create dimension for arbitrary gene

client/src/components/brushableHistogram/index.js

@@ -19,12 +19,9 @@ import * as globals from "../../globals";
   obsAnnotations: _.get(state.controls.world, "obsAnnotations", null)
 }))
 class HistogramBrush extends React.Component {
-  calcHistogramCache = memoize((obsAnnotations, metadataField, ranges) => {
+  calcHistogramCache = memoize((obsAnnotations, field, ranges) => {
     // recalculate expensive stuff
-    const allValuesForContinuousFieldAsArray = _.map(
+    const allValuesForContinuousFieldAsArray = _.map(obsAnnotations, field);
-      obsAnnotations,
-      metadataField
-    );
     const histogramCache = {};
 
     histogramCache.x = d3
@@ -61,17 +58,17 @@ class HistogramBrush extends React.Component {
 
   onBrush(selection, x) {
     return () => {
-      const { dispatch, metadataField } = this.props;
+      const { dispatch, field } = this.props;
       if (d3.event.selection) {
         dispatch({
           type: "continuous metadata histogram brush",
-          selection: metadataField,
+          selection: field,
           range: [x(d3.event.selection[0]), x(d3.event.selection[1])]
         });
       } else {
         dispatch({
           type: "continuous metadata histogram brush",
-          selection: metadataField,
+          selection: field,
           range: null
         });
       }
@@ -79,10 +76,10 @@ class HistogramBrush extends React.Component {
   }
 
   drawHistogram(svgRef) {
-    const { obsAnnotations, metadataField, ranges } = this.props;
+    const { obsAnnotations, field, ranges } = this.props;
     const histogramCache = this.calcHistogramCache(
       obsAnnotations,
-      metadataField,
+      field,
       ranges
     );
 
@@ -109,11 +106,7 @@ class HistogramBrush extends React.Component {
         .select(svgRef)
         .append("g")
         .attr("class", "brush")
-        .call(
+        .call(d3.brushX().on("end", this.onBrush(field, x.invert).bind(this)));
-          d3
-            .brushX()
-            .on("end", this.onBrush(metadataField, x.invert).bind(this))
-        );
 
       const xAxis = d3
         .select(svgRef)
@@ -127,30 +120,40 @@ class HistogramBrush extends React.Component {
         .attr("fill", "#000")
         .attr("text-anchor", "end")
         .attr("font-weight", "bold")
-        .text(metadataField);
+        .text(field);
+
+      d3.select(svgRef)
+        .selectAll(".axis--x text")
+        .style("fill", "rgb(80,80,80)");
+      d3.select(svgRef)
+        .selectAll(".axis--x path")
+        .style("stroke", "rgb(230,230,230)");
+      d3.select(svgRef)
+        .selectAll(".axis--x line")
+        .style("stroke", "rgb(230,230,230)");
 
       this.setState({ brush, xAxis });
     }
   }
 
   handleColorAction() {
-    const { dispatch, metadataField, initializeRanges } = this.props;
+    const { dispatch, field, initializeRanges } = this.props;
     dispatch({
       type: "color by continuous metadata",
-      colorAccessor: metadataField,
+      colorAccessor: field,
-      rangeMaxForColorAccessor: initializeRanges[metadataField].range.max
+      rangeMaxForColorAccessor: initializeRanges[field].range.max
     });
   }
 
   render() {
-    const { metadataField, ranges, colorAccessor } = this.props;
+    const { field, ranges, colorAccessor } = this.props;
     return (
       <div
         style={{
           marginTop: 10,
           position: "flex"
         }}
-        id={`histogram_${metadataField}`}
+        id={`histogram_${field}`}
       >
         <svg
           width={this.width}
@@ -168,11 +171,10 @@ class HistogramBrush extends React.Component {
           style={{
             fontSize: 16,
             marginLeft: 4,
-            // padding: this.props.colorAccessor === this.props.metadataField ? 3 : "auto",
+            // padding: this.props.colorAccessor === this.props.field ? 3 : "auto",
             borderRadius: 3,
-            color:
+            color: colorAccessor === field ? globals.brightBlue : "black",
-              colorAccessor === metadataField ? globals.brightBlue : "black",
+            // backgroundColor: this.props.colorAccessor === this.props.field ? globals.brightBlue : "inherit",
-            // backgroundColor: this.props.colorAccessor === this.props.metadataField ? globals.brightBlue : "inherit",
             position: "relative",
             top: -29,
             cursor: "pointer"

client/src/components/brushableHistogram/util.js

@@ -0,0 +1,27 @@
+import * as globals from "../../globals";
+import _ from "lodash";
+import * as constants from "./constants";
+
+export const calcHistogram = (ranges, allValuesForContinuousFieldAsArray) => {
+  const histogramData = {};
+
+  histogramData.x = d3
+    .scaleLinear()
+    .domain([ranges.min, ranges.max])
+    .range([0, constants.width]);
+
+  histogramData.y = d3
+    .scaleLinear()
+    .range([constants.height - constants.marginBottom, 0]);
+  // .range([height - margin.bottom, margin.top]);
+
+  histogramData.bins = d3
+    .histogram()
+    .domain(histogramData.x.domain())
+    .thresholds(40)(allValuesForContinuousFieldAsArray);
+
+  histogramData.numValues = allValuesForContinuousFieldAsArray.length;
+
+  console.log(histogramData);
+  return histogramData;
+};

client/src/components/continuous/continuous.js

@@ -5,15 +5,12 @@ import React from "react";
 import _ from "lodash";
 import { connect } from "react-redux";
 
-import HistogramBrush from "./histogramBrush";
+import HistogramBrush from "../brushableHistogram/";
 
 @connect(state => {
-  const metadata = _.get(state.controls.world, "obsAnnotations", null);
-  const ranges = _.get(state.controls.world, "summary.obs", null);
-
   return {
-    ranges,
+    ranges: _.get(state.controls.world, "summary.obs", null),
-    metadata,
+    metadata: _.get(state.controls.world, "obsAnnotations", null),
     colorAccessor: state.controls.colorAccessor,
     colorScale: state.controls.colorScale,
     selectionUpdate: _.get(state.controls, "crossfilter.updateTime", null)
@@ -29,16 +26,18 @@ class Continuous extends React.Component {
   }
 
   handleColorAction(key) {
-    const { dispatch, ranges } = this.props;
+    return () => {
-    dispatch({
+      const { dispatch, ranges } = this.props;
-      type: "color by continuous metadata",
+      dispatch({
-      colorAccessor: key,
+        type: "color by continuous metadata",
-      rangeMaxForColorAccessor: ranges[key].range.max
+        colorAccessor: key,
-    });
+        rangeMaxForColorAccessor: ranges[key].range.max
+      });
+    };
   }
 
   render() {
-    const { ranges } = this.props;
+    const { ranges, obsAnnotations } = this.props;
 
     return (
       <div>
@@ -48,8 +47,10 @@ class Continuous extends React.Component {
             return (
               <HistogramBrush
                 key={key}
-                metadataField={key}
+                field={key}
+                fieldValues={obsAnnotations}
                 ranges={value.range}
+                handleColorAction={this.handleColorAction(key).bind(this)}
               />
             );
           }

client/src/components/graph/graph.js

@@ -165,6 +165,7 @@ class Graph extends React.Component {
       if (!this.renderCache.sizes) {
         this.renderCache.sizes = new Float32Array(cellCount);
       }
+
       crossfilter.fillByIsFiltered(this.renderCache.sizes, 4, 0.2);
       sizeBuffer({ data: this.renderCache.sizes, dimension: 1 });
 

client/src/reducers/controls.js

@@ -35,6 +35,7 @@ const Controls = (
     categoricalAsBooleansMap: null,
     crossfilter: null,
     dimensionMap: null,
+    dimensionMapVar: {},
 
     colorAccessor: null,
     colorScale: null,
@@ -115,9 +116,16 @@ const Controls = (
       };
     }
     case "expression load success": {
-      const { world, universe } = state;
+      const {
+        world,
+        universe,
+        crossfilter,
+        dimensionMap,
+        dimensionMapVar
+      } = state;
       let universeVarDataCache = universe.varDataCache;
       let worldVarDataCache = world.varDataCache;
+      let _dimensionMapVar = dimensionMapVar;
       _.forEach(action.expressionData, (val, key) => {
         universeVarDataCache = kvCache.set(universeVarDataCache, key, val);
         if (kvCache.get(worldVarDataCache, key) === undefined) {
@@ -128,8 +136,20 @@ const Controls = (
           );
         }
       });
+
+      _.forEach(action.expressionData, (val, key) => {
+        console.log("got one ", key);
+        dimensionMap[key] = World.createVarDimensionsMap(
+          world,
+          worldVarDataCache,
+          crossfilter,
+          key
+        );
+      });
+
       return {
         ...state,
+        dimensionMapVar,
         universe: {
           ...universe,
           varDataCache: universeVarDataCache
@@ -152,18 +172,6 @@ const Controls = (
     /*******************************
              User Events
      *******************************/
-    case "parallel coordinates axes have been drawn": {
-      return {
-        ...state,
-        axesHaveBeenDrawn: true
-      };
-    }
-    case "continuous selection using parallel coords brushing": {
-      return {
-        ...state,
-        continuousSelection: action.data
-      };
-    }
     case "graph brush selection change": {
       state.dimensionMap.x.filterRange([
         action.brushCoords.northwest[0],