@sjcrh/proteinpaint-client 2.207.1 → 2.209.0

package/dist/CorrelationVolcano-YV4UHOAX.js

@@ -0,0 +1,617 @@
+import {
+  LegendCircleReference,
+  PlotBase,
+  appInit,
+  axisstyle,
+  controlsInit,
+  fillTermWrapper,
+  fillTwLst,
+  formatHeaderText,
+  table2col,
+  to_svg
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import {
+  termType2label
+} from "./chunk-3XBG5HIV.js";
+import "./chunk-SB36AUG7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import {
+  axisBottom,
+  axisLeft
+} from "./chunk-Z2ZITHT4.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import {
+  roundValue
+} from "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/corrVolcano/model/Model.ts
+var Model = class {
+  constructor(config, state, app, settings, variableTwLst, vocabApi) {
+    this.config = config;
+    this.state = state;
+    this.app = app;
+    this.settings = settings;
+    this.variableTwLst = variableTwLst;
+    this.vocabApi = vocabApi;
+  }
+  async getData() {
+    const opts = await this.setRequestOpts();
+    const data = await this.vocabApi.getCorrelationVolcanoData(opts);
+    return data;
+  }
+  async setRequestOpts() {
+    return {
+      featureTw: this.config.featureTw,
+      variableTwLst: this.variableTwLst,
+      filter: this.state.termfilter.filter,
+      filter0: this.state.termfilter.filter0,
+      correlationMethod: this.settings.method
+    };
+  }
+};
+
+// plots/corrVolcano/viewModel/ViewModel.ts
+var ViewModel = class {
+  constructor(config, data, dom, settings, variableTwLst) {
+    this.bottomPad = 60;
+    /** Only one side, left or right */
+    this.horizPad = 70;
+    this.topPad = 40;
+    this.variableTwLst = variableTwLst;
+    const pValueKey = settings.isAdjustedPValue ? "adjusted_pvalue" : "original_pvalue";
+    const d = this.transformPValues(data, pValueKey);
+    const [absYMax, absYMin] = this.setMinMax(d, `transformed_${pValueKey}`);
+    const [absXMax, absXMin] = this.setMinMax(d, "correlation");
+    const [absSampleMax, absSampleMin] = this.setMinMax(d, "sampleSize");
+    const plotDim = this.setPlotDimensions(config, settings, absYMax, absYMin, absXMax, absXMin);
+    this.viewData = {
+      plotDim,
+      variableItems: this.setVariablesData(absSampleMax, absSampleMin, d, dom, pValueKey, plotDim, settings),
+      legendData: this.setLegendData(absSampleMin, absSampleMax, data.skippedVariables)
+    };
+  }
+  transformPValues(data, key) {
+    data.variableItems = data.variableItems.filter((v) => v[key] > 0);
+    for (const item of data.variableItems) {
+      if (item[key] > 0) item[`transformed_${key}`] = -Math.log10(item[key]);
+      else item[key] = null;
+    }
+    return data;
+  }
+  setMinMax(data, key) {
+    const sortedValues = data.variableItems.map((v) => v[key]).sort((a, b) => a - b);
+    const max = sortedValues[sortedValues.length - 1];
+    const min = sortedValues[0];
+    return [max, min];
+  }
+  setPlotDimensions(config, settings, absYMax, absYMin, absXMax, absXMin) {
+    const maxXRange = Math.max(Math.abs(absXMin), absXMax);
+    const xScale = linear().domain(this.setDomain(-maxXRange, maxXRange, 0.05)).range([0, settings.width]);
+    const yScale = linear().domain(this.setDomain(absYMin, absYMax)).range([settings.height, 0]);
+    return {
+      svg: {
+        height: settings.height + this.topPad + this.bottomPad * 2,
+        width: settings.width + this.horizPad * 2
+      },
+      title: {
+        text: `${config.featureTw.term.name} ${termType2label(config.featureTw.term.type)}`,
+        x: this.horizPad + settings.width / 2,
+        y: this.topPad / 2
+      },
+      xAxisLabel: {
+        x: this.horizPad + settings.width / 2,
+        y: this.topPad + settings.height + this.bottomPad
+      },
+      yAxisLabel: {
+        x: this.horizPad / 3,
+        y: this.topPad + settings.height / 2
+      },
+      xScale: {
+        scale: xScale,
+        x: this.horizPad,
+        y: settings.height + this.topPad
+      },
+      yScale: {
+        //Do not use scaleLog() here. scaleLog is for raw values before the log transformation
+        //Using it will distort the values.
+        scale: yScale,
+        x: this.horizPad,
+        y: this.topPad
+      },
+      divideLine: {
+        x: xScale(0) + this.horizPad,
+        y1: settings.height + this.topPad,
+        y2: this.topPad
+      },
+      thresholdLine: {
+        y: yScale(-Math.log10(settings.threshold)) + this.topPad,
+        x1: this.horizPad,
+        x2: settings.width + this.horizPad
+      }
+    };
+  }
+  /** Increase the domain slightly so all data points fit within the plot */
+  setDomain(min, max, percent = 0.1) {
+    const rangeInc = (max - min) * percent;
+    const domain = [min - rangeInc, max + rangeInc];
+    return domain;
+  }
+  setVariablesData(absSampleMax, absSampleMin, data, dom, key, plotDim, settings) {
+    const radiusScale = linear().domain([absSampleMin, absSampleMax]).range([settings.radiusMin, settings.radiusMax]);
+    const renderedCircles = dom.plot?.selectAll("circle").nodes().map((d) => d.__data__);
+    for (const item of data.variableItems) {
+      item.color = item.correlation > 0 ? settings.corrColor : settings.antiCorrColor;
+      item.label = this.variableTwLst.find((t) => t.$id == item.tw$id).term.name;
+      item.x = plotDim.xScale.scale(item.correlation) + this.horizPad;
+      item.y = plotDim.yScale.scale(item[`transformed_${key}`]) + this.topPad;
+      item.radius = radiusScale(item.sampleSize);
+      if (renderedCircles?.length > 0) {
+        const findRenderdCircle = renderedCircles.find((d) => d.tw$id === item.tw$id);
+        if (findRenderdCircle) {
+          item.previousX = findRenderdCircle.x;
+          item.previousY = findRenderdCircle.y;
+        }
+      } else {
+        item.previousX = item.x;
+        item.previousY = item.y;
+      }
+    }
+    return data.variableItems;
+  }
+  setLegendData(absSampleMin, absSampleMax, skippedVariables) {
+    const opts = {
+      absMin: absSampleMin,
+      absMax: absSampleMax,
+      skippedVariables: skippedVariables.length == 0 ? [] : skippedVariables.map((t) => {
+        return { label: this.variableTwLst.find((tw) => tw.$id == t.tw$id).term.name };
+      })
+    };
+    return opts;
+  }
+};
+
+// plots/corrVolcano/view/ItemToolTip.ts
+var ItemToolTip = class {
+  constructor(item, circle, tip, settings) {
+    circle.on("mouseover", () => {
+      tip.clear().showunder(circle.node());
+      const table = table2col({ holder: tip.d.append("table") });
+      table.addRow("Item", item.label);
+      table.addRow("Correlation (\u03C1)", roundValue(item.correlation, 3));
+      const pValue = settings.isAdjustedPValue ? item.adjusted_pvalue : item.original_pvalue;
+      table.addRow(settings.isAdjustedPValue ? "Adjusted p value" : "Original p value", roundValue(pValue, 5));
+      table.addRow("Sample size", item.sampleSize);
+    });
+    circle.on("mouseout", () => {
+      tip.hide();
+    });
+  }
+};
+
+// plots/corrVolcano/view/View.ts
+var View = class {
+  constructor(dom, viewData, interactions, settings, defaultMaxRadius, defaultMinRadius) {
+    this.duration = 500;
+    this.dom = dom;
+    this.viewData = viewData;
+    interactions.clearDom();
+    const plotDim = viewData.plotDim;
+    this.renderDom(plotDim);
+    renderVariables(this, settings, interactions);
+    this.renderLegend(viewData.legendData, settings, interactions, defaultMaxRadius, defaultMinRadius);
+  }
+  renderDom(plotDim) {
+    this.dom.svg.attr("width", plotDim.svg.width).attr("height", plotDim.svg.height);
+    this.dom.title.attr("class", "sjpp-corr-volcano-title").style("font-weight", 600).attr("text-anchor", "middle").attr("x", plotDim.title.x).attr("y", plotDim.title.y).text(plotDim.title.text);
+    this.dom.yAxisLabel.attr("class", "sjpp-corr-volcano-y-axis").style("font-weight", 600).attr("text-anchor", "middle").attr("transform", `translate(${plotDim.yAxisLabel.x}, ${plotDim.yAxisLabel.y}) rotate(-90)`).text("-log10(p value)");
+    this.dom.xAxisLabel.attr("class", "sjpp-corr-volcano-x-axis").style("font-weight", 600).attr("text-anchor", "middle").attr("transform", `translate(${plotDim.xAxisLabel.x}, ${plotDim.xAxisLabel.y})`).html("Correlation Coefficient (ρ)");
+    this.renderScale(plotDim.yScale, true);
+    this.renderScale(plotDim.xScale);
+    this.dom.svg.append("line").attr("class", "sjpp-corr-volcano-divide-line").attr("stroke", "black").attr("stroke-dasharray", "5 4").attr("stroke-opacity", 0.4).attr("x1", plotDim.divideLine.x).attr("x2", plotDim.divideLine.x).attr("y1", plotDim.divideLine.y1).attr("y2", plotDim.divideLine.y2);
+    this.dom.svg.append("line").attr("class", "sjpp-corr-volcano-threshold-line").attr("stroke", "black").attr("stroke-dasharray", "5 4").attr("stroke-opacity", 0.4).attr("x1", plotDim.thresholdLine.x1).attr("x2", plotDim.thresholdLine.x2).attr("y1", plotDim.thresholdLine.y).attr("y2", plotDim.thresholdLine.y);
+  }
+  renderScale(scale, isLeft = false) {
+    const scaleG = this.dom.plot.append("g").attr("transform", `translate(${scale.x}, ${scale.y})`).transition().duration(this.duration).call(isLeft ? axisLeft(scale.scale) : axisBottom(scale.scale));
+    axisstyle({
+      axis: scaleG,
+      color: "black",
+      showline: true
+    });
+  }
+  renderLegend(legendData, settings, interactions, defaultMaxRadius, defaultMinRadius) {
+    const svg = this.dom.legend.attr("width", 400).attr("height", 400).style("display", "inline-block").style("vertical-align", "top").style("padding-top", "20px");
+    const startXPos = 20;
+    const startYPos = 20;
+    new LegendCircleReference({
+      g: svg.append("g").attr("transform", `translate(${startXPos}, ${startYPos})`),
+      inputMax: defaultMaxRadius,
+      inputMin: defaultMinRadius,
+      maxLabel: legendData.absMax,
+      maxRadius: settings.radiusMax,
+      minLabel: legendData.absMin,
+      minRadius: settings.radiusMin,
+      title: "Sample Size",
+      menu: {
+        minMaxLabel: "pixels",
+        callback: async (obj) => {
+          await interactions.changeRadius(obj);
+        }
+      }
+    });
+    if (legendData.skippedVariables.length > 0) {
+      const newYPos = startYPos + settings.radiusMax + 60;
+      let incrY = 30;
+      const skippedVariablesG = svg.append("g").attr("transform", `translate(${startXPos}, ${newYPos})`);
+      skippedVariablesG.append("text").style("font-weight", "bold").style("font-size", "0.8em").text("Skipped Variables");
+      for (const term of legendData.skippedVariables) {
+        skippedVariablesG.append("text").attr("transform", `translate(${startXPos}, ${incrY})`).style("font-size", "0.8em").text(term.label);
+        incrY += 20;
+      }
+    }
+  }
+};
+function renderVariables(self, settings, interactions) {
+  self.dom.plot.selectAll("circle").data(self.viewData.variableItems).enter().append("circle").attr("id", (item) => `sjpp-corr-volcano-circle-${item.label}`).attr("stroke", (item) => item.color).attr("fill", (item) => item.color).attr("fill-opacity", 0.5).attr("cx", (item) => item.previousX).attr("cy", (item) => item.previousY).attr("r", (item) => item.radius * 0.9).transition().duration(self.duration).attr("cx", (item) => item.x).attr("cy", (item) => item.y).attr("r", (item) => item.radius).each(function(item) {
+    const circle = select_default(this);
+    new ItemToolTip(item, circle, self.dom.tip, settings);
+    circle.on("click", () => {
+      interactions.launchSampleScatter(item);
+    });
+  });
+}
+
+// plots/corrVolcano/interactions/CorrVolcanoInteractions.ts
+var CorrVolcanoInteractions = class {
+  constructor(app, dom, id) {
+    this.app = app;
+    this.dom = dom;
+    this.id = id;
+    this.variableTwLst = [];
+  }
+  download() {
+    const svg = this.dom.svg.node();
+    to_svg(svg, `correlationVolcano`, { apply_dom_styles: true });
+  }
+  //If no featureTw is set, show the tree to select a feature
+  async showTree() {
+    this.dom.div.selectAll("*").remove();
+    await appInit({
+      vocabApi: this.app.vocabApi,
+      holder: this.dom.div,
+      state: this.app.getState(),
+      tree: {
+        click_term: (_term) => {
+          const term = _term.term || _term;
+          this.app.dispatch({
+            type: "plot_create",
+            config: {
+              chartType: "correlationVolcano",
+              featureTw: _term.term ? _term : { term }
+            }
+          });
+          this.app.dispatch({
+            type: "plot_delete",
+            id: this.id
+          });
+        }
+      }
+    });
+  }
+  //When clicking on dot, launch the sample scatter by gene and drug
+  launchSampleScatter(item) {
+    const config = this.app.getState();
+    const plot = config.plots.find((p) => p.id === this.id);
+    const term2 = this.variableTwLst?.find((t) => t.$id === item.tw$id)?.term;
+    if (!term2) throw `No term found for ${item.tw$id}`;
+    const scatterConfig = {
+      chartType: "sampleScatter",
+      name: `${plot.featureTw.term.name} ${termType2label(plot.featureTw.term.type)} v ${term2.name}`,
+      term: { term: plot.featureTw.term },
+      term2: { id: term2.id },
+      filter: config.termfilter.filter
+    };
+    this.app.dispatch({
+      type: "plot_create",
+      config: scatterConfig
+    });
+  }
+  //Obj is returned from LegendCircleReference callback
+  async changeRadius(obj) {
+    this.app.dispatch({
+      type: "plot_edit",
+      id: this.id,
+      config: {
+        settings: {
+          correlationVolcano: {
+            radiusMax: obj.max,
+            radiusMin: obj.min
+          }
+        }
+      }
+    });
+  }
+  clearDom() {
+    this.dom.error.style("padding", "").text("");
+    this.dom.plot.selectAll("*").remove();
+    this.dom.legend.selectAll("*").remove();
+    this.dom.svg.selectAll("line").remove();
+    this.dom.title.text("");
+    this.dom.yAxisLabel.text("");
+    this.dom.xAxisLabel.text("");
+  }
+};
+
+// plots/corrVolcano/CorrelationVolcano.ts
+var CorrelationVolcano = class _CorrelationVolcano extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    /** Max radius user may enter in control or legend menu */
+    this.defaultInputMaxRadius = 35;
+    /** Min radius user may enter in control or legend menu */
+    this.defaultInputMinRadius = 1;
+    this.type = _CorrelationVolcano.type;
+    this.components = {
+      controls: {}
+    };
+    const holder = opts.holder.classed("sjpp-corrVolcano-main", true);
+    const controls = opts.controls ? holder : holder.append("div");
+    const div = holder.append("div").style("padding", "5px").style("display", "inline-block");
+    const errorDiv = div.append("div").attr("id", "sjpp-corrVolcano-error").style("opacity", 0.75);
+    const svg = div.append("svg").style("display", "inline-block").attr("id", "sjpp-corrVolcano-svg");
+    this.dom = {
+      controls: controls.style("display", "block"),
+      div,
+      error: errorDiv,
+      svg,
+      plot: svg.append("g"),
+      title: svg.append("text"),
+      yAxisLabel: svg.append("text"),
+      xAxisLabel: svg.append("text"),
+      legend: div.append("svg"),
+      tip: new Menu({ padding: "" })
+    };
+    if (opts.header) formatHeaderText({
+      header: opts.header,
+      chartType: "CORRELATION VOLCANO"
+    });
+    this.variableTwLst = [];
+  }
+  static {
+    this.type = "correlationVolcano";
+  }
+  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 {
+      termdbConfig: appState.termdbConfig,
+      termfilter: appState.termfilter,
+      correlationVolcano: appState.termdbConfig.correlationVolcano,
+      config: Object.assign({}, config, {
+        settings: {
+          correlationVolcano: config.settings.correlationVolcano
+        }
+      })
+    };
+  }
+  async setControls() {
+    const inputs = [
+      {
+        type: "term",
+        configKey: "featureTw",
+        chartType: "correlationVolcano",
+        usecase: { target: "correlationVolcano", detail: "numeric" },
+        label: "Feature",
+        vocabApi: this.app.vocabApi,
+        numericEditMenuVersion: ["continuous"],
+        menuOptions: "replace"
+      },
+      {
+        label: "Correlation method",
+        title: "Change the correlation method",
+        type: "radio",
+        chartType: "correlationVolcano",
+        settingsKey: "method",
+        options: [
+          { label: "Pearson", value: "pearson" },
+          { label: "Spearman", value: "spearman" }
+        ]
+      },
+      {
+        label: "P value",
+        title: "Change the p value",
+        type: "radio",
+        chartType: "correlationVolcano",
+        settingsKey: "isAdjustedPValue",
+        options: [
+          { label: "Adjusted", value: true },
+          { label: "Original", value: false }
+        ]
+      },
+      {
+        label: "Significant p value",
+        title: "Set the significant p value threshold",
+        type: "number",
+        chartType: "correlationVolcano",
+        settingsKey: "threshold",
+        debounceInterval: 0.05
+      },
+      {
+        label: "Maximum radius size",
+        title: "Set maximum radius size in pixels",
+        type: "number",
+        chartType: "correlationVolcano",
+        settingsKey: "radiusMax",
+        min: this.defaultInputMinRadius,
+        max: this.defaultInputMaxRadius,
+        debounceInterval: 500
+      },
+      {
+        label: "Minimum radius size",
+        title: "Set minimum radius size in pixels",
+        type: "number",
+        chartType: "correlationVolcano",
+        settingsKey: "radiusMin",
+        min: this.defaultInputMinRadius,
+        max: this.defaultInputMaxRadius,
+        debounceInterval: 500
+      },
+      {
+        label: "Height",
+        title: "Set the height of the plot",
+        type: "number",
+        chartType: "correlationVolcano",
+        settingsKey: "height",
+        debounceInterval: 500
+      },
+      {
+        label: "Width",
+        title: "Set the width of the plot",
+        type: "number",
+        chartType: "correlationVolcano",
+        settingsKey: "width",
+        debounceInterval: 500
+      },
+      {
+        label: "Correlation color",
+        type: "color",
+        chartType: "correlationVolcano",
+        settingsKey: "corrColor",
+        title: "Color of correlated values"
+      },
+      {
+        label: "Anticorrelation color",
+        type: "color",
+        chartType: "correlationVolcano",
+        settingsKey: "antiCorrColor",
+        title: "Color of anticorrelated values"
+      }
+    ];
+    this.components.controls = await controlsInit({
+      app: this.app,
+      id: this.id,
+      holder: this.dom.controls.style("display", "inline-block"),
+      inputs
+    });
+    this.components.controls.on("downloadClick.correlationVolcano", () => {
+      this.interactions.download();
+    });
+    this.components.controls.on("helpClick.correlationVolcano", () => {
+      window.open("https://github.com/stjude/proteinpaint/wiki/Correlation-volcano", "_blank");
+    });
+  }
+  async init(appState) {
+    this.interactions = new CorrVolcanoInteractions(this.app, this.dom, this.id);
+    const state = this.getState(appState);
+    if (state.config["featureTw"]) await this.setControls();
+    const dsCorrVolcano = state.termdbConfig.correlationVolcano;
+    this.variableTwLst = dsCorrVolcano.variables.termIds.map((id) => {
+      return { id };
+    });
+    this.interactions.variableTwLst = this.variableTwLst;
+    await fillTwLst(this.variableTwLst, this.app.vocabApi);
+  }
+  async main() {
+    const config = structuredClone(this.state.config);
+    if (config.childType != this.type && config.chartType != this.type) return;
+    if (!this.interactions) throw "Interactions not initialized [correlationVolcano main()]";
+    if (config.featureTw == null) {
+      this.interactions.showTree();
+      return;
+    }
+    const settings = config.settings.correlationVolcano;
+    const model = new Model(config, this.state, this.app, settings, this.variableTwLst, this.vocabApi);
+    const data = await model.getData();
+    if (!data || data.error || !data.variableItems.length) {
+      this.interactions.clearDom();
+      this.dom.error.style("padding", "20px 20px 20px 60px").text(data.error || "No correlation data to render.");
+      return;
+    }
+    const viewModel = new ViewModel(config, data, this.dom, settings, this.variableTwLst);
+    new View(
+      this.dom,
+      viewModel.viewData,
+      this.interactions,
+      settings,
+      this.defaultInputMaxRadius,
+      this.defaultInputMinRadius
+    );
+  }
+};
+var corrVolcanoInit = getCompInit(CorrelationVolcano);
+var componentInit = corrVolcanoInit;
+function getDefaultCorrVolcanoSettings(overrides = {}) {
+  const defaults = {
+    antiCorrColor: "#ff0000",
+    //red
+    corrColor: "#0000ff",
+    //blue
+    isAdjustedPValue: false,
+    method: "pearson",
+    threshold: 0.05,
+    height: 500,
+    width: 500,
+    radiusMax: 20,
+    radiusMin: 5
+  };
+  return Object.assign(defaults, overrides);
+}
+async function getPlotConfig(opts, app) {
+  if (opts.numeric && !opts.featureTw) opts.featureTw = { term: opts.numeric.term };
+  if (opts.featureTw) {
+    try {
+      await fillTermWrapper(opts.featureTw, app.vocabApi);
+    } catch (e) {
+      console.error(new Error(`${e} [correlationVolcano getPlotConfig()]`));
+      throw `correlationVolcano getPlotConfig() failed`;
+    }
+  }
+  const config = {
+    chartType: "correlationVolcano",
+    featureTw: opts.featureTw ?? null,
+    settings: {
+      controls: {
+        term2: null,
+        term0: null
+      },
+      correlationVolcano: getDefaultCorrVolcanoSettings(opts.overrides || {})
+    }
+  };
+  return copyMerge(config, opts);
+}
+export {
+  componentInit,
+  corrVolcanoInit,
+  getDefaultCorrVolcanoSettings,
+  getPlotConfig
+};
+//# sourceMappingURL=CorrelationVolcano-YV4UHOAX.js.map