@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/chunk-VWGRKOVJ.js

@@ -1,170 +0,0 @@
-import {
-  getEmptyCell,
-  maySetEmptyCell,
-  setCellProps
-} from "./chunk-74C6G6JD.js";
-import {
-  TermTypeGroups
-} from "./chunk-4EZLVENZ.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.serieses.js
-var matrix_serieses_exports = {};
-__export(matrix_serieses_exports, {
-  getSerieses: () => getSerieses
-});
-function getSerieses(data) {
-  const s = this.settings.matrix;
-  const serieses = [];
-  const { colw, dx, dy, xMin, xMax } = this.dimensions;
-  const dvt = this.config.divideBy || {};
-  const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
-  const legendGroups = {};
-  this.colorScaleByTermId = {};
-  for (const t of this.termOrder) {
-    const $id = t.tw.$id;
-    const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
-    const isDivideByTerm = termid === divideByTermId;
-    const emptyGridCells = [];
-    const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
-    const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
-    const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
-    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
-    const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
-    const series = {
-      t,
-      tw: t.tw,
-      cells: [],
-      y,
-      hoverY0,
-      hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
-    };
-    for (const so of this.unfilteredSampleOrder) {
-      const { totalIndex, grpIndex, row } = so;
-      series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
-      const anno = row[$id];
-      const cellTemplate = {
-        s: so,
-        sample: row.sample,
-        tw: t.tw,
-        term: t.tw.term,
-        termid,
-        $id,
-        totalIndex,
-        grpIndex,
-        row,
-        t,
-        seriesY: y
-      };
-      if (!anno) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      const key = anno.key;
-      const values = anno.filteredValues || anno.values || [anno.value];
-      const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
-      const height = !s.transpose ? s.rowh / numRects : colw;
-      const width = !s.transpose ? colw : colw / values.length;
-      const siblingCells = [];
-      if (!anno || !anno.renderedValues?.length) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      for (const [i, value] of values.entries()) {
-        const cell = Object.assign({ key, siblingCells }, cellTemplate);
-        cell.valueIndex = i;
-        let legend;
-        if (typeof t.tw.setCellProps == "function") {
-          legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
-        } else {
-          const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
-          legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
-        }
-        if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
-        if (legend) {
-          for (const l of [legendGroups, so.grp.legendGroups]) {
-            if (!l) continue;
-            if (!l[legend.group]) {
-              l[legend.group] = {
-                ref: legend.ref,
-                values: {},
-                order: legend.order,
-                $id,
-                origin: legend.entry.origin
-              };
-              if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
-            }
-            const lg = l[legend.group];
-            if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
-            const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
-            if (!lg.values[legendK]) {
-              lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
-              if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
-            }
-            if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
-            if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
-              if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
-            } else lg.values[legendK].samples.add(row.sample);
-            if (isDivideByTerm) {
-              lg.values[legend.value].isExcluded = so.grp.isExcluded;
-            }
-          }
-        }
-        if (!so.grp.isExcluded) {
-          if (anno.renderedValues.includes(value)) series.cells.push(cell);
-          siblingCells.push(cell);
-        }
-      }
-      if (s.showGrid == "rect" && !so.grp.isExcluded) {
-        const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this);
-        if (cell) emptyGridCells.push(cell);
-      }
-    }
-    if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
-    if (series.cells.length) serieses.push(series);
-  }
-  addAllHiddenLegendGroups(legendGroups, this);
-  this.legendData = this.getLegendData(legendGroups, data.refs, this);
-  for (const grp of this.sampleGroups) {
-    grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
-  }
-  return serieses;
-}
-function addAllHiddenLegendGroups(legendGroups, self) {
-  for (const valueFilter of self.config.legendValueFilter.lst) {
-    if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
-      legendGroups[valueFilter.legendGrpName] = {
-        ref: {},
-        values: {},
-        dt: [valueFilter.tvs.values[0].dt],
-        origin: valueFilter.tvs.values[0].origin
-      };
-    } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    }
-  }
-}
-
-export {
-  getSerieses,
-  matrix_serieses_exports
-};
-//# sourceMappingURL=chunk-VWGRKOVJ.js.map

package/dist/chunk-WCTKHF5T.js

@@ -1,197 +0,0 @@
-import {
-  DATermTypes
-} from "./chunk-QJ3HYZH3.js";
-import {
-  dofetch3
-} from "./chunk-VMRO6DMC.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;
-      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;
-      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() {
-    await this.getOtherSamples(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() {
-    await this.getOtherSamples(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 } : {},
-      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";
-    return {
-      significanceThresholds: {
-        pValueCutoff: this.settings.pValue,
-        pValueType: this.settings.pValueType,
-        foldChangeCutoff: useDeltaBeta ? this.settings.deltaBetaCutoff : this.settings.foldChangeCutoff
-      },
-      ...useDeltaBeta ? { xField: "delta_beta" } : {},
-      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
-    };
-  }
-  //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()
-    };
-  }
-  /** retrieve the sampleId/sampleName for samples in
-   * the "others" group instead of using {in: false} */
-  async getOtherSamples(samplelst) {
-    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
-    if (!othersSamplesGroup) return;
-    const state = this.app.getState();
-    const samplesGroup = samplelst.groups.find((g) => g.in);
-    othersSamplesGroup.values = [];
-    for (const s of await this.plot.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
-      if (!samplesGroup.values.some((i) => i.sampleId == s.id)) {
-        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
-      }
-    }
-    othersSamplesGroup.in = true;
-  }
-};
-
-export {
-  getGroupColors,
-  VolcanoModel
-};
-//# sourceMappingURL=chunk-WCTKHF5T.js.map

package/dist/chunk-WCTKHF5T.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/volcano/colors.ts", "../plots/volcano/model/VolcanoModel.ts"],
-  "sourcesContent": ["import { rgb } from 'd3-color'\n\n/** Resolve the case/control dot colors for a volcano plot in one place so the\n * interactive SVG overlay (VolcanoViewModel) and the server-rendered PNG\n * (VolcanoModel \u2192 Rust) paint each dot the same color.\n *\n * `caseColor` maps to points with `fold_change > 0` (group 2 in samplelst),\n * `controlColor` to `fold_change < 0` (group 1). Every returned color is a\n * `#rrggbb` hex string \u2014 CSS names like `'red'` are normalized via d3-color\n * so the Rust renderer's hex-only parser doesn't fall back to a muted tuple.\n */\nexport function getGroupColors(config: any): { caseColor: string; controlColor: string } {\n\tconst groups = config?.samplelst?.groups\n\tconst termValues = config?.tw?.term?.values\n\tconst rawDown = termValues?.[groups?.[0]?.name]?.color || 'red'\n\tconst rawUp = termValues?.[groups?.[1]?.name]?.color || 'blue'\n\treturn {\n\t\tcontrolColor: toHex(rawDown, 'red'),\n\t\tcaseColor: toHex(rawUp, 'blue')\n\t}\n}\n\n/** Normalize any CSS-accepted color string into `#rrggbb`. */\nexport function toHex(color: string | undefined, fallback: string): string {\n\tconst c = rgb(color || fallback)\n\treturn c.displayable() ? c.formatHex() : rgb(fallback).formatHex()\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { dofetch3 } from '#common/dofetch'\nimport type { DERequest, DiffMethRequest, TermdbSingleCellDEgenesRequest, VolcanoRenderRequest } from '#types'\nimport { DATermTypes as tt } from '../../diffAnalysis/enabledTermTypes'\nimport { getGroupColors, toHex } from '../colors'\n// import type { Volcano } from '../Volcano'\n\nexport class VolcanoModel {\n\tplot: any\n\tapp: MassAppApi\n\tconfig!: any\n\tsettings!: any\n\ttermType: string\n\n\t/** TODO: This model is used in both the volcano and gsea.\n\t * In the future, create base model in DA and use specific\n\t * classes for the volcano and gsea. */\n\tconstructor(plot: any, termType: string) {\n\t\tthis.plot = plot\n\t\tthis.app = plot.app\n\t\tthis.termType = termType\n\t}\n\n\t/** May use mapper instead as more termTypes are added */\n\tasync getData(config: any, settings: any) {\n\t\tthis.config = config\n\t\tthis.settings = settings\n\n\t\tif (this.termType === tt.GENE_EXPRESSION) {\n\t\t\tconst body = await this.getGERequestBody()\n\t\t\tconst response = await dofetch3('termdb/DE', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DE request so downstream plots (GSEA) can snapshot\n\t\t\t// it and later ask the server to recompute the DA cache if the\n\t\t\t// file is missing on a peer node or after TTL eviction.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.DNA_METHYLATION) {\n\t\t\tconst body = await this.getDMRequestBody()\n\t\t\tconst response = await dofetch3('termdb/diffMeth', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DM request the same way the GE branch above does so\n\t\t\t// the GSEA tab can snapshot it and the server can recompute the DM\n\t\t\t// cache if the file is missing on a peer node or after TTL.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_CELLTYPE) {\n\t\t\tconst body = await this.getSCCTRequestBody()\n\t\t\treturn await dofetch3('termdb/singlecellDEgenes', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.PROTEOME_DAP) {\n\t\t\tconst body = this.getDapRequestBody()\n\t\t\treturn await dofetch3('termdb/dapVolcano', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_GENE_EXPRESSION) {\n\t\t\t//TODO\n\t\t}\n\t\tthrow new Error(`Volcano plot does not support route for termType='${this.termType}'`)\n\t}\n\n\t//Gene expression\n\tasync getGERequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DE',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tmethod: this.settings.method,\n\t\t\tmin_count: this.settings.minCount,\n\t\t\tmin_total_count: this.settings.minTotalCount,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tcpm_cutoff: this.settings.cpmCutoff,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DERequest> //remove Partial when storage_type is removed from DERequest\n\t\tconst pseudobulk = this.config.tw?.pseudobulk\n\t\tif (pseudobulk) body.pseudobulk = pseudobulk\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//DNA methylation\n\tasync getDMRequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DM',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tmin_samples_per_group: this.settings.minSamplesPerGroup,\n\t\t\texclude_sex_chr: this.settings.excludeSexChr,\n\t\t\t/* Omitted rather than sent as 'promoter' when it is the default, so a request\n\t\t\tfrom a promoter-only dataset is byte-identical to what this client sent before\n\t\t\tthe element picker existed. The server resolves an absent element_type to\n\t\t\t'promoter'. This does NOT preserve cache keys -- the key object gained the\n\t\t\tfield server-side, so every pre-existing dm/ entry is orphaned on deploy\n\t\t\tregardless of what the client sends. */\n\t\t\t...(this.settings.elementType && this.settings.elementType != 'promoter'\n\t\t\t\t? { element_type: this.settings.elementType }\n\t\t\t\t: {}),\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DiffMethRequest>\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t/** Parameters telling the server to run the `volcano` Rust renderer and return a\n\t * volcano PNG + top-significant rows instead of the full dot list. */\n\tgetVolcanoRender(): VolcanoRenderRequest {\n\t\t// Match the client overlay's radius (see VolcanoViewModel.setPointData)\n\t\t// so the PNG rings and the interactive overlay rings line up; otherwise\n\t\t// a smaller PNG ring sits inside the larger overlay ring and looks like\n\t\t// a stray dot at the center.\n\t\tconst dotRadius = Math.max(this.settings.width, this.settings.height) / 80\n\t\t// Resolve case/control colors via the shared helper (see colors.ts) so the\n\t\t// PNG and the SVG overlay paint each side with the exact same hex string.\n\t\tconst { caseColor, controlColor } = getGroupColors(this.config)\n\t\t/* Only differential methylation carries delta_beta, and only it offers the axis toggle, so\n\t\tother term types always fall through to fold_change. The cutoff sent must be in the units\n\t\tof the field sent -- otherwise the server draws threshold lines that do not correspond to\n\t\twhat it classified. */\n\t\tconst useDeltaBeta = this.termType === tt.DNA_METHYLATION && this.settings.xAxis == 'delta_beta'\n\t\treturn {\n\t\t\tsignificanceThresholds: {\n\t\t\t\tpValueCutoff: this.settings.pValue,\n\t\t\t\tpValueType: this.settings.pValueType,\n\t\t\t\tfoldChangeCutoff: useDeltaBeta ? this.settings.deltaBetaCutoff : this.settings.foldChangeCutoff\n\t\t\t},\n\t\t\t...(useDeltaBeta ? { xField: 'delta_beta' as const } : {}),\n\t\t\tpixelWidth: this.settings.width,\n\t\t\tpixelHeight: this.settings.height,\n\t\t\tcolorSignificant: toHex(this.settings.defaultSignColor, 'red'),\n\t\t\tcolorSignificantUp: caseColor,\n\t\t\tcolorSignificantDown: controlColor,\n\t\t\tcolorNonsignificant: toHex(this.settings.defaultNonSignColor, 'black'),\n\t\t\tdotRadius,\n\t\t\tmaxInteractiveDots: this.settings.maxInteractiveDots,\n\t\t\t// Render the PNG at device-pixel resolution so it stays sharp on\n\t\t\t// retina screens. The server reports the plot extent in CSS-space,\n\t\t\t// so SVG overlay coords are unaffected.\n\t\t\t//\n\t\t\t// Oversample by 2\u00D7 so the PNG also stays sharp when the user\n\t\t\t// *zooms in after* the initial render (the captured DPR is frozen\n\t\t\t// at fetch time \u2014 bigger headroom = more tolerable post-render\n\t\t\t// zoom before pixelation appears). The server clamp keeps the\n\t\t\t// bitmap memory bounded.\n\t\t\tdevicePixelRatio: (typeof window !== 'undefined' ? window.devicePixelRatio : 1) * 2\n\t\t}\n\t}\n\n\t//This is a workaround until the server can accept an arr of confounder tws\n\taddConfounderTw(body) {\n\t\tconst confounders = this.config?.confounderTws\n\t\tif (confounders?.length) {\n\t\t\tbody.tw = this.config.confounderTws[0]\n\t\t\tif (confounders.length > 1) body.tw2 = this.config.confounderTws[1]\n\t\t}\n\t}\n\n\t//Single cell cell type\n\tgetSCCTRequestBody(): TermdbSingleCellDEgenesRequest {\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsample: this.config.sample,\n\t\t\ttermId: this.config.termId,\n\t\t\tcategoryName: this.config.categoryName,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t}\n\t\treturn body\n\t}\n\n\tgetDapRequestBody() {\n\t\tconst { organism, assay, cohort } = this.config.proteomeDetails\n\t\treturn {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\torganism,\n\t\t\tassay,\n\t\t\tcohort,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t}\n\t}\n\n\t/** retrieve the sampleId/sampleName for samples in\n\t * the \"others\" group instead of using {in: false} */\n\tasync getOtherSamples(samplelst) {\n\t\tconst othersSamplesGroup = samplelst.groups.find(g => !g.in)\n\t\tif (!othersSamplesGroup) return\n\n\t\tconst state = this.app.getState()\n\t\tconst samplesGroup = samplelst.groups.find(g => g.in)\n\t\tothersSamplesGroup.values = []\n\t\t// retrieve full list of samples based on current filter. put samples not in samplesGroup in \"others\" group.\n\t\t// the plot-scoped vocabApi from PlotBase is used, so that an unrelated app dispatch does not cancel this request\n\t\tfor (const s of await this.plot.vocabApi.getFilteredSampleList(state.termfilter.filter)) {\n\t\t\t// s={id,name}, samplelst.groups[].values[]={sampleId,sample}\n\t\t\t// NOTE: must not use indexOf() here, it compares by strict equality and not by predicate,\n\t\t\t// which would never match and would put every sample in the \"others\" group\n\t\t\tif (!samplesGroup.values.some(i => i.sampleId == s.id)) {\n\t\t\t\tothersSamplesGroup.values.push({ sampleId: s.id, sample: s.name })\n\t\t\t}\n\t\t}\n\t\tothersSamplesGroup.in = true\n\t}\n}\n"],
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package/dist/chunk-WOMERKMR.js

@@ -1,31 +0,0 @@
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-4EZLVENZ.js";
-
-// src/spliceevent.exonskip.getdefault.js
-function spliceevent_exonskip_getdefault_default(events) {
-  let evt2showidx = 0;
-  for (let i = 1; i < events.length; i++) {
-    const e = events[i];
-    const e2show = events[evt2showidx];
-    if (e.isskipexon && e2show.isaltexon) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == OUT_frame && e2show.framenocheck) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == IN_frame && e2show.frame != IN_frame) {
-      evt2showidx = i;
-      continue;
-    }
-  }
-  return evt2showidx;
-}
-
-export {
-  spliceevent_exonskip_getdefault_default
-};
-//# sourceMappingURL=chunk-WOMERKMR.js.map

package/dist/chunk-WXX2YD4Q.js

@@ -1,59 +0,0 @@
-import {
-  plotColor
-} from "./chunk-4EZLVENZ.js";
-
-// plots/scatter/settings/defaults.ts
-function getDefaultScatterSettings(opts = {}) {
-  const overrides = opts?.overrides || {};
-  const defaults = {
-    size: 0.8,
-    minShapeSize: 0.5,
-    maxShapeSize: 4,
-    scaleDotOrder: "Ascending",
-    refSize: 0.8,
-    svgw: 600,
-    svgh: 600,
-    svgd: 600,
-    axisTitleFontSize: 16,
-    showAxes: true,
-    showRef: true,
-    opacity: 0.6,
-    defaultColor: plotColor,
-    regression: "None",
-    fov: 50,
-    threeSize: 5e-3,
-    threeFOV: 70,
-    maxSvgSamplesCutoff: 2e4,
-    // if a cohort is larger than this, switch from svg to webgl/canvas rendering
-    //ColorScale settings
-    colorScaleMode: "auto",
-    colorScalePercentile: 95,
-    colorScaleMinFixed: null,
-    colorScaleMaxFixed: null,
-    noExpColor: "#F5F5F5",
-    // light gray, for dots with no gene expression value
-    expColor: "#ff000d",
-    // default color for the maximum gene expression value
-    //3D Plot settings
-    showContour: false,
-    colorContours: false,
-    contourBandwidth: 30,
-    contourThresholds: 10,
-    duration: 500,
-    useGlobalMinMax: true,
-    saveZoomTransform: false,
-    // Axis scale settings
-    minXScale: null,
-    maxXScale: null,
-    minYScale: null,
-    maxYScale: null,
-    itemLabel: opts?.singleCellPlot ? "Cell" : "Sample",
-    maxTooltipRows: 5
-  };
-  return Object.assign(defaults, overrides);
-}
-
-export {
-  getDefaultScatterSettings
-};
-//# sourceMappingURL=chunk-WXX2YD4Q.js.map