left sidebar improvements (#368)

* left sidebar improvements

* lint

.gitignore

@@ -33,7 +33,4 @@ npm-debug.log
 *.idea*
 __pycache__
 *.DS_Store*
-
-
-
-
+data

client/index.html

@@ -6,7 +6,7 @@
     <title>cellxgene</title>
     <link href="https://fonts.googleapis.com/css?family=Roboto+Condensed:400,400i,700" rel="stylesheet">
     <style>
-      html, body, p, h1, h2, h3, h4, h5, h6, span, button, input, label, text {
+      html, body, p, h1, h2, h3, h4, h5, h6, span, button, input, label, text, div {
         font-family: 'Roboto Condensed','Helvetica Neue','Helvetica','Arial',sans-serif;
         font-size: 14px;
       }

client/index_template.html

@@ -6,7 +6,7 @@
     <title>cellxgene</title>
     <link href="https://fonts.googleapis.com/css?family=Roboto+Condensed:400,400i,700" rel="stylesheet">
     <style>
-      html, body, p, h1, h2, h3, h4, h5, h6, span, button, input, label, text {
+      html, body, p, h1, h2, h3, h4, h5, h6, span, button, input, label, text, div {
         font-family: 'Roboto Condensed','Helvetica Neue','Helvetica','Arial',sans-serif;
         font-size: 14px;
       }

client/src/components/brushableHistogram/index.js

@@ -6,8 +6,8 @@ https://bl.ocks.org/SpaceActuary/2f004899ea1b2bd78d6f1dbb2febf771
 // jshint esversion: 6
 import React from "react";
 import _ from "lodash";
+import { Button, ButtonGroup } from "@blueprintjs/core";
 import { connect } from "react-redux";
-import { FaPaintBrush } from "react-icons/fa";
 import * as d3 from "d3";
 import memoize from "memoize-one";
 import { kvCache } from "../../util/stateManager";
@@ -74,7 +74,7 @@ class HistogramBrush extends React.Component {
   constructor(props) {
     super(props);
 
-    this.width = 300;
+    this.width = 340;
     this.height = 100;
     this.marginBottom = 20;
 
@@ -156,8 +156,7 @@ class HistogramBrush extends React.Component {
 
       d3.select(svgRef)
         .selectAll(".axis--x text")
-        .style("fill", "rgb(80,80,80)")
-        .style("font-size", 12);
+        .style("fill", "rgb(80,80,80)");
 
       d3.select(svgRef)
         .selectAll(".axis--x path")
@@ -234,110 +233,62 @@ class HistogramBrush extends React.Component {
       set1AvgExp,
       set2AvgExp,
       scatterplotXXaccessor,
-      scatterplotYYaccessor
+      scatterplotYYaccessor,
+      zebra
     } = this.props;
 
     return (
       <div
-        style={{
-          marginTop: 10,
-          position: "flex"
-        }}
         id={`histogram_${field}`}
+        style={{
+          padding: globals.leftSidebarSectionPadding,
+          backgroundColor: zebra ? globals.lightestGrey : "white"
+        }}
       >
-        <div>
-          <span style={{ fontSize: globals.tiniestFontSize }}> {field} </span>
+        <div style={{ display: "flex", justifyContent: "flex-end" }}>
+          {isDiffExp ? (
+            <span>
+              <span
+                style={{ marginRight: 7 }}
+                className="bp3-icon-standard bp3-icon-scatter-plot"
+              />
+              <ButtonGroup style={{ marginRight: 7 }}>
+                <Button
+                  onClick={this.handleSetGeneAsScatterplotX(field).bind(this)}
+                  active={scatterplotXXaccessor === field}
+                  intent={scatterplotXXaccessor === field ? "primary" : "none"}
+                >
+                  plot x
+                </Button>
+                <Button
+                  onClick={this.handleSetGeneAsScatterplotY(field).bind(this)}
+                  active={scatterplotYYaccessor === field}
+                  intent={scatterplotYYaccessor === field ? "primary" : "none"}
+                >
+                  plot y
+                </Button>
+              </ButtonGroup>
+            </span>
+          ) : null}
           {isUserDefined ? (
-            <span
+            <Button
+              minimal
               onClick={this.removeHistogram.bind(this)}
               style={{
-                fontSize: globals.tiniestFontSize,
                 color: globals.blue,
                 cursor: "pointer",
                 marginLeft: 7
               }}
             >
               remove
-            </span>
-          ) : null}
-          {isDiffExp ? (
-            <span>
-              <span
-                style={{
-                  fontSize: globals.tiniestFontSize,
-                  marginLeft: 7
-                }}
-              >
-                <strong>1:</strong>
-                {` ${set1AvgExp.toPrecision(2)}`}
-              </span>
-              <span
-                style={{
-                  fontSize: globals.tiniestFontSize,
-                  marginLeft: 7,
-                  backgroundColor: globals.lighterGrey,
-                  padding: 2
-                }}
-              >
-                <strong>2:</strong>
-                {` ${set2AvgExp.toPrecision(2)}`}
-              </span>
-              <span
-                style={{
-                  fontSize: globals.tiniestFontSize,
-                  marginLeft: 7
-                }}
-              >
-                {`Av. Diff: ${avgDiff.toFixed(2)}`}
-              </span>
-              <span
-                onClick={this.handleSetGeneAsScatterplotX(field).bind(this)}
-                style={{
-                  fontSize: 16,
-                  color:
-                    scatterplotXXaccessor === field
-                      ? "white"
-                      : globals.brightBlue,
-                  cursor: "pointer",
-                  position: "relative",
-                  top: 1,
-                  fontWeight: 700,
-                  marginRight: 4,
-                  borderRadius: 3,
-                  padding: "2px 3px",
-                  backgroundColor:
-                    scatterplotXXaccessor === field
-                      ? globals.brightBlue
-                      : "inherit"
-                }}
-              >
-                X
-              </span>
-              <span
-                onClick={this.handleSetGeneAsScatterplotY(field).bind(this)}
-                style={{
-                  fontSize: 16,
-                  color:
-                    scatterplotYYaccessor === field
-                      ? "white"
-                      : globals.brightBlue,
-                  cursor: "pointer",
-                  position: "relative",
-                  top: 1,
-                  fontWeight: 700,
-                  marginRight: 4,
-                  borderRadius: 3,
-                  padding: "2px 3px",
-                  backgroundColor:
-                    scatterplotYYaccessor === field
-                      ? globals.brightBlue
-                      : "inherit"
-                }}
-              >
-                Y
-              </span>
-            </span>
+            </Button>
           ) : null}
+          <Button
+            onClick={this.handleColorAction.bind(this)}
+            active={colorAccessor === field}
+            intent={colorAccessor === field ? "primary" : "none"}
+            icon="tint"
+          />
         </div>
         <svg
           width={this.width}
@@ -346,22 +297,46 @@ class HistogramBrush extends React.Component {
             this.drawHistogram(svgRef);
           }}
         />
-        <span
-          onClick={this.handleColorAction.bind(this)}
+        <div
           style={{
-            fontSize: 14,
-            marginLeft: 4,
-            // padding: this.props.colorAccessor === this.props.field ? 3 : "auto",
-            borderRadius: 3,
-            color: colorAccessor === field ? globals.brightBlue : "black",
-            // backgroundColor: this.props.colorAccessor === this.props.field ? globals.brightBlue : "inherit",
-            position: "relative",
-            top: -29,
-            cursor: "pointer"
+            display: "flex",
+            justifyContent: "center"
           }}
         >
-          <FaPaintBrush />
-        </span>
+          <span style={{ fontStyle: "italic" }}>{field}</span>
+        </div>
+
+        {isDiffExp ? (
+          <div
+            style={{
+              display: "flex",
+              justifyContent: "center",
+              alignItems: "baseline"
+            }}
+          >
+            <span>
+              <strong>1:</strong>
+              {` ${set1AvgExp.toPrecision(2)}`}
+            </span>
+            <span
+              style={{
+                marginLeft: 7,
+                backgroundColor: globals.lighterGrey,
+                padding: 2
+              }}
+            >
+              <strong>2:</strong>
+              {` ${set2AvgExp.toPrecision(2)}`}
+            </span>
+            <span
+              style={{
+                marginLeft: 7
+              }}
+            >
+              {`Av. Diff: ${avgDiff.toFixed(2)}`}
+            </span>
+          </div>
+        ) : null}
       </div>
     );
   }

client/src/components/categorical/category.js

@@ -1,8 +1,9 @@
 import React from "react";
 import _ from "lodash";
 import { connect } from "react-redux";
-import { FaChevronRight, FaChevronDown, FaPaintBrush } from "react-icons/fa";
+import { FaChevronRight, FaChevronDown } from "react-icons/fa";
 import memoize from "memoize-one";
+import { Button } from "@blueprintjs/core";
 
 import * as globals from "../../globals";
 import Value from "./value";
@@ -119,55 +120,58 @@ class Category extends React.Component {
         <div
           style={{
             display: "flex",
-            justifyContent: "flex-start",
+            justifyContent: "space-between",
             alignItems: "baseline"
           }}
         >
-          <label className="bp3-control bp3-checkbox">
-            <input
-              onChange={this.handleToggleAllClick.bind(this)}
-              ref={el => {
-                this.checkbox = el;
-                return el;
+          <div
+            style={{
+              display: "flex",
+              justifyContent: "flex-start",
+              alignItems: "baseline"
+            }}
+          >
+            <label className="bp3-control bp3-checkbox">
+              <input
+                onChange={this.handleToggleAllClick.bind(this)}
+                ref={el => {
+                  this.checkbox = el;
+                  return el;
+                }}
+                checked={isChecked}
+                type="checkbox"
+              />
+              <span className="bp3-control-indicator" />
+              {""}
+            </label>
+
+            <span
+              style={{
+                cursor: "pointer",
+                display: "inline-block"
               }}
-              checked={isChecked}
-              type="checkbox"
-            />
-            <span className="bp3-control-indicator" />
-            {""}
-          </label>
-
-          <span
-            style={{
-              cursor: "pointer",
-              display: "inline-block"
-            }}
-            onClick={() => {
-              this.setState({ isExpanded: !isExpanded });
-            }}
-          >
-            {metadataField}
-            {isExpanded ? (
-              <FaChevronDown style={{ fontSize: 10, marginLeft: 5 }} />
-            ) : (
-              <FaChevronRight style={{ fontSize: 10, marginLeft: 5 }} />
-            )}
-          </span>
-
-          <span
+              onClick={() => {
+                this.setState({ isExpanded: !isExpanded });
+              }}
+            >
+              {metadataField}
+              {isExpanded ? (
+                <FaChevronDown style={{ fontSize: 10, marginLeft: 5 }} />
+              ) : (
+                <FaChevronRight style={{ fontSize: 10, marginLeft: 5 }} />
+              )}
+            </span>
+          </div>
+          <Button
             onClick={this.handleColorChange.bind(this)}
-            style={{
-              marginLeft: 4,
-              color:
-                colorAccessor === metadataField ? globals.brightBlue : "black",
-              display: "inline-block",
-              cursor: "pointer"
-            }}
-          >
-            <FaPaintBrush style={{ fontSize: 12, marginLeft: 10 }} />
-          </span>
+            active={colorAccessor === metadataField}
+            intent={colorAccessor === metadataField ? "primary" : "none"}
+            icon={"tint"}
+          />
+        </div>
+        <div style={{ marginLeft: 26 }}>
+          {isExpanded ? this.renderCategoryItems() : null}
         </div>
-        <div style={{ marginLeft: 26 }}>{isExpanded ? this.renderCategoryItems() : null}</div>
         <div>
           {isExpanded && isTruncated ? (
             <p style={{ paddingLeft: 15 }}>... truncated list ...</p>

client/src/components/continuous/continuous.js

@@ -48,16 +48,16 @@ class Continuous extends React.Component {
       this.continuousChecked = true; /* only do this once */
     }
 
+    /* initial value for iterator to simulate index, ranges is an object */
+    let zebra = -1;
+
     return (
-      <div
-        style={{
-          padding: globals.leftSidebarSectionPadding
-        }}
-      >
+      <div>
         {this.hasContinuous ? (
           <p
             style={Object.assign({}, globals.leftSidebarSectionHeading, {
-              marginTop: 40
+              marginTop: 40,
+              paddingLeft: globals.leftSidebarSectionPadding
             })}
           >
             Continuous metadata
@@ -65,12 +65,14 @@ class Continuous extends React.Component {
         ) : null}
         {_.map(ranges, (value, key) => {
           const isColorField = key.includes("color") || key.includes("Color");
+          zebra += 1;
           if (value.range && key !== "name" && !isColorField) {
             return (
               <HistogramBrush
                 key={key}
                 field={key}
                 isObs
+                zebra={zebra % 2 === 0}
                 fieldValues={obsAnnotations}
                 ranges={value.range}
                 handleColorAction={this.handleColorAction(key).bind(this)}

client/src/components/continuousLegend/index.js

@@ -6,7 +6,7 @@ import { interpolateViridis } from "d3-scale-chromatic";
 
 // create continuous color legend
 // http://bl.ocks.org/syntagmatic/e8ccca52559796be775553b467593a9f
-const continuous = (selectorId, colorscale, colorAccessor) => {
+const continuous = (selectorId, colorscale) => {
   const legendheight = 200;
   const legendwidth = 80;
   const margin = { top: 10, right: 60, bottom: 10, left: 2 };

client/src/components/geneExpression/cellSetButtons.js

@@ -3,7 +3,6 @@ import React from "react";
 import _ from "lodash";
 import { Button } from "@blueprintjs/core";
 import { connect } from "react-redux";
-import * as globals from "../../globals";
 
 @connect()
 class CellSetButton extends React.Component {

client/src/components/geneExpression/expressionButtons.js

@@ -37,6 +37,9 @@ class Expression extends React.Component {
       type: "clear differential expression",
       diffExp: differential.diffExp
     });
+    dispatch({
+      type: "clear scatterplot"
+    });
   }
 
   render() {
@@ -47,7 +50,13 @@ class Expression extends React.Component {
     const haveBothCellSets =
       !!differential.celllist1 && !!differential.celllist2;
     return (
-      <div style={{ marginRight: 10, marginBottom: 10 }}>
+      <div
+        style={{
+          marginRight: 10,
+          marginBottom: 10,
+          paddingLeft: globals.leftSidebarSectionPadding
+        }}
+      >
         <CellSetButton {...this.props} eitherCellSetOneOrTwo={1} />
         <CellSetButton {...this.props} eitherCellSetOneOrTwo={2} />
         {!differential.diffExp ? (
@@ -55,6 +64,7 @@ class Expression extends React.Component {
             style={{ marginTop: 10 }}
             disabled={!haveBothCellSets}
             intent="primary"
+            fill
             type="button"
             onClick={this.computeDiffExp.bind(this)}
           >
@@ -64,6 +74,7 @@ class Expression extends React.Component {
         {differential.diffExp ? (
           <Button
             type="button"
+            fill
             style={{ marginTop: 10 }}
             intent="warning"
             onClick={this.clearDifferentialExpression.bind(this)}

client/src/components/geneExpression/index.js

@@ -76,14 +76,22 @@ class GeneExpression extends React.Component {
       <div>
         <div
           style={{
-            padding: globals.leftSidebarSectionPadding,
             marginTop: 30
           }}
         >
-          <p style={globals.leftSidebarSectionHeading}>Custom genes</p>
-          <div style={{ marginTop: 11 }} className="bp3-control-group">
-            <div className="bp3-input-group">
-              <span className="bp3-icon bp3-icon-symbol-cross" />
+          <p
+            style={Object.assign({}, globals.leftSidebarSectionHeading, {
+              paddingLeft: globals.leftSidebarSectionPadding,
+              margin: 0
+            })}
+          >
+            Custom genes
+          </p>
+          <div
+            style={{ padding: globals.leftSidebarSectionPadding }}
+            className="bp3-control-group"
+          >
+            <div className="bp3-input-group bp3-fill">
               <input
                 onKeyDown={this.keyPress.bind(this)}
                 onChange={e => {
@@ -105,7 +113,7 @@ class GeneExpression extends React.Component {
             </button>
           </div>
           {world && userDefinedGenes.length > 0
-            ? _.map(userDefinedGenes, geneName => {
+            ? _.map(userDefinedGenes, (geneName, index) => {
                 const values = world.varDataCache[geneName];
                 if (!values) {
                   return null;
@@ -114,6 +122,7 @@ class GeneExpression extends React.Component {
                   <HistogramBrush
                     key={geneName}
                     field={geneName}
+                    zebra={index % 2 === 0}
                     ranges={d3.extent(values)}
                     isUserDefined
                   />
@@ -121,21 +130,18 @@ class GeneExpression extends React.Component {
               })
             : null}
         </div>
-        <div
-          style={{
-            padding: globals.leftSidebarSectionPadding
-          }}
-        >
+        <div>
           <p
             style={Object.assign({}, globals.leftSidebarSectionHeading, {
-              marginTop: 40
+              marginTop: 40,
+              paddingLeft: globals.leftSidebarSectionPadding
             })}
           >
             Differentially Expressed Genes
           </p>
           <ExpressionButtons />
           {differential.diffExp
-            ? _.map(differential.diffExp, value => {
+            ? _.map(differential.diffExp, (value, index) => {
                 const annotations = world.varAnnotations[value[0]];
                 const { name } = annotations;
                 const values = world.varDataCache[name];
@@ -146,6 +152,7 @@ class GeneExpression extends React.Component {
                   <HistogramBrush
                     key={name}
                     field={name}
+                    zebra={index % 2 === 0}
                     ranges={d3.extent(values)}
                     isDiffExp
                     avgDiff={value[1]}

client/src/components/graph/graph.js

@@ -96,7 +96,8 @@ class Graph extends React.Component {
       camera,
       pointBuffer,
       colorBuffer,
-      sizeBuffer
+      sizeBuffer,
+      svg
     } = this.state;
 
     if (reglRender && this.reglRenderState === "rendering" && mode !== "zoom") {
@@ -183,19 +184,19 @@ class Graph extends React.Component {
       prevProps.responsive.height !== responsive.height ||
       prevProps.responsive.width !== responsive.width ||
       /* first time */
-      (responsive.height && responsive.width && !this.state.svg)
+      (responsive.height && responsive.width && !svg)
     ) {
       /* clear out whatever was on the div, even if nothing, but usually the brushes etc */
       d3.select("#graphAttachPoint")
         .selectAll("svg")
         .remove();
-      const { svg: newSvg, brush, brushContainer } = setupSVGandBrushElements(
+      const { svg: newSvg, brush } = setupSVGandBrushElements(
         this.handleBrushSelectAction.bind(this),
         this.handleBrushDeselectAction.bind(this),
         responsive,
         this.graphPaddingTop
       );
-      this.setState({ svg: newSvg, brush, brushContainer });
+      this.setState({ svg: newSvg, brush });
     }
   }
 

client/src/components/leftsidebar.js

@@ -15,15 +15,7 @@ import DynamicScatterplot from "./scatterplot/scatterplot";
   scatterplotYYaccessor: state.controls.scatterplotYYaccessor
 }))
 class LeftSideBar extends React.Component {
-  constructor(props) {
-    super(props);
-    this.state = {
-      currentTab: "metadata"
-    };
-  }
-
   render() {
-    const { currentTab } = this.state;
     const {
       responsive,
       datasetTitle,

client/src/components/scatterplot/scatterplot.js

@@ -258,6 +258,7 @@ class Scatterplot extends React.Component {
       .attr("x", 10)
       .attr("y", 10)
       .attr("class", "label")
+      .style("font-style", "italic")
       .text(scatterplotYYaccessor);
 
     svg
@@ -266,6 +267,7 @@ class Scatterplot extends React.Component {
       .attr("y", height - 10)
       .attr("text-anchor", "end")
       .attr("class", "label")
+      .style("font-style", "italic")
       .text(scatterplotXXaccessor);
   }
 
@@ -285,7 +287,6 @@ class Scatterplot extends React.Component {
         id="scatterplot_wrapper"
       >
         <ButtonGroup
-          minimal
           style={{
             position: "absolute",
             right: 5,
@@ -294,14 +295,16 @@ class Scatterplot extends React.Component {
         >
           <Button
             type="button"
-            icon={minimized ? "plus" : "minus"}
+            minimal
             onClick={() => {
               this.setState({ minimized: !minimized });
             }}
-          />
+          >
+            {minimized ? "show scatterplot" : "hide"}
+          </Button>
           <Button
             type="button"
-            icon="cross"
+            minimal
             onClick={() => {
               dispatch({
                 type: "clear scatterplot"
@@ -310,7 +313,9 @@ class Scatterplot extends React.Component {
                 type: "reset colorscale"
               });
             }}
-          />
+          >
+            remove
+          </Button>
         </ButtonGroup>
         <div
           className={styles.scatterplot}

client/src/index.js

@@ -3,6 +3,7 @@
 import React from "react";
 import ReactDOM from "react-dom";
 import { Provider } from "react-redux";
+import { FocusStyleManager } from "@blueprintjs/core";
 
 import "./index.css";
 
@@ -10,6 +11,8 @@ import "./index.css";
 import App from "./components/app";
 import store from "./reducers";
 
+FocusStyleManager.onlyShowFocusOnTabs();
+
 ReactDOM.render(
   <Provider store={store}>
     <App />