@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-7OOZHEUC.js

@@ -0,0 +1,302 @@
+import {
+  appear2 as appear,
+  axisstyle,
+  bwSetting,
+  disappear2 as disappear,
+  makeNumericAxisConfig,
+  rgb2hex
+} from "./chunk-2XPDA6NL.js";
+import {
+  dofetch3
+} from "./chunk-MYWJQRTD.js";
+import {
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import {
+  format,
+  linear
+} from "./chunk-OAWQ6LOO.js";
+
+// src/block.tk.bigwig.js
+function bigwigfromtemplate(tk, template) {
+  tk.scale = {};
+  if (template.scale) {
+    for (const k in template.scale) {
+      tk.scale[k] = template.scale[k];
+    }
+  } else {
+    tk.scale.auto = 1;
+  }
+  if (tk.normalize) {
+  } else {
+    tk.normalize = {
+      dividefactor: 1,
+      disable: 1
+    };
+  }
+  tk.barheight = template.height || 50;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  if (!tk.ncolor) tk.ncolor = "#BD005E";
+  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
+  if (!tk.pcolor) tk.pcolor = "#005EBD";
+  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
+}
+function bigwigmaketk(tk, block) {
+  tk.img = tk.glider.append("image");
+  tk.tklabel.attr("y", tk.barheight / 2);
+  tk.leftaxis = tk.gleft.append("g");
+  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
+    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
+  });
+}
+async function bigwigload(tk, block) {
+  block.tkcloakon(tk);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
+  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  tk.img.attr("width", block.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    let data;
+    if (tk.imgData) {
+      data = tk.imgData;
+    } else {
+      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    }
+    if (data.error) throw data.error;
+    if (!data.src) throw "data.src missing";
+    tk.tklabel.transition().attr("y", tk.barheight / 2);
+    tk.img.attr("xlink:href", data.src);
+    if (data.minv != void 0) {
+      tk.scale.min = data.minv;
+    }
+    if (data.maxv != void 0) {
+      tk.scale.max = data.maxv;
+    }
+    tk.leftaxis.selectAll("*").remove();
+    if (data.nodata) {
+      throw "No data in view range";
+    }
+    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
+    const axis = axisLeft().scale(scale).tickValues([tk.scale.min, tk.scale.max]);
+    if (tk.integer4axis) {
+      axis.tickFormat(format("d"));
+    }
+    axisstyle({
+      axis: tk.leftaxis.call(axis),
+      color: "black",
+      showline: true
+    });
+  } catch (err) {
+    tk.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff(tk, { error: errtext });
+    block.block_setheight();
+    for (const panel of tk.subpanels) {
+      bigwigloadsubpanel(tk, block, panel);
+    }
+  }
+}
+async function bigwigloadsubpanel(tk, block, panel) {
+  block.tkcloakon_subpanel(panel);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) {
+    par.dotplotfactor = tk.dotplotfactor;
+  }
+  par.width = panel.width;
+  par.rglst = [
+    {
+      chr: panel.chr,
+      start: panel.start,
+      stop: panel.stop,
+      width: panel.width
+    }
+  ];
+  delete par.percentile;
+  delete par.autoscale;
+  panel.img.attr("width", panel.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    if (tk.imgData) throw "subpanel not supported by imgData yet";
+    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    if (data.error) throw data.error;
+    panel.img.attr("xlink:href", data.src);
+  } catch (err) {
+    panel.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff_subpanel(panel, { error: errtext });
+  }
+}
+function bigwigconfigpanel(tk, block, holder, loader) {
+  const config = {
+    pcolor: {},
+    ncolor: {},
+    pcolor2: {},
+    ncolor2: {},
+    // .row
+    // .lab
+    dotplot: {},
+    // .row
+    dividefactor: {}
+  };
+  {
+    const row = holder.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Height  ");
+    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
+      if (event.code != "Enter") return;
+      const s = event.target.value;
+      if (s == "") return;
+      const v = Number.parseInt(s);
+      if (Number.isNaN(v) || v <= 1) {
+        alert("track height must be positive integer");
+        return;
+      }
+      tk.barheight = v;
+      loader(bwSetting.height);
+    });
+  }
+  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
+  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
+    tk.pcolor = event.target.value;
+    loader(bwSetting.pcolor);
+  });
+  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
+  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
+    tk.ncolor = event.target.value;
+    loader(bwSetting.ncolor);
+  });
+  if (!tk.scale.auto) {
+    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
+    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
+      tk.pcolor2 = event.target.value;
+      loader(bwSetting.pcolor2);
+    });
+    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
+    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
+      tk.ncolor2 = event.target.value;
+      loader(bwSetting.ncolor2);
+    });
+  }
+  {
+    const setting = {};
+    if (tk.scale.auto) {
+      setting.auto = 1;
+    } else if (tk.scale.percentile) {
+      setting.percentile = tk.scale.percentile;
+    } else {
+      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
+    }
+    makeNumericAxisConfig({
+      holder: holder.append("div").style("margin-bottom", "15px"),
+      setting,
+      callback: (s) => {
+        if (s.auto) {
+          tk.scale.auto = 1;
+          loader(bwSetting.autoscale);
+          return;
+        }
+        if (s.fixed) {
+          delete tk.scale.auto;
+          delete tk.scale.percentile;
+          tk.scale.max = s.fixed.max;
+          tk.scale.min = s.fixed.min;
+          loader(bwSetting.fixedscale);
+          return;
+        }
+        delete tk.scale.auto;
+        tk.scale.percentile = s.percentile;
+        loader(bwSetting.percentilescale);
+      }
+    });
+  }
+  {
+    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
+    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
+    const s = config.dotplot.row.append("select").on("change", (event) => {
+      const i = event.target.selectedIndex;
+      if (i == 0) {
+        delete tk.dotplotfactor;
+      } else {
+        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
+      }
+      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
+    });
+    let o = s.append("option").text("no");
+    if (!tk.dotplotfactor) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("5");
+    if (tk.dotplotfactor == 5) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("10");
+    if (tk.dotplotfactor == 10) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("15");
+    if (tk.dotplotfactor == 15) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("20");
+    if (tk.dotplotfactor == 20) {
+      o.property("selected", 1);
+    }
+  }
+  config.dividefactor.row = holder.append("div");
+  {
+    const id = Math.random().toString();
+    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
+    if (!tk.normalize.disable) {
+      input.property("checked", 1);
+    }
+    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
+    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
+    folder.append("span").html("Divide raw value by&nbsp;");
+    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      const v = event.target.value;
+      if (v <= 0) {
+        return;
+      }
+      tk.normalize.dividefactor = v;
+      loader(bwSetting.usedividefactor);
+    });
+    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
+    input.on("change", (event) => {
+      if (event.target.checked) {
+        appear(folder);
+        delete tk.normalize.disable;
+        factorinput.property("value", tk.normalize.dividefactor);
+        loader(bwSetting.usedividefactor);
+        return;
+      }
+      disappear(folder);
+      tk.normalize.disable = 1;
+      loader(bwSetting.nodividefactor);
+    });
+  }
+  return config;
+}
+
+export {
+  bigwigfromtemplate,
+  bigwigmaketk,
+  bigwigload,
+  bigwigloadsubpanel,
+  bigwigconfigpanel
+};
+//# sourceMappingURL=chunk-7OOZHEUC.js.map

package/dist/chunk-A4VLWLYF.js

@@ -0,0 +1,226 @@
+import {
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-FDK4UJMN.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-A4VLWLYF.js.map