map