@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-FOJWYEGV.js

@@ -0,0 +1,228 @@
+import {
+  appInit
+} from "./chunk-CVRYZMDE.js";
+import {
+  getDefaultViolinSettings
+} from "./chunk-6WBIZXNI.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/regression.inputs.values.table.js
+var row_hover_bgcolor = "#fff6dc";
+var InputValuesTable = class {
+  constructor(opts) {
+    this.opts = opts;
+    this.input = opts.input;
+    setRenderers(this);
+    this.setDOM(opts.holder);
+  }
+  main() {
+    try {
+      const term = this.input.term;
+      if (!term || !this.input.termStatus) {
+        this.dom.holder.style("display", "none");
+        this.dom.loading_div.style("display", "none");
+        return;
+      } else if (term) {
+        this.dom.holder.style("display", "block");
+        this.dom.loading_div.style("display", "block");
+        this.updateValueCount();
+        this.dom.loading_div.style("display", "none");
+        this.render();
+        return;
+      }
+    } catch (e) {
+      this.dom.loading_div.style("display", "none");
+      throw e;
+    }
+  }
+  updateValueCount() {
+    const i = this.input;
+    try {
+      if (i.pill && i.pill.validateQ) {
+        i.pill.validateQ({
+          term: i.term.term,
+          q: i.term.q,
+          sampleCounts: i.termStatus.sampleCounts
+        });
+      }
+    } catch (e) {
+      i.term.error = e;
+    }
+  }
+};
+function setRenderers(self) {
+  self.setDOM = (holder) => {
+    self.dom = {
+      holder: holder.style("margin", "10px").style("font-size", ".8em").style("text-align", "left").style("color", "#999"),
+      loading_div: holder.append("div").text("Loading..").style("display", "none"),
+      top_info_div: holder.append("div").style("padding-bottom", "5px"),
+      violin_div: holder.append("div").style("color", "black").style("padding-top", "5px"),
+      table_div: holder.append("table").style("margin", "5px 0px 15px 0px").style("border-collapse", "collapse").style("color", "black"),
+      bottom_info_div: holder.append("div"),
+      excluded_div: holder.append("table").style("display", "none").style("margin", "5px 10px").style("border-collapse", "collapse")
+    };
+  };
+  self.render = async () => {
+    const input = self.input;
+    renderTopInfo(input);
+    await renderValuesTable(input);
+    renderBottomInfo(input);
+    renderExcludedValues(input);
+  };
+  function renderTopInfo(input) {
+    if (input.termStatus.topInfoStatus?.length) {
+      self.dom.top_info_div.style("display", "block").html(input.termStatus.topInfoStatus.join("<br>"));
+    } else {
+      self.dom.top_info_div.style("display", "none");
+    }
+  }
+  async function renderValuesTable(input) {
+    if (input.term.q.mode == "continuous" || input.term.q.mode == "spline") {
+      self.dom.violin_div.style("display", "block");
+      self.dom.table_div.style("display", "none");
+      if (self.plotAppApi) {
+        const action = {
+          type: "app_refresh",
+          state: {
+            termfilter: {
+              filter: self.input.parent.parent.filter
+            }
+          },
+          subactions: [
+            {
+              type: "plot_edit",
+              id: self.violinApi.id,
+              config: {
+                term: input.term
+              }
+            }
+          ]
+        };
+        self.plotAppApi.dispatch(action);
+      } else {
+        const opts = {
+          holder: self.dom.violin_div,
+          vocabApi: self.input.parent.app.vocabApi,
+          state: {
+            vocab: {
+              genome: self.input.parent.app.vocabApi.genome,
+              dslabel: self.input.parent.app.vocabApi.dslabel
+            },
+            termfilter: {
+              filter: self.input.parent.parent.filter
+            },
+            plots: [
+              {
+                chartType: "violin",
+                term: input.term,
+                settings: {
+                  violin: getDefaultViolinSettings(null, {
+                    svgw: 350,
+                    axisHeight: 25,
+                    rightMargin: 10,
+                    datasymbol: "rug",
+                    radius: 8,
+                    plotThickness: 80
+                  })
+                }
+              }
+            ]
+          },
+          // global options for plotAppApi
+          // opts.violin will apply to all violin plots within the plotApp
+          // rx will pass options by component type, which are not tracked in state
+          // examples are callbacks, event listeners, etc
+          violin: {
+            mode: "minimal"
+          }
+        };
+        self.plotAppApi = await appInit(opts);
+        const plotId = self.plotAppApi.getState().plots[0].id;
+        self.violinApi = self.plotAppApi.getComponents(`plots.${plotId}`);
+      }
+    } else {
+      self.dom.violin_div.style("display", "none");
+      const data = input.termStatus.sampleCounts;
+      if (!data || !data.length) {
+        self.dom.table_div.style("display", "none");
+        return;
+      }
+      self.dom.table_div.style("display", "block");
+      const l = self.input.orderedLabels;
+      const sortFxn = l && l.length ? (a, b) => l.indexOf(a.label) - l.indexOf(b.label) : (a, b) => b.samplecount - a.samplecount;
+      const tr_data = data.sort(sortFxn);
+      const maxCount = Math.max(...tr_data.map((v) => v.samplecount), 0);
+      tr_data.forEach((v) => v.bar_width_frac = Number((1 - (maxCount - v.samplecount) / maxCount).toFixed(4)));
+      self.dom.table_div.selectAll("tr").remove();
+      const trs = self.dom.table_div.selectAll("tr").data(tr_data, (b) => b.key);
+      trs.enter().append("tr").each(trEnter);
+    }
+  }
+  function renderBottomInfo(input) {
+    if (input.termStatus.bottomSummaryStatus) {
+      self.dom.bottom_info_div.style("display", "block").html(input.termStatus.bottomSummaryStatus);
+    } else {
+      self.dom.bottom_info_div.style("display", "none");
+    }
+  }
+  function renderExcludedValues(input) {
+    const data = input.termStatus.excludeCounts;
+    if (!data || !data.length) {
+      self.dom.excluded_div.style("display", "none");
+      return;
+    }
+    self.dom.excluded_div.style("display", "block").selectAll("tr").remove();
+    const trs = self.dom.excluded_div.selectAll("tr").data(data, (b) => b.key);
+    trs.enter().append("tr").each(trEnter);
+    self.dom.excluded_div.selectAll("td").style("color", "#999");
+  }
+  function trEnter(item) {
+    const tr = select_default(this);
+    const input = this.parentNode.__data__;
+    const t = input.term;
+    const maxBarWidth = 150;
+    tr.style("text-align", "left").style("cursor", input.termStatus.allowToSelectRefGrp ? "pointer" : "default");
+    const tdSpacing = "1px 10px 1px 0px";
+    tr.append("td").style("padding", tdSpacing).style("text-align", "left").style("color", "black").text(item.samplecount !== void 0 ? "n=" + item.samplecount : "");
+    tr.append("td").style("padding", tdSpacing).style("text-align", "left").style("color", "black").text(item.label);
+    const bar_td = tr.append("td").style("padding", tdSpacing);
+    const barWidth = maxBarWidth * item.bar_width_frac;
+    bar_td.append("div").style("margin", tdSpacing).style("width", barWidth + "px").style("height", "15px").style("background-color", "#ddd");
+    addTrBehavior({ input, item, tr, rendered: false });
+  }
+  function addTrBehavior({ input, item, tr, rendered }) {
+    if (!item.bar_width_frac) return;
+    const t = input.term;
+    const hover_flag = input.termStatus.allowToSelectRefGrp;
+    let ref_text;
+    if (rendered) {
+      tr.style("background", "white");
+      ref_text = select_default(tr.node().lastChild).select("div").style("display", item.key === t.refGrp && hover_flag ? "inline-block" : "none").style("border", item.key === t.refGrp && hover_flag ? "1px solid #bbb" : "");
+    } else if (input.term.q.mode != "cutoff") {
+      const reference_td = tr.append("td").style("padding", "1px 5px").style("text-align", "left");
+      ref_text = reference_td.append("div").style("display", item.key === t.refGrp && hover_flag ? "inline-block" : "none").style("padding", "2px 10px").style("border", item.key === t.refGrp && hover_flag ? "1px solid #bbb" : "").style("border-radius", "10px").style("color", "#999").style("font-size", ".7em").text("REFERENCE");
+      if (hover_flag) {
+        tr.on("mouseover", () => {
+          if (t.refGrp !== item.key) {
+            tr.style("background", row_hover_bgcolor);
+            ref_text.style("display", "inline-block").style("border", "").text("Set as reference");
+          } else tr.style("background", "white");
+        }).on("mouseout", () => {
+          tr.style("background", "white");
+          if (t.refGrp !== item.key) ref_text.style("display", "none");
+        }).on("click", () => {
+          t.refGrp = item.key;
+          ref_text.style("border", "1px solid #bbb").text("REFERENCE");
+          self.opts.callback(t);
+        });
+      }
+    }
+  }
+}
+
+export {
+  InputValuesTable
+};
+//# sourceMappingURL=chunk-FOJWYEGV.js.map

package/dist/chunk-FTN7Y34O.js

@@ -0,0 +1,158 @@
+import {
+  appInit
+} from "./chunk-CVRYZMDE.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-2YC6ZVE4.js";
+import {
+  mclass
+} from "./chunk-AMYSEKPF.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 5) {
+      errors.push("snv input not equal to 5 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-FTN7Y34O.js.map