@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

package/dist/DE-7TPZWAKI.js

@@ -1,95 +0,0 @@
-import {
-  appInit
-} from "./chunk-G6WVVRDA.js";
-import "./chunk-OSWTQVAX.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-S6OIEQXG.js";
-import "./chunk-XUFWJJM5.js";
-import "./chunk-WKMZ4ZQ3.js";
-import "./chunk-NPTHYZY4.js";
-import "./chunk-DNM2DKYE.js";
-import "./chunk-RRWP2LM4.js";
-import "./chunk-OHELNDGK.js";
-import "./chunk-NWAUBRGM.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.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";
-
-// gdc/DE.ts
-async function init(arg, holder, genomes) {
-  const useGenome = arg.genome || "hg38";
-  const useDslabel = arg.dslabel || "GDC";
-  const genome = genomes[useGenome];
-  const massApi = await appInit({
-    //debug: arg.debugmode, // is debug accepted?
-    genome,
-    holder,
-    state: {
-      genome: useGenome,
-      dslabel: useDslabel,
-      termfilter: { filter0: arg.filter0 },
-      nav: { activeTab: 1, header_mode: "hidden" },
-      plots: [{ chartType: "DEinput" }]
-    },
-    opts: Object.assign(
-      {
-        // todo additional customizations
-        // dictionary:{header:'Select a variable to build Correlation Plot'}
-        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
-      },
-      arg.opts || {}
-    ),
-    app: arg.opts?.app || {}
-  });
-  const api = {
-    update: async (updateArg) => {
-      if (!massApi) return;
-      if ("filter0" in updateArg) {
-        massApi.dispatch({
-          type: "app_refresh",
-          subactions: [
-            {
-              type: "filter_replace",
-              filter0: updateArg.filter0
-            }
-          ]
-        });
-      }
-    },
-    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
-  };
-  return api;
-}
-export {
-  init
-};
-//# sourceMappingURL=DE-7TPZWAKI.js.map

package/dist/DEinput-WQJEXWGY.js

@@ -1,301 +0,0 @@
-import {
-  PlotBase,
-  excludeFilterByTag,
-  filterInit,
-  filterJoin,
-  filterPromptInit,
-  getNormalRoot,
-  negateFilter,
-  renderPreAnalysisData,
-  renderTable
-} from "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import {
-  dofetch3
-} from "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import {
-  getColors
-} from "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/DEinput.ts
-var colorScale = getColors(5);
-var DEinputPlot = class _DEinputPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    this.type = _DEinputPlot.type;
-    this.opts = opts;
-    this.dom = this.getDom();
-    this.groups = [];
-  }
-  static {
-    this.type = "DEinput";
-  }
-  getDom() {
-    const header = this.opts?.header?.html("Differential Gene Expression") || void 0;
-    const holder = this.opts.holder.append("div").style("margin", "10px");
-    const table = holder.append("div");
-    const btns = holder.append("div").style("margin-top", "5px");
-    const addGroup = btns.append("div").style("display", "inline-block");
-    const submit = btns.append("div").style("display", "none").style("margin-left", "15px").attr("class", "sja_new_filter_btn sja_menuoption");
-    const loading = holder.append("div").style("display", "none").style("margin", "20px 10px").text("Loading...");
-    const preAnalysis = holder.append("div").style("display", "none").style("margin-top", "20px").style("margin-left", "5px");
-    const dom = { header, table, addGroup, submit, loading, preAnalysis };
-    return dom;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async init() {
-  }
-  // TODO: handle errors
-  async main() {
-    this.dom.preAnalysis.selectAll("*").remove();
-    this.makeGroupsUI();
-    this.mayRenderSubmit();
-  }
-  async makeGroupsUI() {
-    if (!this.filterPrompt) {
-      this.filterPrompt = await filterPromptInit({
-        holder: this.dom.addGroup,
-        vocabApi: this.app.vocabApi,
-        emptyLabel: "Add group",
-        /** 'hide_search' by default expands all terms. Passing the
-         * header_mode in opts gives the caller the flexibility to choose. */
-        header_mode: this.opts?.header_mode || "hide_search",
-        callback: async (f) => {
-          const filter2 = getNormalRoot(f);
-          this.addNewGroup(filter2, this.groups);
-          await this.main();
-        },
-        debug: this.opts.debug
-      });
-    }
-    const filter = structuredClone(this.state.termfilter.filter);
-    this.filterPrompt.main(excludeFilterByTag(filter, "cohortFilter"));
-    if (!this.groups.length) {
-      this.dom.table.style("display", "none");
-      return;
-    }
-    this.dom.table.style("display", "block").selectAll("*").remove();
-    const tableArg = {
-      div: this.dom.table,
-      columns: [
-        {},
-        // blank column to add delete buttons
-        {
-          label: "NAME",
-          editCallback: async (i, cell) => {
-            const newName = cell.value;
-            const index = this.groups.findIndex((group) => group.name == newName);
-            if (index != -1) {
-              alert(`Group named ${newName} already exists`);
-              await this.main();
-            } else {
-              this.groups[i].name = newName;
-              await this.main();
-            }
-          }
-        },
-        {
-          label: "COLOR",
-          editCallback: async (i, cell) => {
-            this.groups[i].color = cell.color;
-            this.main();
-          }
-        },
-        //{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc
-        { label: "FILTER" }
-      ],
-      rows: [],
-      striped: false,
-      // no alternating row bg color so delete button appears more visible
-      showLines: false
-    };
-    for (const g of this.groups) {
-      tableArg.rows.push([
-        {},
-        // blank cell to add delete button
-        { value: g.name },
-        // to allow click to show <input>
-        { color: g.color },
-        // { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc
-        {}
-        // blank cell to show filter ui
-      ]);
-    }
-    renderTable(tableArg);
-    for (const [i, row] of tableArg.rows.entries()) {
-      row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
-        this.groups.splice(i, 1);
-        this.main();
-      });
-      const group = this.groups[i];
-      filterInit({
-        holder: row[3].__td,
-        vocabApi: this.app.vocabApi,
-        header_mode: "hide_search",
-        callback: (f) => {
-          if (!f || f.lst.length == 0) {
-            const i2 = this.groups.findIndex((g) => g.name == group.name);
-            this.groups.splice(i2, 1);
-          } else {
-            group.filter = f;
-          }
-          this.main();
-        }
-      }).main(group.filter);
-    }
-    this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "auto").style("opacity", 1);
-  }
-  addNewGroup(filter, groups, name) {
-    if (!groups) throw "groups is missing";
-    if (!name) {
-      const base = "New group";
-      name = base;
-      for (let i = 0; ; i++) {
-        name = base + (i === 0 ? "" : " " + i);
-        if (!groups.find((g) => g.name === name)) break;
-      }
-    }
-    const newGroup = {
-      name,
-      filter,
-      color: rgb(colorScale(groups.length)).formatHex()
-    };
-    groups.push(newGroup);
-  }
-  mayRenderSubmit() {
-    if (!this.groups.length) {
-      this.dom.submit.style("display", "none");
-      return;
-    }
-    this.dom.submit.style("display", "inline-block");
-    if (this.groups.length == 1) {
-      this.dom.submit.text(`Submit (${this.groups[0].name} vs others)`);
-      this.dom.submit.on("click", async () => {
-        const groups = [this.groups[0]];
-        const otherGroup = {
-          name: "Not in " + groups[0].name,
-          color: "#ccc",
-          filter: negateFilter(groups[0].filter)
-        };
-        groups.push(otherGroup);
-        await this.clickSubmit(groups);
-      });
-    } else if (this.groups.length == 2) {
-      this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "none").style("opacity", 0.5);
-      this.dom.submit.text(`Submit (${this.groups[0].name} vs ${this.groups[1].name})`);
-      this.dom.submit.on("click", async () => {
-        await this.clickSubmit(this.groups);
-      });
-    } else {
-      throw new Error("cannot exceed 2 groups");
-    }
-  }
-  async clickSubmit(groups) {
-    this.dom.loading.style("display", "block");
-    const samplelstTW = {
-      q: { groups: [] },
-      term: {
-        name: groups.map((g) => g.name).join(" vs "),
-        type: "samplelst",
-        values: {}
-      }
-    };
-    for (const g of groups) {
-      const samples = await this.app.vocabApi.getFilteredSampleList(
-        filterJoin([g.filter, this.state.termfilter.filter])
-      );
-      const sampleIds = samples.map((s) => {
-        return { sampleId: s };
-      });
-      samplelstTW.q.groups.push({
-        name: g.name,
-        in: true,
-        values: sampleIds
-      });
-      samplelstTW.term.values[g.name] = {
-        color: g.color,
-        key: g.name,
-        label: g.name,
-        list: sampleIds
-      };
-    }
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      samplelst: { groups: samplelstTW.q.groups },
-      filter: this.state.termfilter.filter,
-      filter0: this.state.termfilter.filter0,
-      preAnalysis: true
-    };
-    const preAnalysisData = await dofetch3("termdb/DE", { body });
-    this.dom.loading.style("display", "none");
-    this.dom.preAnalysis.style("display", "block");
-    this.dom.preAnalysis.append("div").style("font-weight", "bold").text("Samples with gene expression data:");
-    renderPreAnalysisData({
-      preAnalysisData,
-      samplelstTW,
-      groups: samplelstTW.q.groups,
-      holder: this.dom.preAnalysis,
-      self: this
-    });
-  }
-};
-var DEinputInit = getCompInit(DEinputPlot);
-var componentInit = DEinputInit;
-async function getPlotConfig(opts) {
-  const config = {
-    chartType: "DEinput",
-    settings: {}
-  };
-  return copyMerge(config, opts);
-}
-export {
-  DEinputInit,
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=DEinput-WQJEXWGY.js.map

package/dist/DifferentialAnalysis-FPG7RDNN.js

@@ -1,245 +0,0 @@
-import {
-  getDefaultGseaSettings
-} from "./chunk-QZVCFDJ7.js";
-import "./chunk-PSQETQZZ.js";
-import {
-  PlotBase,
-  getDefaultVolcanoSettings,
-  validateVolcanoSettings
-} from "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import {
-  importPlot
-} from "./chunk-IFA3COXY.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import {
-  DNA_METHYLATION,
-  GENE_EXPRESSION,
-  PROTEOME_DAP,
-  SINGLECELL_CELLTYPE,
-  termType2label
-} from "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.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";
-
-// plots/diffAnalysis/view/DiffAnalysisView.ts
-var DiffAnalysisView = class {
-  constructor(app, config, dom) {
-    this.app = app;
-    this.config = config;
-    this.dom = dom;
-    setRenderers(this);
-    this.tabsData = this.getTabsOptions(this);
-    this.tabs = new Tabs({ holder: this.dom.tabsDiv, tabs: this.tabsData });
-    this.tabs.main();
-  }
-  update(plotConfig) {
-    const activeTabIndex = this.tabsData.findIndex((tab) => tab.id == plotConfig.childType);
-    this.tabs.update(activeTabIndex);
-  }
-};
-function setRenderers(self) {
-  self.getTabsOptions = (self2) => {
-    const tabs = [
-      {
-        active: self2.config.childType === "volcano",
-        id: "volcano",
-        label: "Volcano",
-        isVisible: () => true,
-        // isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,
-        getPlotConfig: () => {
-          return {
-            childType: "volcano"
-          };
-        },
-        callback: self2.tabCallback
-      },
-      {
-        active: self2.config.childType === "gsea",
-        id: "gsea",
-        label: "Gene Set Enrichment Analysis",
-        isVisible: () => true,
-        // isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,
-        getPlotConfig: () => {
-          return {
-            childType: "gsea"
-          };
-        },
-        callback: self2.tabCallback
-      }
-    ];
-    return tabs;
-  };
-  self.tabCallback = async (event, tab) => {
-    if (!event || !tab || !tab.id) return;
-    const plotConfig = tab.getPlotConfig();
-    await self.app.dispatch({
-      type: "plot_edit",
-      id: self.config.id,
-      config: plotConfig
-    });
-  };
-}
-
-// plots/diffAnalysis/DifferentialAnalysis.ts
-var DifferentialAnalysis = class extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = "differentialAnalysis";
-    this.components = {
-      plots: {}
-    };
-    this.termType = opts.termType;
-    const holder = opts.holder.classed("sjpp-diff-analysis-main", true);
-    const controls = opts.controls ? holder : holder.append("div");
-    const div = holder.append("div").style("padding", "5px").style("display", "inline-block").style("vertical-align", "top");
-    const tabsDiv = div.append("div").attr("id", "sjpp-diff-analysis-tabs").style("display", "inline-block");
-    const plots = div.append("div").attr("id", "sjpp-diff-analysis-tabs-content");
-    this.dom = {
-      controls: controls.style("display", "inline-block"),
-      div,
-      tabsDiv,
-      plots,
-      tip: new Menu({ padding: "" })
-    };
-    this.plotsControlsDiv = {};
-    this.plotsDiv = {};
-    if (opts.parentId) this.parentId = opts.parentId;
-    if (opts.header) {
-      this.dom.header = {
-        title: opts.header.append("span").style("margin-right", "5px").style("color", "darkslategray"),
-        plot: opts.header.append("span").style("font-size", "0.7em").style("opacity", 0.6)
-      };
-    }
-  }
-  static {
-    this.type = "differentialAnalysis";
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw new Error(
-        `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
-      );
-    }
-    return {
-      config
-    };
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.startsWith("plot_")) {
-      return action.id === this.id || action.id == this.parentId;
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const config = structuredClone(state.config);
-    this.plotTabs = new DiffAnalysisView(this.app, config, this.dom);
-  }
-  async setComponent(config) {
-    this.plotsControlsDiv[config.childType] = this.dom.controls.append("div");
-    this.plotsDiv[config.childType] = this.dom.plots.append("div");
-    const opts = {
-      app: this.app,
-      holder: this.plotsDiv[config.childType],
-      id: this.id,
-      parent: this.api,
-      controls: this.plotsControlsDiv[config.childType],
-      termType: config.termType
-    };
-    const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
-    this.components.plots[config.childType] = await _.componentInit(opts);
-  }
-  async main() {
-    const config = structuredClone(this.state.config);
-    if (config.chartType != this.type) return;
-    if (!this.components.plots[config.childType]) await this.setComponent(config);
-    for (const childType in this.components.plots) {
-      const chart = this.components.plots[childType];
-      if (chart.type != config.childType) {
-        this.plotsDiv[chart.type].style("display", "none");
-        this.plotsControlsDiv[chart.type].style("display", "none");
-      }
-    }
-    this.plotsDiv[config.childType].style("display", "");
-    this.plotsControlsDiv[config.childType].style("display", "");
-    if (this.dom.header) {
-      if (config.tw) this.dom.header.title.text(config.tw.term.name);
-      if (config.headerText) this.dom.header.title.text(config.headerText);
-      const typeStr = termType2label(config.termType).toUpperCase();
-      this.dom.header.plot.text(` DIFFERENTIAL ${typeStr} ANALYSIS`);
-    }
-    if (this.plotTabs) this.plotTabs.update(config);
-  }
-};
-var DiffAnalysisInit = getCompInit(DifferentialAnalysis);
-var componentInit = DiffAnalysisInit;
-var enabledTermTypes = [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION, PROTEOME_DAP];
-function getPlotConfig(opts) {
-  if (!opts.termType) throw new Error(".termType is required");
-  if (!enabledTermTypes.includes(opts.termType))
-    throw new Error(`termType = '${opts.termType}' not supported by Differential Analysis`);
-  const config = {
-    chartType: "differentialAnalysis",
-    childType: "volcano",
-    termType: opts.termType,
-    settings: {},
-    highlightedData: opts.highlightedData || [],
-    hidePlotFilter: true
-    //TODO: Support filtering and reactivity in child plots
-  };
-  if (opts?.tw?.term?.name && opts.headerText)
-    throw new Error("Cannot provide both tw.term.name and headerText. Please choose one to use as the plot title.");
-  if (opts.termType == SINGLECELL_CELLTYPE) {
-    Object.assign(config, {
-      categoryName: opts.categoryName || "",
-      termId: opts.termId || "",
-      sample: opts.sample || { sID: "", eID: "" }
-    });
-  }
-  config.settings.volcano = getDefaultVolcanoSettings(opts.overrides, opts);
-  config.settings.gsea = getDefaultGseaSettings(opts.overrides);
-  validateVolcanoSettings(config, opts);
-  return copyMerge(config, opts);
-}
-export {
-  DiffAnalysisInit,
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=DifferentialAnalysis-FPG7RDNN.js.map