@sjcrh/proteinpaint-client 2.190.2 → 2.191.0

package/dist/chunk-FRGACC2C.js

@@ -0,0 +1,182 @@
+import {
+  dofetch3
+} from "./chunk-H5BIGL3W.js";
+import {
+  DNA_METHYLATION,
+  GENE_EXPRESSION,
+  PROTEOME_DAP,
+  SINGLECELL_CELLTYPE
+} from "./chunk-TVADJLMF.js";
+import {
+  rgb
+} from "./chunk-OMR2DT66.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 {
+  constructor(app, termType) {
+    this.app = 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 === GENE_EXPRESSION) {
+      const body = await this.getGERequestBody();
+      const response = await dofetch3("termdb/DE", { body });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === DNA_METHYLATION) {
+      const body = await this.getDMRequestBody();
+      const response = await dofetch3("termdb/diffMeth", { body });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === SINGLECELL_CELLTYPE) {
+      const body = await this.getSCCTRequestBody();
+      return await dofetch3("termdb/singlecellDEgenes", { body });
+    }
+    if (this.termType === PROTEOME_DAP) {
+      const body = this.getDapRequestBody();
+      return await dofetch3("termdb/dapVolcano", { body });
+    }
+    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()
+    };
+    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,
+      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);
+    return {
+      significanceThresholds: {
+        pValueCutoff: this.settings.pValue,
+        pValueType: this.settings.pValueType,
+        foldChangeCutoff: this.settings.foldChangeCutoff
+      },
+      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.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
+      if (samplesGroup.values.indexOf((i) => i.sampleId == s.id) == -1) {
+        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
+      }
+    }
+    othersSamplesGroup.in = true;
+  }
+};
+
+export {
+  getGroupColors,
+  VolcanoModel
+};
+//# sourceMappingURL=chunk-FRGACC2C.js.map

package/dist/chunk-FZ63VOSX.js

@@ -0,0 +1,226 @@
+import {
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-TVADJLMF.js";
+
+// test/testdata/data.ts
+function getSamplelstTw() {
+  const values = [
+    {
+      sampleId: 42,
+      sample: "2660"
+    },
+    {
+      sampleId: 44,
+      sample: "2688"
+    },
+    {
+      sampleId: 45,
+      sample: "2702"
+    },
+    {
+      sampleId: 46,
+      sample: "2716"
+    },
+    {
+      sampleId: 59,
+      sample: "2898"
+    },
+    {
+      sampleId: 60,
+      sample: "2912"
+    },
+    {
+      sampleId: 67,
+      sample: "3010"
+    },
+    {
+      sampleId: 68,
+      sample: "3024"
+    },
+    {
+      sampleId: 69,
+      sample: "3038"
+    },
+    {
+      sampleId: 70,
+      sample: "3052"
+    },
+    {
+      sampleId: 73,
+      sample: "3094"
+    },
+    {
+      sampleId: 79,
+      sample: "3178"
+    },
+    {
+      sampleId: 80,
+      sample: "3192"
+    }
+  ];
+  return {
+    term: {
+      name: "termdbtest samplelst",
+      type: "samplelst",
+      values: {
+        "Group 1": {
+          key: "Group 1",
+          label: "Group 1",
+          list: values
+        },
+        "Not in Group 1": {
+          key: "Not in Group 1",
+          label: "Not in Group 1",
+          list: values
+        }
+      }
+    },
+    q: {
+      mode: "discrete",
+      groups: [
+        {
+          name: "Group 1",
+          in: true,
+          values
+        },
+        {
+          name: "Not in Group 1",
+          in: false,
+          values
+        }
+      ],
+      isAtomic: true
+    }
+  };
+}
+function getCategoryGroupsetting() {
+  return {
+    id: "diaggrp",
+    q: {
+      type: "custom-groupset",
+      customset: {
+        name: "A versus B",
+        groups: [
+          {
+            name: "Test A",
+            type: "values",
+            values: [{ key: "Acute lymphoblastic leukemia" }, { key: "Wilms tumor" }]
+          },
+          {
+            name: "Test B",
+            type: "values",
+            values: [
+              { key: "Central nervous system (CNS)" },
+              { key: "Acute myeloid leukemia" },
+              { key: "Non-Hodgkin lymphoma" }
+            ]
+          }
+        ]
+      }
+    }
+  };
+}
+function getGenesetMutTw() {
+  return {
+    term: {
+      genes: [
+        { kind: "gene", gene: "TP53", type: "geneVariant" },
+        { kind: "gene", gene: "KRAS", type: "geneVariant" },
+        { kind: "gene", gene: "AKT1", type: "geneVariant" },
+        { kind: "gene", gene: "BCR", type: "geneVariant" }
+      ],
+      type: "geneVariant"
+    },
+    q: { type: "predefined-groupset" }
+  };
+}
+function getGeneVariantTw(position = false) {
+  return {
+    term: {
+      genes: [
+        position ? { kind: "coord", chr: "chr12", start: 25205246, stop: 25250936, name: "KRASregion", type: "geneVariant" } : { kind: "gene", gene: "TP53", type: "geneVariant" }
+      ],
+      type: "geneVariant"
+    },
+    q: { type: "predefined-groupset", predefined_groupset_idx: 0, hiddenValues: {} }
+  };
+}
+function getSsgseaTw(isBin = false) {
+  return {
+    term: { id: "HALLMARK_ADIPOGENESIS", type: "ssGSEA", name: "HALLMARK_ADIPOGENESIS" },
+    q: isBin ? {
+      type: "regular-bin",
+      startinclusive: true,
+      bin_size: 0.2,
+      first_bin: { stop: -0.4 },
+      last_bin: { start: 0.8 },
+      mode: "discrete"
+    } : { mode: "continuous" }
+  };
+}
+function getScgeneexpTw(gene = "KRAS") {
+  return {
+    term: {
+      type: SINGLECELL_GENE_EXPRESSION,
+      id: gene,
+      gene,
+      name: gene,
+      sample: {
+        sID: "1_patient"
+      }
+    },
+    q: {
+      mode: "continuous"
+    }
+  };
+}
+function getScctTw() {
+  return {
+    term: {
+      type: SINGLECELL_CELLTYPE,
+      id: "CellType",
+      name: "Cell Type",
+      sample: {
+        sID: "1_patient"
+      },
+      plot: "UMAP",
+      colorBy: "CellType",
+      values: {
+        T_NK: {
+          key: "T_NK",
+          value: "T_NK"
+        },
+        Blast: {
+          key: "Blast",
+          value: "Blast"
+        },
+        Monocyte: {
+          key: "Monocyte",
+          value: "Monocyte"
+        }
+      },
+      groupsetting: {
+        disabled: false
+      }
+    }
+  };
+}
+function getCategoricalTermcollectionTw() {
+  return {
+    type: "TermCollectionTWQual",
+    term: { type: "termCollection", name: "Assay Availability" }
+  };
+}
+
+export {
+  getSamplelstTw,
+  getCategoryGroupsetting,
+  getGenesetMutTw,
+  getGeneVariantTw,
+  getSsgseaTw,
+  getScgeneexpTw,
+  getScctTw,
+  getCategoricalTermcollectionTw
+};
+//# sourceMappingURL=chunk-FZ63VOSX.js.map