test data

client/src/components/brushableHistogram/histogramMini.js

@@ -0,0 +1,178 @@
+import React, { useEffect, useRef, useState } from "react";
+import { interpolateCool } from "d3-scale-chromatic";
+import * as d3 from "d3";
+
+import maybeScientific from "./maybeScientific";
+import clamp from "./clamp";
+
+const Histogram = ({
+  field,
+  fieldForId,
+  display,
+  histogram,
+  width,
+  height,
+  onBrush,
+  onBrushEnd,
+  margin,
+  isColorBy,
+  selectionRange,
+}) => {
+  const svgRef = useRef(null);
+  const [brush, setBrush] = useState(null);
+
+  useEffect(() => {
+    /*
+      Create the d3 histogram
+      */
+    const { marginLeft, marginRight, marginBottom, marginTop } = margin;
+    const { x, y, bins, binStart, binEnd, binWidth } = histogram;
+    const svg = d3.select(svgRef.current);
+
+    /* Remove everything */
+    svg.selectAll("*").remove();
+
+    /* Set margins within the SVG */
+    const container = svg
+      .attr("width", width + marginLeft + marginRight)
+      .attr("height", height + marginTop + marginBottom)
+      .append("g")
+      .attr("class", "histogram-container")
+      .attr("transform", `translate(${marginLeft},${marginTop})`);
+
+    const colorScale = d3
+      .scaleSequential(interpolateCool)
+      .domain([0, bins.length]);
+
+    const histogramScale = d3
+      .scaleLinear()
+      .domain(x.domain())
+      .range([
+        colorScale.domain()[1],
+        colorScale.domain()[0],
+      ]); /* we flip this to make colors dark if high in the color scale */
+
+    if (binWidth > 0) {
+      /* BINS */
+      container
+        .insert("g", "*")
+        .selectAll("rect")
+        .data(bins)
+        .enter()
+        .append("rect")
+        .attr("x", (d, i) => x(binStart(i)) + 1)
+        .attr("y", (d) => y(d))
+        .attr("width", (d, i) => x(binEnd(i)) - x(binStart(i)) - 1)
+        .attr("height", (d) => y(0) - y(d))
+        .style(
+          "fill",
+          isColorBy ? (d, i) => colorScale(histogramScale(binStart(i))) : "#bbb"
+        );
+    }
+
+    // BRUSH
+    // Note the brushable area is bounded by the data on three sides, but goes down to cover the x-axis
+    const brushX = d3
+      .brushX()
+      .extent([
+        [x.range()[0], y.range()[1]],
+        [x.range()[1], marginTop + height + marginBottom],
+      ])
+      /*
+        emit start so that the Undoable history can save an undo point
+        upon drag start, and ignore the subsequent intermediate drag events.
+        */
+      .on("start", onBrush(field, x.invert, "start"))
+      .on("brush", onBrush(field, x.invert, "brush"))
+      .on("end", onBrushEnd(field, x.invert));
+
+    const brushXselection = container
+      .insert("g")
+      .attr("class", "brush")
+      .attr("data-testid", `${svgRef.current.dataset.testid}-brushable-area`)
+      .call(brushX);
+
+    /* X AXIS */
+    container
+      .insert("g")
+      .attr("class", "axis axis--x")
+      .attr("transform", `translate(0,${marginTop + height})`)
+      .call(
+        d3
+          .axisBottom(x)
+          .ticks(4)
+          .tickFormat(d3.format(maybeScientific(x)))
+      );
+
+    /* Y AXIS */
+    container
+      .insert("g")
+      .attr("class", "axis axis--y")
+      .attr("transform", `translate(${marginLeft + width},0)`)
+      .call(
+        d3
+          .axisRight(y)
+          .ticks(3)
+          .tickFormat(
+            d3.format(
+              y.domain().some((n) => Math.abs(n) >= 10000) ? ".0e" : ","
+            )
+          )
+      );
+
+    /* axis style */
+    svg.selectAll(".axis text").style("fill", "rgb(80,80,80)");
+    svg.selectAll(".axis path").style("stroke", "rgb(230,230,230)");
+    svg.selectAll(".axis line").style("stroke", "rgb(230,230,230)");
+
+    setBrush({ brushX, brushXselection });
+  }, [histogram, isColorBy]);
+
+  useEffect(() => {
+    /*
+      paint/update selection brush
+      */
+    if (!brush) return;
+    const { brushX, brushXselection } = brush;
+    const selection = d3.brushSelection(brushXselection.node());
+    if (!selectionRange && selection) {
+      /* no active selection - clear brush */
+      brushXselection.call(brushX.move, null);
+    } else if (selectionRange) {
+      const { x, domain } = histogram;
+      const [min, max] = domain;
+      const x0 = x(clamp(selectionRange[0], [min, max]));
+      const x1 = x(clamp(selectionRange[1], [min, max]));
+      if (!selection) {
+        /* there is an active selection, but no brush - set the brush */
+        brushXselection.call(brushX.move, [x0, x1]);
+      } else {
+        /* there is an active selection and a brush - make sure they match */
+        const moveDeltaThreshold = 1;
+        const dX0 = Math.abs(x0 - selection[0]);
+        const dX1 = Math.abs(x1 - selection[1]);
+        /*
+          only update the brush if it is grossly incorrect,
+          as defined by the moveDeltaThreshold
+          */
+        if (dX0 > moveDeltaThreshold || dX1 > moveDeltaThreshold) {
+          brushXselection.call(brushX.move, [x0, x1]);
+        }
+      }
+    }
+  }, [brush, selectionRange]);
+
+  return (
+    <svg
+      style={{ display }}
+      width={width}
+      height={height}
+      id={`histogram_${fieldForId}_svg`}
+      data-testclass="histogram-plot"
+      data-testid={`histogram-${field}-plot`}
+      ref={svgRef}
+    />
+  );
+};
+
+export default Histogram;

client/src/components/geneExpression/gene.js

@@ -86,6 +86,8 @@ class Gene extends React.Component {
                 {gene}
               </span>
             </Truncate>
+            <HistogramBrush isUserDefined field={gene} />
+
             {/* <TestMiniHisto /> */}
           </span>
         </div>
@@ -113,7 +115,6 @@ class Gene extends React.Component {
             icon={<Icon icon="maximize" iconSize={10} />}
           />
         </div>
-        <HistogramBrush isUserDefined field={gene} />
       </div>
     );
   }

client/src/components/geneExpression/geneSet.js

@@ -12,7 +12,7 @@ import { memoize } from "../../util/dataframe/util";
 import Truncate from "../util/truncate";
 // import TestMiniHisto from "./test_miniHisto";
 import * as globals from "../../globals";
-// import GenesetMenus from "./menus/genesetMenus";
+import GenesetMenus from "./menus/genesetMenus";
 
 @connect((state, ownProps) => {
   return {
@@ -150,7 +150,7 @@ class GeneSet extends React.Component {
           </span>
           <div>
             {/* <TestMiniHisto /> */}
-            {/* <GenesetMenus genesetsEditable geneset={setName} /> */}
+            <GenesetMenus genesetsEditable geneset={setName} />
             <Tooltip
               content="Color by geneset"
               position={Position.LEFT}