@sjcrh/proteinpaint-client 2.221.0 → 2.222.0

package/dist/chunk-QNCE6EOK.js

@@ -1,82 +0,0 @@
-import {
-  addGeneSearchbox,
-  getGEunit,
-  getSelectedSampleTypes,
-  mayGetSampleTypeLabel,
-  renderSampleTypeSelect,
-  renderSampleTypesByTermsSelect,
-  table2col
-} from "./chunk-WD7FZ5EE.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  TermTypes
-} from "./chunk-WJLRU5OF.js";
-
-// termdb/handlers/geneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    this.dom = {};
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    this.dom.sampleTypeDiv = holder.append("div");
-    this.mayRenderSampleTypeSelect();
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch)
-    });
-    holder.select(".sja_genesearchinput").style("margin", "0px");
-  }
-  mayRenderSampleTypeSelect() {
-    this.dom.sampleTypeDiv.selectAll("*").remove();
-    this.querySampleTypes = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypes;
-    this.querySampleTypesByTerms = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypesByTerms;
-    if (Array.isArray(this.querySampleTypes) && this.querySampleTypes.length >= 2 || this.querySampleTypesByTerms) {
-      const table = table2col({ holder: this.dom.sampleTypeDiv, margin: "0px 0px 15px 0px" });
-      const [td1, td2] = table.addRow();
-      td1.text("Sample Type");
-      td2.style("padding-left", "10px");
-      if (this.querySampleTypesByTerms) {
-        this.sampleTypeSelect = renderSampleTypesByTermsSelect(
-          td2,
-          this.querySampleTypesByTerms,
-          this.app.vocabApi.termdbConfig
-        );
-      } else {
-        this.sampleTypeSelect = renderSampleTypeSelect(td2, this.querySampleTypes, this.app.vocabApi.termdbConfig);
-      }
-    }
-  }
-  async selectGene(geneSearch) {
-    const gene = geneSearch?.geneSymbol;
-    if (!gene) throw new Error("No gene selected");
-    const sampleTypes = getSelectedSampleTypes({
-      sampleTypeSelect: this.sampleTypeSelect,
-      querySampleTypes: this.querySampleTypes,
-      querySampleTypesByTerms: this.querySampleTypesByTerms
-    });
-    if (this.sampleTypeSelect && !sampleTypes?.length) {
-      return;
-    }
-    const unit = getGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    const term = { gene, name, type: TermTypes.GENE_EXPRESSION, sampleTypes };
-    term.sampleTypeLabel = mayGetSampleTypeLabel({
-      sampleTypeSelect: this.sampleTypeSelect,
-      querySampleTypes: this.querySampleTypes,
-      querySampleTypesByTerms: this.querySampleTypesByTerms,
-      termdbConfig: this.app.vocabApi.termdbConfig
-    });
-    this.callback(term);
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-QNCE6EOK.js.map

package/dist/chunk-RV335DF2.js

@@ -1,266 +0,0 @@
-import {
-  DATermTypes,
-  DMRCATE_DEFAULTS,
-  getOthersGroup
-} from "./chunk-WD7FZ5EE.js";
-import {
-  dofetch3
-} from "./chunk-4TJO2DGU.js";
-import {
-  DMR_SCAN_ELEMENT_TYPE
-} from "./chunk-WJLRU5OF.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-
-// plots/volcano/colors.ts
-function getGroupColors(config) {
-  const groups = config?.samplelst?.groups;
-  const termValues = config?.tw?.term?.values;
-  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
-  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
-  return {
-    controlColor: toHex(rawDown, "red"),
-    caseColor: toHex(rawUp, "blue")
-  };
-}
-function toHex(color, fallback) {
-  const c = rgb(color || fallback);
-  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
-}
-
-// plots/volcano/model/VolcanoModel.ts
-var VolcanoModel = class {
-  /** TODO: This model is used in both the volcano and gsea.
-   * In the future, create base model in DA and use specific
-   * classes for the volcano and gsea. */
-  constructor(plot, termType) {
-    this.plot = plot;
-    this.app = plot.app;
-    this.termType = termType;
-  }
-  /** May use mapper instead as more termTypes are added */
-  async getData(config, settings) {
-    this.config = config;
-    this.settings = settings;
-    if (this.termType === DATermTypes.GENE_EXPRESSION) {
-      const body = await this.getGERequestBody();
-      const response = await dofetch3("termdb/DE", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) {
-        response.daRequest = body;
-        this.setGroupSizes(response);
-      }
-      return response;
-    }
-    if (this.termType === DATermTypes.DNA_METHYLATION) {
-      const body = await this.getDMRequestBody();
-      const response = await dofetch3("termdb/diffMeth", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) {
-        response.daRequest = body;
-        this.setGroupSizes(response);
-      }
-      return response;
-    }
-    if (this.termType === DATermTypes.JUNCTION) {
-      const body = await this.getDSRequestBody();
-      const response = await dofetch3("termdb/diffSplice", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) {
-        response.daRequest = body;
-        this.setGroupSizes(response);
-      }
-      return response;
-    }
-    if (this.termType === DATermTypes.SINGLECELL_CELLTYPE) {
-      const body = await this.getSCCTRequestBody();
-      return await dofetch3("termdb/singlecellDEgenes", { body, signal: this.plot.api?.getAbortSignal() });
-    }
-    if (this.termType === DATermTypes.PROTEOME_DAP) {
-      const body = this.getDapRequestBody();
-      return await dofetch3("termdb/dapVolcano", { body, signal: this.plot.api?.getAbortSignal() });
-    }
-    if (this.termType === DATermTypes.SINGLECELL_GENE_EXPRESSION) {
-    }
-    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
-  }
-  //Gene expression
-  async getGERequestBody() {
-    this.setOthersGroup(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DE",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      method: this.settings.method,
-      min_count: this.settings.minCount,
-      min_total_count: this.settings.minTotalCount,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      cpm_cutoff: this.settings.cpmCutoff,
-      volcanoRender: this.getVolcanoRender()
-    };
-    const pseudobulk = this.config.tw?.pseudobulk;
-    if (pseudobulk) body.pseudobulk = pseudobulk;
-    this.addConfounderTw(body);
-    return body;
-  }
-  //DNA methylation
-  async getDMRequestBody() {
-    this.setOthersGroup(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DM",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      min_samples_per_group: this.settings.minSamplesPerGroup,
-      exclude_sex_chr: this.settings.excludeSexChr,
-      /* Omitted rather than sent as 'promoter' when it is the default, so a request
-      from a promoter-only dataset is byte-identical to what this client sent before
-      the element picker existed. The server resolves an absent element_type to
-      'promoter'. This does NOT preserve cache keys -- the key object gained the
-      field server-side, so every pre-existing dm/ entry is orphaned on deploy
-      regardless of what the client sends. */
-      ...this.settings.elementType && this.settings.elementType != "promoter" ? { element_type: this.settings.elementType } : {},
-      // the scan's own knobs; the server ignores them for any other element type
-      ...this.settings.elementType == DMR_SCAN_ELEMENT_TYPE ? {
-        scan: {
-          ...this.settings.scanChromosome ? { chromosome: this.settings.scanChromosome } : {},
-          backgroundCorrection: !!this.settings.backgroundCorrection,
-          minCpgs: this.settings.minCpgs,
-          profileBinBp: this.settings.profileBinBp,
-          // only when changed: an explicit default would orphan every cached scan
-          ...this.settings.lambda != DMRCATE_DEFAULTS.lambda ? { lambda: this.settings.lambda } : {},
-          ...this.settings.C != DMRCATE_DEFAULTS.C ? { C: this.settings.C } : {},
-          ...this.settings.fdrCutoff != DMRCATE_DEFAULTS.fdrCutoff ? { fdrCutoff: this.settings.fdrCutoff } : {}
-        }
-      } : {},
-      volcanoRender: this.getVolcanoRender()
-    };
-    if (this.settings.elementType != DMR_SCAN_ELEMENT_TYPE) this.addConfounderTw(body);
-    return body;
-  }
-  //Splicing
-  async getDSRequestBody() {
-    this.setOthersGroup(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DS",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      method: this.settings.method,
-      /* leafcutter's own cluster filters, applied by the edgeR screen too so both engines
-      rank the same cluster set. Sent already scaled to cohort size by validateDSSettings --
-      as absolute counts they silently loosen as N grows. */
-      minSamplesPerIntron: this.settings.minSamplesPerIntron,
-      minSamplesPerGroup: this.settings.minSamplesPerGroup,
-      minCountsPerCluster: this.settings.minCountsPerCluster,
-      volcanoRender: this.getVolcanoRender()
-    };
-    this.addConfounderTw(body);
-    return body;
-  }
-  /** Parameters telling the server to run the `volcano` Rust renderer and return a
-   * volcano PNG + top-significant rows instead of the full dot list. */
-  getVolcanoRender() {
-    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
-    const { caseColor, controlColor } = getGroupColors(this.config);
-    const useDeltaBeta = this.termType === DATermTypes.DNA_METHYLATION && this.settings.xAxis == "delta_beta";
-    const render = {
-      significanceThresholds: {
-        pValueCutoff: this.settings.pValue,
-        pValueType: this.settings.pValueType,
-        foldChangeCutoff: useDeltaBeta ? this.settings.deltaBetaCutoff : this.settings.foldChangeCutoff
-      },
-      ...useDeltaBeta ? { xField: "delta_beta" } : {},
-      // Tied to the delta-beta axis: the control that sets it is only offered for
-      // methylation, and centering a log2 fold-change axis is a different conversation.
-      ...useDeltaBeta && this.settings.centerDeltaBeta ? { centerX: true } : {},
-      pixelWidth: this.settings.width,
-      pixelHeight: this.settings.height,
-      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
-      colorSignificantUp: caseColor,
-      colorSignificantDown: controlColor,
-      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
-      dotRadius,
-      maxInteractiveDots: this.settings.maxInteractiveDots,
-      // Render the PNG at device-pixel resolution so it stays sharp on
-      // retina screens. The server reports the plot extent in CSS-space,
-      // so SVG overlay coords are unaffected.
-      //
-      // Oversample by 2× so the PNG also stays sharp when the user
-      // *zooms in after* the initial render (the captured DPR is frozen
-      // at fetch time — bigger headroom = more tolerable post-render
-      // zoom before pixelation appears). The server clamp keeps the
-      // bitmap memory bounded.
-      devicePixelRatio: (typeof window !== "undefined" ? window.devicePixelRatio : 1) * 2
-    };
-    if (this.termType === DATermTypes.JUNCTION) {
-      render.xField = "delta_psi";
-      render.significanceThresholds.foldChangeCutoff = this.settings.deltaPsiCutoff;
-    }
-    return render;
-  }
-  //This is a workaround until the server can accept an arr of confounder tws
-  addConfounderTw(body) {
-    const confounders = this.config?.confounderTws;
-    if (confounders?.length) {
-      body.tw = this.config.confounderTws[0];
-      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
-    }
-  }
-  //Single cell cell type
-  getSCCTRequestBody() {
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      sample: this.config.sample,
-      termId: this.config.termId,
-      categoryName: this.config.categoryName,
-      volcanoRender: this.getVolcanoRender()
-    };
-    return body;
-  }
-  getDapRequestBody() {
-    const { organism, assay, cohort } = this.config.proteomeDetails;
-    return {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      organism,
-      assay,
-      cohort,
-      volcanoRender: this.getVolcanoRender()
-    };
-  }
-  /** The "others" group arrives as a placeholder with {in: false}. Replace it with the group that
-   * it stands for: the filter of the app without the samples of the other group, which the server
-   * resolves. */
-  setOthersGroup(samplelst) {
-    const i = samplelst.groups.findIndex((g) => !g.in);
-    if (i == -1) return;
-    const samplesGroup = samplelst.groups.find((g) => g.in);
-    samplelst.groups[i] = getOthersGroup(
-      { name: samplelst.groups[i].name, values: samplesGroup.values },
-      this.app.getState().termfilter
-    );
-  }
-  /** A group that the server resolved from a filter lists no sample here. Keep the number of its
-   * samples that the analysis ran on, where the group does not carry one, for getSampleNum(). */
-  setGroupSizes(response) {
-    for (const [i, g] of this.config.samplelst.groups.entries()) {
-      const n = response[`sample_size${i + 1}`];
-      if (!Array.isArray(g.values) && g.sampleCount === void 0 && Number.isFinite(n)) g.sampleCount = n;
-    }
-  }
-};
-
-export {
-  getGroupColors,
-  VolcanoModel
-};
-//# sourceMappingURL=chunk-RV335DF2.js.map