@sjcrh/proteinpaint-client 2.205.0 → 2.206.0

package/dist/chunk-GT6WJUJY.js

@@ -0,0 +1,480 @@
+import {
+  renderTable
+} from "./chunk-Q5SK3U2T.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst
+} from "./chunk-RPDVFM7E.js";
+import {
+  termType2label
+} from "./chunk-5ILEFNXJ.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import {
+  __export
+} from "./chunk-HS5PO5ZQ.js";
+
+// plots/matrix/hierCluster.interactivity.js
+var hierCluster_interactivity_exports = {};
+__export(hierCluster_interactivity_exports, {
+  addSelectedRowsOptions: () => addSelectedRowsOptions,
+  addSelectedSamplesOptions: () => addSelectedSamplesOptions,
+  getAllChildrenClusterIds: () => getAllChildrenClusterIds,
+  getClusterFromLeftDendrogram: () => getClusterFromLeftDendrogram,
+  getClusterFromTopDendrogram: () => getClusterFromTopDendrogram,
+  setClusteringBtn: () => setClusteringBtn,
+  showTable4selectedRows: () => showTable4selectedRows,
+  showTable4selectedSamples: () => showTable4selectedSamples,
+  triggerZoomBranch: () => triggerZoomBranch
+});
+function getAllChildrenClusterIds(clickedClusterId, left) {
+  const mergedClusters = left ? this.hierClusterData.clustering.row.mergedClusters : this.hierClusterData.clustering.col.mergedClusters;
+  const children = mergedClusters.get(clickedClusterId).childrenClusters || [];
+  let allChildren = [...children];
+  for (const child of children) {
+    allChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left));
+  }
+  return allChildren;
+}
+function addSelectedSamplesOptions(clickedSampleNames, event) {
+  const l = this.settings.matrix.controlLabels;
+  const ss = this.opts.allow2selectSamples;
+  const optionArr = [
+    {
+      label: "Zoom in",
+      callback: () => {
+        this.triggerZoomBranch(this, clickedSampleNames);
+      }
+    },
+    {
+      label: `List ${clickedSampleNames.length} ${l.samples}`,
+      callback: () => this.showTable4selectedSamples(clickedSampleNames)
+    }
+  ];
+  if (ss) {
+    optionArr.push({
+      label: ss.buttonText || `Select ${l.samples}`,
+      callback: async () => {
+        const samples = clickedSampleNames.map((c) => this.data.samples[c]);
+        ss.callback({
+          samples: await this.app.vocabApi.convertSampleId(samples, ss.attributes),
+          source: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`
+        });
+      }
+    });
+  } else {
+    if (this.state.nav && this.state.nav.header_mode !== "hidden") {
+      const samples = clickedSampleNames.map((c) => this.sampleOrder.find((s) => s.row.sample == c).row);
+      for (const s of samples) {
+        if (!s.sampleId) s.sampleId = s.sample;
+      }
+      optionArr.push({
+        label: "Add to a group",
+        callback: async () => {
+          const group = {
+            name: "Group",
+            items: samples
+          };
+          this.addGroup(group);
+        }
+      });
+    }
+  }
+  this.mouseout();
+  this.dom.tip.hide();
+  this.dom.dendroClickMenu.d.selectAll("*").remove();
+  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", "sja_menuoption").style("border-radius", "0px").html((d) => d.label).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
+    this.dom.dendroClickMenu.d.selectAll("*").remove();
+    event2.target.__data__.callback();
+  });
+  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
+}
+function addSelectedRowsOptions(clickedRowNames, event) {
+  const rowType = this.config.settings.matrix.controlLabels.terms;
+  const optionArr = [
+    {
+      label: `List ${clickedRowNames.length} ${rowType}`,
+      callback: () => this.showTable4selectedRows(clickedRowNames, rowType)
+    }
+  ];
+  if (this.config.dataType == "geneExpression" && this.app.opts.genome.termdbs) {
+    const minGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.minCutoff;
+    const maxGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.maxCutoff;
+    optionArr.push({
+      label: `Gene set overrepresentation analysis`,
+      disabled: clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff,
+      callback: () => {
+        if (clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff) return;
+        this.dom.dendroClickMenu.d.selectAll("*").remove();
+        const lst = [];
+        for (const x of clickedRowNames) {
+          const j = this.terms?.find?.((t) => t.tw.$id == x);
+          if (j) {
+            const n = j.tw?.term?.gene;
+            if (n) lst.push(n);
+          }
+        }
+        const config = {
+          chartType: "geneORA",
+          geneORAparams: {
+            sample_genes: lst.join(","),
+            genome: this.app.vocabApi.opts.state.vocab.genome
+          }
+        };
+        this.app.dispatch({
+          type: "plot_create",
+          config
+        });
+      }
+    });
+  }
+  this.mouseout();
+  this.dom.tip.hide();
+  this.dom.dendroClickMenu.d.selectAll("*").remove();
+  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", (d) => d.disabled ? "sja_menuoption_not_interactive" : "sja_menuoption").style("opacity", (d) => d.disabled ? 0.5 : 1).style("border-radius", "0px").html(
+    (d) => d.disabled ? `${d.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>` : d.label
+  ).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
+    if (event2.target.__data__?.callback) event2.target.__data__.callback();
+  });
+  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
+}
+function triggerZoomBranch(self, clickedSampleNames) {
+  if (self.zoomArea) {
+    self.zoomArea.remove();
+    delete self.zoomArea;
+  }
+  const c = {
+    startCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[0]),
+    endCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[clickedSampleNames.length - 1])
+  };
+  const s = self.settings.matrix;
+  const d = self.dimensions;
+  const start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell;
+  const zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2);
+  const centerCell = self.sampleOrder[zoomIndex];
+  const colw = self.computedSettings.colw || self.settings.matrix.colw;
+  const maxZoomLevel = s.colwMax / colw;
+  const minZoomLevel = s.colwMin / colw;
+  const tentativeZoomLevel = Math.max(
+    1,
+    s.zoomLevel * d.mainw / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw) * 0.7
+  );
+  const zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel));
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: {
+      settings: {
+        matrix: {
+          zoomLevel,
+          zoomCenterPct: 0.5,
+          //zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,
+          zoomIndex,
+          zoomGrpIndex: centerCell.grpIndex
+        }
+      }
+    }
+  });
+  self.resetInteractions();
+}
+function showTable4selectedSamples(clickedSampleNames) {
+  const templates = this.state.termdbConfig.urlTemplates;
+  const rows = templates?.sample ? clickedSampleNames.map((c) => [
+    { value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }
+  ]) : clickedSampleNames.map((c) => [{ value: this.hierClusterData.bySampleId[c].label }]);
+  const columns = [{ label: this.settings.matrix.controlLabels.Sample }];
+  renderTable({
+    rows,
+    columns,
+    div: this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px"),
+    showLines: true,
+    maxHeight: "35vh",
+    resize: true
+  });
+}
+function showTable4selectedRows(clickedRowNames, rowType) {
+  const templates = this.state.termdbConfig.urlTemplates;
+  const rows = [];
+  if (templates?.gene && this.config.dataType == "geneExpression" && this.hierClusterData.byTermId) {
+    for (const i of clickedRowNames) {
+      const genesymbol = this.terms.find((t) => t.tw?.$id == i)?.tw?.term?.gene;
+      if (!genesymbol) continue;
+      const gencode = this.hierClusterData.byTermId[i]?.gencodeId;
+      if (gencode) {
+        rows.push([{ value: genesymbol, url: `${templates.gene.base}${gencode}` }]);
+      } else {
+        rows.push([{ value: genesymbol }]);
+      }
+    }
+  } else {
+    for (const i of clickedRowNames) {
+      const tw = this.terms.find((t) => t.tw?.$id == i)?.tw;
+      if (!tw) continue;
+      const n = tw.term?.gene || tw.term?.name;
+      if (!n) continue;
+      rows.push([{ value: n }]);
+    }
+  }
+  const div = this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px");
+  const buttonDiv = div.append("div").style("padding", "5px");
+  const copyButton = buttonDiv.append("button").html(`Copy ${rowType}`).attr("class", ".sja_menu_div button").style("margin-top", "2px").style("padding", "5px").on("click", () => {
+    const geneNames = rows.map((row) => row[0].value).join("\n");
+    navigator.clipboard.writeText(geneNames).then(() => {
+    }, console.warn);
+    copyButton.html(`Copy ${rowType}&nbsp;&check;`);
+  });
+  renderTable({
+    rows,
+    columns: [{ label: rowType }],
+    div: div.append("div"),
+    showLines: true,
+    maxHeight: "35vh",
+    resize: true
+  });
+}
+function getClusterFromTopDendrogram(event) {
+  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
+  else return;
+  const y = event.clientY - this.imgBox.y - event.target.clientTop;
+  const xMin = this.dimensions.xMin;
+  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
+  for (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {
+    const { x1, y1, x2, y2, clusterY } = cluster.clusterPosition;
+    if (x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5 || clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5 || clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5) {
+      return clusterId;
+    }
+  }
+}
+function getClusterFromLeftDendrogram(event) {
+  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
+  else return;
+  const y = event.clientY - this.imgBox.y - event.target.clientTop;
+  const xMin = this.dimensions.xMin;
+  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
+  for (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {
+    const { x1, y1, x2, y2, clusterX } = cluster.clusterPosition;
+    if (y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5 || clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5 || clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5) {
+      return clusterId;
+    }
+  }
+}
+function setClusteringBtn(holder, callback) {
+  const cl = this.config.settings.matrix.controlLabels;
+  const dataType = this.config.dataType;
+  const clusterRowLabel = cl.Terms;
+  const cluteringButtonLabel = `${termType2label(dataType)} Clustering`;
+  holder.append("button").datum({
+    label: cluteringButtonLabel,
+    getCount: () => this.hcTermGroup?.lst.length || 0,
+    showCount: "hide",
+    rows: [
+      {
+        label: `Cluster ${cl.Samples}`,
+        title: `Option to enable ${cl.samples} clustering, instead of enabling ${cl.samples} sorting.`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "clusterSamples",
+        boxLabel: `Cluster ${cl.Samples} (Disable ${cl.Samples} Sorting)`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.yDendrogramHeight = 0;
+            this.config.settings.hierCluster.clusterSamples = false;
+          } else {
+            this.config.divideBy = null;
+            this.config.settings.hierCluster.yDendrogramHeight = 200;
+            this.config.settings.hierCluster.clusterSamples = true;
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Cluster ${clusterRowLabel}`,
+        title: `Option to enable ${clusterRowLabel} clustering, instead of enabling ${clusterRowLabel} sorting.`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "clusterRows",
+        boxLabel: `Cluster ${clusterRowLabel} (Disable ${clusterRowLabel} Sorting)`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.clusterRows = false;
+            this.config.settings.hierCluster.sortClusterRows = "asListed";
+          } else {
+            this.config.settings.hierCluster.clusterRows = true;
+            this.config.settings.hierCluster.sortClusterRows = void 0;
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Sort ${clusterRowLabel}`,
+        title: `Set how to order the ${clusterRowLabel} as rows`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "sortClusterRows",
+        options: [
+          { label: `By input ${clusterRowLabel} order`, value: "asListed" },
+          { label: `By ${clusterRowLabel} name`, value: "byName" }
+        ],
+        styles: { padding: 0, "padding-right": "10px", margin: 0, display: "inline-block" },
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterRows ? "none" : "table-row";
+        }
+      },
+      {
+        label: "Z-score Transformation",
+        title: `Option to do Z-score transformation`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "zScoreTransformation",
+        boxLabel: `Perform Z-score Transformation`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.zScoreTransformation = false;
+            this.config.settings.hierCluster.colorScale = "whiteRed";
+          } else {
+            this.config.settings.hierCluster.zScoreTransformation = true;
+            this.config.settings.hierCluster.colorScale = "blueWhiteRed";
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Clustering Method`,
+        title: `Sets which clustering method to use`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "clusterMethod",
+        options: clusterMethodLst
+      },
+      {
+        label: `Distance Method`,
+        title: `Sets which distance method to use for clustering`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "distanceMethod",
+        options: distanceMethodLst
+      },
+      {
+        label: `Column Dendrogram Height`,
+        title: `The maximum height to render the column dendrogram`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "yDendrogramHeight",
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterSamples ? "table-row" : "none";
+        }
+      },
+      {
+        label: `Row Dendrogram Width`,
+        title: `The maximum width to render the row dendrogram`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "xDendrogramHeight",
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterRows ? "table-row" : "none";
+        }
+      },
+      {
+        label: `Z-score Cap`,
+        title: `Cap the Z-score scale to not exceed this absolute value`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "zScoreCap"
+      },
+      {
+        label: `Color Scheme`,
+        title: `Sets which color scheme to use`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "colorScale",
+        options: [
+          {
+            label: "Blue-White-Red",
+            value: "blueWhiteRed",
+            title: `color scheme Blue-White-Red`
+          },
+          {
+            label: "Green-Black-Red",
+            value: "greenBlackRed",
+            title: `color scheme Green-Black-Red`
+          },
+          {
+            label: "Blue-Yellow-Red",
+            value: "blueYellowRed",
+            title: `color scheme Blue-Yellow-Red`
+          },
+          {
+            label: "Green-White-Red",
+            value: "greenWhiteRed",
+            title: `color scheme Green-White-Red`
+          },
+          {
+            label: "Blue-Black-Yellow",
+            value: "blueBlackYellow",
+            title: `color scheme Blue-Black-Yellow`
+          }
+        ]
+      }
+    ],
+    customInputs: updateClusteringControls
+  }).html((d) => d.label).style("margin", "2px 0").on("click", callback);
+}
+function updateClusteringControls(self, app, parent, table) {
+  if (parent.chartType == "hierCluster" && !parent.config.settings.hierCluster.zScoreTransformation) {
+    const zScoreCapControl = select_default(
+      table.selectAll("td").filter(function() {
+        return select_default(this).text() == "Z-score Cap";
+      }).node().closest("tr")
+    );
+    zScoreCapControl.style("display", "none");
+    const colorSchemeControl = select_default(
+      table.selectAll("td").filter(function() {
+        return select_default(this).text() == "Color Scheme";
+      }).node().closest("tr")
+    );
+    colorSchemeControl.style("display", "none");
+  }
+  if (parent.chartType == "hierCluster" && parent.config.dataType !== "geneExpression") {
+    const geneInputTr = table.insert("tr", () => table.select("tr").node());
+    geneInputTr.append("td").attr("class", "sja-termdb-config-row-label").html("Hierarchical Clustering Term Set");
+    const td1 = geneInputTr.append("td").style("display", "block").style("padding", "5px 0px");
+    const editGrpDiv = td1.append("div").append("label");
+    const clusteringBtn = self.btns.node();
+    editGrpDiv.append("button").html("Edit Set").on("click", () => {
+      app.tip.clear();
+      const backDiv = app.tip.d.append("div").style("padding", "5px");
+      backDiv.attr("tabindex", 0).style("padding", "5px").style("text-decoration", "underline").style("cursor", "pointer").style("margin-bottom", "12px").html(`&#171; Back`).on("click", () => clusteringBtn.click()).on("keyup", (event) => {
+        if (event.key == "Enter") event.target.click();
+      });
+      const setEdiUiHolder = app.tip.d.append("div");
+      parent.showDictTermSelection(setEdiUiHolder);
+    });
+  }
+}
+
+export {
+  getAllChildrenClusterIds,
+  addSelectedSamplesOptions,
+  addSelectedRowsOptions,
+  triggerZoomBranch,
+  showTable4selectedSamples,
+  showTable4selectedRows,
+  getClusterFromTopDendrogram,
+  getClusterFromLeftDendrogram,
+  setClusteringBtn,
+  hierCluster_interactivity_exports
+};
+//# sourceMappingURL=chunk-GT6WJUJY.js.map

package/dist/chunk-GWCK5QGV.js

@@ -0,0 +1,70 @@
+import {
+  junctionCustomTermSource
+} from "./chunk-L32KMIC3.js";
+import {
+  mayRenderFractionSelection
+} from "./chunk-Q5SK3U2T.js";
+
+// termdb/handlers/junction.ts
+var SearchHandler = class {
+  async init(opts) {
+    if (!opts?.holder) throw new Error("opts.holder is required");
+    if (typeof opts.callback != "function") throw new Error("opts.callback is required");
+    const entries = getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms);
+    render(opts, entries);
+  }
+};
+function getJunctionCustomTerms(customTerms) {
+  if (!Array.isArray(customTerms)) return [];
+  return customTerms.filter((term) => term?.source === junctionCustomTermSource && term.tw?.term);
+}
+function render(opts, entries) {
+  const holder = opts.holder;
+  holder.selectAll("*").remove();
+  const div = holder.append("div").style("padding", "10px 0px");
+  if (!entries.length) {
+    div.append("div").text("Junctions selected from genome browser will be shown here.");
+    return;
+  }
+  const listDiv = div.append("div");
+  const fractionDiv = div.append("div");
+  for (const entry of entries) {
+    if (entry.eventlabel) renderJunctionEvent(listDiv, fractionDiv, entry, opts);
+    else renderJunction(listDiv, entry, opts);
+  }
+  listDiv.append("div").style("font-size", ".7em").style("margin-top", "10px").style("opacity", 0.7).text("Select additional junctions from genome browser.");
+}
+function renderJunction(holder, entry, opts) {
+  const choice = holder.append("div");
+  choice.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.tw.term.name).on("click", () => opts.callback(entry.tw.term));
+  addDeleteButton(choice, entry, opts);
+}
+function renderJunctionEvent(holder, fractionDiv, entry, opts) {
+  const eventHolder = holder.append("div");
+  const pillRow = eventHolder.append("div");
+  pillRow.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.eventlabel).on("click", () => selectJunctionEvent(holder, fractionDiv, entry, opts));
+  addDeleteButton(pillRow, entry, opts);
+  eventHolder.append("div").style("margin-left", "10px").style("font-size", ".7em").selectAll("div").data(entry.tw.term.termlst, (term) => term.id).enter().append("div").text((term) => term.name);
+}
+function selectJunctionEvent(listDiv, fractionDiv, entry, opts) {
+  const isStaged = mayRenderFractionSelection({
+    term: entry.tw.term,
+    selectionMode: opts.termCollectionSelectionMode,
+    listDiv,
+    fractionDiv,
+    callback: (tw) => opts.callback(tw)
+  });
+  if (!isStaged) opts.callback(entry.tw.term);
+}
+function addDeleteButton(holder, entry, opts) {
+  holder.append("button").attr("data-testid", "sjpp-junction-delete").style("margin-left", "4px").attr("aria-label", `Delete ${entry.name}`).text("\xD7").on("click", async () => {
+    await opts.app.vocabApi.deleteCustomTermById(entry.id);
+    render(opts, getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms));
+  });
+}
+
+export {
+  SearchHandler,
+  getJunctionCustomTerms
+};
+//# sourceMappingURL=chunk-GWCK5QGV.js.map