mini

client/src/components/brushableHistogram/footer.js

@@ -10,6 +10,7 @@ const HistogramFooter = React.memo(
     rangeColorMax,
     logFoldChange,
     pvalAdj,
+    isObs,
   }) => {
     /*
     Footer of each histogram.  Will render range, title, and optionally 
@@ -43,7 +44,7 @@ const HistogramFooter = React.memo(
             data-testclass="brushable-histogram-field-name"
             style={{ fontStyle: "italic" }}
           >
-            {displayName}
+            {isObs ? displayName : null}
           </span>
           <div style={{ display: hideRanges ? "block" : "none" }}>
             : {rangeMin}

client/src/components/brushableHistogram/histogram.js

@@ -75,62 +75,64 @@ const Histogram = ({
         );
     }
 
-    // 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],
-      ])
-      /*
+    if (!mini) {
+      // 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));
+        .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", `${svgRef.current.dataset.testid}-brushable-area`)
-      .call(brushX);
+      const brushXselection = container
+        .insert("g")
+        .attr("class", "brush")
+        .attr("data-testid", `${svgRef.current.dataset.testid}-brushable-area`)
+        .call(brushX);
 
-    /* X AXIS */
-    container
-      .insert("g")
-      .attr("class", "axis axis--x")
-      .attr("transform", `translate(0,${marginTop + height})`)
-      .call(
-        d3
-          .axisBottom(x)
-          .ticks(4)
-          .tickFormat(d3.format(maybeScientific(x)))
-      );
+      /* X AXIS */
+      container
+        .insert("g")
+        .attr("class", "axis axis--x")
+        .attr("transform", `translate(0,${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(${marginLeft + width},0)`)
-      .call(
-        d3
-          .axisRight(y)
-          .ticks(3)
-          .tickFormat(
-            d3.format(
-              y.domain().some((n) => Math.abs(n) >= 10000) ? ".0e" : ","
+      /* Y AXIS */
+      container
+        .insert("g")
+        .attr("class", "axis axis--y")
+        .attr("transform", `translate(${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)");
+      /* 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 });
+      setBrush({ brushX, brushXselection });
+    }
   }, [histogram, isColorBy]);
 
   useEffect(() => {

client/src/components/brushableHistogram/histogramMini.js

@@ -1,178 +0,0 @@
-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/brushableHistogram/index.js

@@ -54,11 +54,6 @@ class HistogramBrush extends React.PureComponent {
     const marginBottom = 25; // space for X axis & labels
     const marginTop = 3;
 
-    const marginLeftMini = 10; // Space for 0 tick label on X axis
-    const marginRightMini = 54; // space for Y axis & labels
-    const marginBottomMini = 25; // space for X axis & labels
-    const marginTopMini = 3;
-
     this.state = {
       margin: {
         marginLeft,
@@ -69,13 +64,13 @@ class HistogramBrush extends React.PureComponent {
       width: 340 - marginLeft - marginRight,
       height: 135 - marginTop - marginBottom,
       marginMini: {
-        marginLeftMini,
-        marginRightMini,
-        marginBottomMini,
-        marginTopMini,
+        marginLeft: 0, // Space for 0 tick label on X axis
+        marginRight: 0, // space for Y axis & labels
+        marginBottom: 0, // space for X axis & labels
+        marginTop: 0,
       },
-      widthMini: 340 - marginLeft - marginRight,
-      heightMini: 135 - marginTop - marginBottom,
+      widthMini: 120,
+      heightMini: 15,
     };
   }
 
@@ -271,16 +266,20 @@ class HistogramBrush extends React.PureComponent {
 
   // eslint-disable-next-line class-methods-use-this -- instance method allows for memoization per annotation
   calcHistogramCache(col, margin, width, height) {
+    /* make this more structured and doing a forEach */
     /*
      recalculate expensive stuff, notably bins, summaries, etc.
     */
-    const histogramCache = {};
-    const summary = col.summarize();
+    const histogramCache = {}; /* maybe change this so that it computes ... */
+    const summary = col.summarize(); /* this is memoized, so it's free the second time you call it */
     const { min: domainMin, max: domainMax } = summary;
     const numBins = 40;
-    const { marginTop, marginLeft } = margin;
+    const { marginTop, marginLeft } = margin; /* changes with mini */
 
-    histogramCache.domain = [domainMin, domainMax];
+    histogramCache.domain = [
+      domainMin,
+      domainMax,
+    ]; /* doesn't change with mini */
 
     histogramCache.x = d3
       .scaleLinear()
@@ -290,7 +289,7 @@ class HistogramBrush extends React.PureComponent {
     histogramCache.bins = histogramContinuous(col, numBins, [
       domainMin,
       domainMax,
-    ]);
+    ]); /* memoized */
     histogramCache.binWidth = (domainMax - domainMin) / numBins;
 
     histogramCache.binStart = (i) => domainMin + i * histogramCache.binWidth;
@@ -377,11 +376,11 @@ class HistogramBrush extends React.PureComponent {
                     : "histogram-continuous-metadata"
                 }
                 style={{
-                  padding: globals.leftSidebarSectionPadding,
+                  padding: mini ? 0 : globals.leftSidebarSectionPadding,
                   backgroundColor: zebra ? globals.lightestGrey : "white",
                 }}
               >
-                {!mini ? (
+                {!mini && isObs ? (
                   <HistogramHeader
                     fieldId={field}
                     isColorBy={isColorAccessor}
@@ -416,6 +415,7 @@ class HistogramBrush extends React.PureComponent {
                 />
                 {!mini ? (
                   <HistogramFooter
+                    isObs={isObs}
                     displayName={field}
                     hideRanges={asyncProps.isSingleValue}
                     rangeMin={asyncProps.unclippedRange[0]}

client/src/components/geneExpression/gene.js

@@ -11,10 +11,18 @@ import HistogramBrush from "../brushableHistogram";
 
 // import TestMiniHisto from "./test_miniHisto";
 import * as globals from "../../globals";
+import actions from "../../actions";
+
 // import GeneMenus from "./menus/geneMenus";
 
-@connect(() => {
-  return {};
+@connect((state, ownProps) => {
+  const { gene } = ownProps;
+
+  return {
+    isColorAccessor: state.colors.colorAccessor === gene,
+    isScatterplotXXaccessor: state.controls.scatterplotXXaccessor === gene,
+    isScatterplotYYaccessor: state.controls.scatterplotYYaccessor === gene,
+  };
 })
 class Gene extends React.Component {
   constructor(props) {
@@ -26,10 +34,7 @@ class Gene extends React.Component {
 
   onColorChangeClick = () => {
     const { dispatch, gene } = this.props;
-    dispatch({
-      type: "color by expression",
-      colorAccessor: gene,
-    });
+    dispatch(actions.requestSingleGeneExpressionCountsForColoringPOST(gene));
   };
 
   handleGeneExpandClick = () => {
@@ -37,26 +42,42 @@ class Gene extends React.Component {
     this.setState({ geneIsExpanded: !geneIsExpanded });
   };
 
+  handleSetGeneAsScatterplotX = () => {
+    const { dispatch, gene } = this.props;
+    dispatch({
+      type: "set scatterplot x",
+      data: gene,
+    });
+  };
+
+  handleSetGeneAsScatterplotY = () => {
+    const { dispatch, gene } = this.props;
+    dispatch({
+      type: "set scatterplot y",
+      data: gene,
+    });
+  };
+
   render() {
-    const { gene } = this.props;
+    const {
+      gene,
+      isColorAccessor,
+      isScatterplotXXaccessor,
+      isScatterplotYYaccessor,
+    } = this.props;
     const { geneIsExpanded } = this.state;
     return (
       <div>
         <div
           style={{
             marginLeft: 15,
+            marginRight: 0,
+            marginTop: 2,
+            display: "flex",
+            justifyContent: "space-between",
+            alignItems: "center",
           }}
         >
-          <Icon
-            icon="drag-handle-horizontal"
-            iconSize={12}
-            style={{
-              marginRight: 10,
-              cursor: "grab",
-              position: "relative",
-              top: -2,
-            }}
-          />
           <span
             role="menuitem"
             tabIndex="0"
@@ -65,8 +86,20 @@ class Gene extends React.Component {
             onKeyPress={/* todo_genesets */ () => {}}
             style={{
               cursor: "pointer",
+              display: "flex",
+              justifyContent: "space-between",
             }}
           >
+            <Icon
+              icon="drag-handle-horizontal"
+              iconSize={12}
+              style={{
+                marginRight: 7,
+                cursor: "grab",
+                position: "relative",
+                top: 3,
+              }}
+            />
             <Truncate>
               <span
                 style={{
@@ -79,22 +112,58 @@ class Gene extends React.Component {
                 {gene}
               </span>
             </Truncate>
+            {!geneIsExpanded ? (
+              <HistogramBrush isUserDefined field={gene} mini />
+            ) : null}
+          </span>
+          <span>
+            <AnchorButton
+              minimal
+              small
+              data-testid={`plot-x-${gene}`}
+              onClick={this.handleSetGeneAsScatterplotX}
+              active={isScatterplotXXaccessor}
+              intent={isScatterplotXXaccessor ? "primary" : "none"}
+              style={{ fontWeight: 700, marginRight: 2 }}
+            >
+              x
+            </AnchorButton>
+            <AnchorButton
+              minimal
+              small
+              data-testid={`plot-y-${gene}`}
+              onClick={this.handleSetGeneAsScatterplotY}
+              active={isScatterplotYYaccessor}
+              intent={isScatterplotYYaccessor ? "primary" : "none"}
+              style={{ fontWeight: 700, marginRight: 2 }}
+            >
+              y
+            </AnchorButton>
             <AnchorButton
               minimal
               small
               data-testclass="maximize"
               data-testid={`maximize-${gene}`}
               onClick={this.handleGeneExpandClick}
-              active={false /* todo gene sets */}
+              active={geneIsExpanded}
               intent="none"
               icon={<Icon icon="maximize" iconSize={10} />}
+              style={{ marginRight: 2 }}
+            />
+            <AnchorButton
+              minimal
+              small
+              data-testclass="colorby"
+              data-testid={`colorby-${gene}`}
+              onClick={this.onColorChangeClick}
+              active={isColorAccessor}
+              intent={isColorAccessor ? "primary" : "none"}
+              icon={<Icon icon="tint" iconSize={12} />}
             />
-            {/* <TestMiniHisto /> */}
           </span>
+          {/* <TestMiniHisto /> */}
         </div>
-
-        <HistogramBrush isUserDefined field={gene} mini={!geneIsExpanded} />
-
+        {geneIsExpanded ? <HistogramBrush isUserDefined field={gene} /> : null}
         {/* <GeneMenus genesetsEditable gene={gene} /> */}
       </div>
     );
@@ -103,17 +172,6 @@ class Gene extends React.Component {
 
 export default Gene;
 
-// <AnchorButton
-//   minimal
-//   small
-//   data-testclass="colorby"
-//   data-testid={`colorby-${gene}`}
-//   onClick={/* todo gene sets */ () => {}}
-//   active={false /* todo gene sets */}
-//   intent="none"
-//   icon={<Icon icon="tint" iconSize={12} />}
-// />
-
 // {geneIsExpanded ? (
 //   <FaChevronDown
 //     data-testclass="gene-expand-is-expanded"