feat(geneset): save diff exp result as geneset (#2216)

* update package lock

* allow falsey vals

* remove old diff exp handling

* save diff exp results as geneset

* delete test

* check for undefined or null

* use global geneset description for diffexp

* remove diffexp special code, no longer showing adjpval + logfoldchange

* remove differential map to state

* remove clear from FSM, since we no longer support those actions

* restore controlHelpers test with todo

client/__tests__/util/stateManager/controlsHelpers.test.js

@@ -1,38 +1,8 @@
 /*
 test controls helpers
 */
-import { subsetAndResetGeneLists } from "../../../src/util/stateManager/controlsHelpers";
-import * as globals from "../../../src/globals";
 
 describe("controls helpers", () => {
-  test("subsetAndResetGeneLists", () => {
+  // TODO #2227 test: improve test coverage on control helper functions
-    const geneList = [];
+  // (`topNCategories()`, `isSelectableCategoryName()`, `selectableCategoryNames()`, `createCategorySummaryFromDfCol()`, `createCategoricalSelection()`, )
-    const genRandGene = () => Math.random().toString(36).substring(2, 6);
-
-    // build a unique set of genes
-    for (let i = 0; i < 150; i += 1) {
-      let randGene = genRandGene();
-      while (geneList.includes(randGene)) randGene = genRandGene();
-      geneList.push(randGene);
-    }
-    // insert duplicates
-    geneList[0] = "dupl";
-    geneList[20] = "dupl";
-    const state = {
-      userDefinedGenes: geneList.slice(0, 20),
-      diffexpGenes: geneList.slice(20),
-    };
-    const [newUserDefinedGenes, newDiffExpGenes] = subsetAndResetGeneLists(
-      state
-    );
-    const expectedNewUserDefinedGenes = [
-      ...geneList.slice(0, 20),
-      ...geneList.slice(21),
-    ].slice(0, globals.maxGenes);
-    expect(globals.maxUserDefinedGenes).toBeLessThan(globals.maxGenes);
-    expect(geneList.length).toBeGreaterThan(globals.maxGenes);
-    expect(newUserDefinedGenes).toHaveLength(globals.maxGenes);
-    expect(newUserDefinedGenes).toStrictEqual(expectedNewUserDefinedGenes);
-    expect(newDiffExpGenes).toStrictEqual([]);
-  });
 });

client/src/components/brushableHistogram/footer.js

@@ -8,22 +8,17 @@ const HistogramFooter = React.memo(
     rangeMax,
     rangeColorMin,
     rangeColorMax,
-    logFoldChange,
-    pvalAdj,
     isObs,
     isGeneSetSummary,
   }) => {
     /*
-    Footer of each histogram.  Will render range, title, and optionally 
+    Footer of each histogram.  Will render range and title.
-    differential expression info.
 
     Required props:
       * displayName - the displayName, aka "n_genes", "FOXP2", etc.
       * hideRanges - true/false, enables/disable rendering of ranges
       * range - length two array, [min, max], containing the range values to display
       * rangeColor - length two array, [mincolor, maxcolor], each a CSS color
-      * logFoldChange - lfc to display, optional.
-      * pValue - pValue to display, optional.
     */
     return (
       <div>
@@ -60,30 +55,6 @@ const HistogramFooter = React.memo(
             max {rangeMax.toPrecision(4)}
           </span>
         </div>
-
-        {logFoldChange && pvalAdj ? (
-          <div
-            style={{
-              display: "flex",
-              justifyContent: "center",
-              alignItems: "baseline",
-            }}
-          >
-            <span>
-              <strong>log fold change:</strong>
-              {` ${logFoldChange.toPrecision(4)}`}
-            </span>
-            <span
-              style={{
-                marginLeft: 7,
-                padding: 2,
-              }}
-            >
-              <strong>p-value (adj):</strong>
-              {pvalAdj < 0.0001 ? " < 0.0001" : ` ${pvalAdj.toFixed(4)}`}
-            </span>
-          </div>
-        ) : null}
       </div>
     );
   }

client/src/components/brushableHistogram/index.js

@@ -14,9 +14,9 @@ import StillLoading from "./loading";
 import ErrorLoading from "./error";
 
 @connect((state, ownProps) => {
-  const { isObs, isUserDefined, isDiffExp, isGeneSetSummary, field } = ownProps;
+  const { isObs, isUserDefined, isGeneSetSummary, field } = ownProps;
   const myName = makeContinuousDimensionName(
-    { isObs, isUserDefined, isDiffExp, isGeneSetSummary },
+    { isObs, isUserDefined, isGeneSetSummary },
     field
   );
   return {
@@ -80,7 +80,6 @@ class HistogramBrush extends React.PureComponent {
         field,
         isObs,
         isUserDefined,
-        isDiffExp,
         isGeneSetSummary,
       } = this.props;
 
@@ -98,7 +97,6 @@ class HistogramBrush extends React.PureComponent {
         continuousNamespace: {
           isObs,
           isUserDefined,
-          isDiffExp,
           isGeneSetSummary,
         },
       };
@@ -115,7 +113,6 @@ class HistogramBrush extends React.PureComponent {
         field,
         isObs,
         isUserDefined,
-        isDiffExp,
         isGeneSetSummary,
       } = this.props;
       const minAllowedBrushSize = 10;
@@ -156,7 +153,6 @@ class HistogramBrush extends React.PureComponent {
         continuousNamespace: {
           isObs,
           isUserDefined,
-          isDiffExp,
           isGeneSetSummary,
         },
       };
@@ -362,10 +358,7 @@ class HistogramBrush extends React.PureComponent {
       field,
       isColorAccessor,
       isUserDefined,
-      isDiffExp,
-      logFoldChange,
       isGeneSetSummary,
-      pvalAdj,
       isScatterplotXXaccessor,
       isScatterplotYYaccessor,
       zebra,
@@ -383,7 +376,7 @@ class HistogramBrush extends React.PureComponent {
       heightMini,
     } = this.state;
     const fieldForId = field.replace(/\s/g, "_");
-    const showScatterPlot = isDiffExp || isUserDefined;
+    const showScatterPlot = isUserDefined;
 
     return (
       <Async
@@ -406,9 +399,7 @@ class HistogramBrush extends React.PureComponent {
                 id={`histogram_${fieldForId}`}
                 data-testid={`histogram-${field}`}
                 data-testclass={
-                  isDiffExp
+                  isUserDefined
-                    ? "histogram-diffexp"
-                    : isUserDefined
                     ? "histogram-user-gene"
                     : "histogram-continuous-metadata"
                 }
@@ -454,15 +445,12 @@ class HistogramBrush extends React.PureComponent {
                   <HistogramFooter
                     isGeneSetSummary={isGeneSetSummary}
                     isObs={isObs}
-                    isDiffExp={isDiffExp}
                     displayName={field}
                     hideRanges={asyncProps.isSingleValue}
                     rangeMin={asyncProps.unclippedRange[0]}
                     rangeMax={asyncProps.unclippedRange[1]}
                     rangeColorMin={asyncProps.unclippedRangeColor[0]}
                     rangeColorMax={asyncProps.unclippedRangeColor[1]}
-                    logFoldChange={logFoldChange}
-                    pvalAdj={pvalAdj}
                   />
                 )}
               </div>

client/src/components/categorical/category/index.js

@@ -45,7 +45,6 @@ const LABEL_WIDTH_ANNO = LABEL_WIDTH - ANNO_BUTTON_WIDTH;
     crossfilter: state.obsCrossfilter,
     isUserAnno,
     genesets: state.genesets.genesets,
-    differential: state.differential,
   };
 })
 class Category extends React.PureComponent {
@@ -144,15 +143,14 @@ class Category extends React.PureComponent {
     */
     const { schema } = annoMatrix;
     const { colorAccessor, colorMode } = colors;
-    const { genesets, differential } = this.props;
+    const { genesets } = this.props;
     let colorDataPromise = Promise.resolve(null);
     if (colorAccessor) {
       const query = createColorQuery(
         colorMode,
         colorAccessor,
         schema,
-        genesets,
+        genesets
-        differential.diffExp
       );
       if (query) colorDataPromise = annoMatrix.fetch(...query);
     }

client/src/components/continuousLegend/index.js

@@ -107,11 +107,10 @@ const continuous = (selectorId, colorScale, colorAccessor) => {
   annoMatrix: state.annoMatrix,
   colors: state.colors,
   genesets: state.genesets.genesets,
-  differential: state.differential,
 }))
 class ContinuousLegend extends React.Component {
   async componentDidUpdate(prevProps) {
-    const { annoMatrix, colors, genesets, differential } = this.props;
+    const { annoMatrix, colors, genesets } = this.props;
     if (!colors || !annoMatrix) return;
 
     if (colors !== prevProps?.colors || annoMatrix !== prevProps?.annoMatrix) {
@@ -122,8 +121,7 @@ class ContinuousLegend extends React.Component {
         colorMode,
         colorAccessor,
         schema,
-        genesets,
+        genesets
-        differential.diffExp
       );
 
       const colorDf = colorQuery ? await annoMatrix.fetch(...colorQuery) : null;

client/src/components/geneExpression/gene.js

@@ -63,9 +63,6 @@ class Gene extends React.Component {
       isColorAccessor,
       isScatterplotXXaccessor,
       isScatterplotYYaccessor,
-      isDiffExp,
-      pvalAdj,
-      logFoldChange,
     } = this.props;
     const { geneIsExpanded } = this.state;
     const genesetNameLengthVisible = 310; /* this magic number determines how much of a long geneset name we see */
@@ -120,25 +117,20 @@ class Gene extends React.Component {
               </Truncate>
             </div>
             {!geneIsExpanded ? (
-              isDiffExp ? (
+              <HistogramBrush isUserDefined field={gene} mini />
-                <HistogramBrush isDiffExp field={gene} mini />
-              ) : (
-                <HistogramBrush isUserDefined field={gene} mini />
-              )
             ) : null}
           </div>
           <div style={{ flexShrink: 0, marginLeft: 2 }}>
-            {!isDiffExp ? (
+            <AnchorButton
-              <AnchorButton
+              minimal
-                minimal
+              small
-                small
+              data-testid={`delete-from-geneset-${gene}`}
-                data-testid={`delete-from-geneset-${gene}`}
+              onClick={this.handleDeleteGeneFromSet}
-                onClick={this.handleDeleteGeneFromSet}
+              intent="none"
-                intent="none"
+              style={{ fontWeight: 700, marginRight: 2 }}
-                style={{ fontWeight: 700, marginRight: 2 }}
+              icon={<Icon icon="trash" iconSize={10} />}
-                icon={<Icon icon="trash" iconSize={10} />}
+            />
-              />
+            )
-            ) : null}
             <AnchorButton
               minimal
               small
@@ -184,17 +176,7 @@ class Gene extends React.Component {
             />
           </div>
         </div>
-        {geneIsExpanded &&
+        {geneIsExpanded && <HistogramBrush isUserDefined field={gene} />}
-          (isDiffExp ? (
-            <HistogramBrush
-              isDiffExp
-              field={gene}
-              pvalAdj={pvalAdj}
-              logFoldChange={logFoldChange}
-            />
-          ) : (
-            <HistogramBrush isUserDefined field={gene} />
-          ))}
       </div>
     );
   }

client/src/components/geneExpression/geneSet.js

@@ -79,33 +79,8 @@ class GeneSet extends React.Component {
   };
 
   renderGenes() {
-    const {
+    const { setName, setGenes, setGenesWithDescriptions } = this.props;
-      setName,
-      setGenes,
-      setGenesWithDescriptions,
-      isDiffExp,
-      diffExp,
-    } = this.props;
 
-    if (isDiffExp) {
-      // [ [gene, logfoldchange, pval, pval_adj], ...]
-      return setGenes.map((gene, idx) => {
-        const logFoldChange = diffExp[idx][1];
-        const pvalAdj = diffExp[idx][3];
-        return (
-          <Gene
-            key={gene}
-            gene={gene}
-            geneset={setName}
-            isDiffExp
-            logFoldChange={logFoldChange}
-            pvalAdj={pvalAdj}
-          />
-        );
-      });
-    }
-
-    // otherwise...
     return setGenes.map((gene) => {
       const { geneDescription } = setGenesWithDescriptions.get(gene);
 

client/src/components/geneExpression/index.js

@@ -7,7 +7,6 @@ import CreateGenesetDialogue from "./menus/createGenesetDialogue";
 
 @connect((state) => {
   return {
-    differential: state.differential,
     genesets: state.genesets.genesets,
   };
 })
@@ -30,24 +29,6 @@ class GeneExpression extends React.Component {
     return sets;
   };
 
-  renderDiffexpGeneSets = () => {
-    const { differential } = this.props;
-    const { diffExp } = differential;
-    if (!diffExp) return null;
-
-    // [ [gene, logfoldchange, pval, pval_adj], ...]
-    const setGenes = diffExp.map((diffExpGene) => diffExpGene[0]);
-    return (
-      <GeneSet
-        key="Temp DiffExp Set"
-        setGenes={setGenes}
-        isDiffExp
-        diffExp={diffExp}
-        setName="Temp DiffExp Set"
-      />
-    );
-  };
-
   handleActivateCreateGenesetMode = () => {
     const { dispatch } = this.props;
     dispatch({ type: "geneset: activate add new geneset mode" });
@@ -68,7 +49,6 @@ class GeneExpression extends React.Component {
           </div>
           <CreateGenesetDialogue />
         </div>
-        <div>{this.renderDiffexpGeneSets()}</div>
         <div>{this.renderGeneSets()}</div>
       </div>
     );

client/src/components/geneExpression/menus/addGenes.js

@@ -54,7 +54,6 @@ const filterGenes = (query, genes) =>
     annoMatrix: state.annoMatrix,
     userDefinedGenes: state.controls.userDefinedGenes,
     userDefinedGenesLoading: state.controls.userDefinedGenesLoading,
-    differential: state.differential,
   };
 })
 class AddGenes extends React.Component {

client/src/components/graph/graph.js

@@ -77,7 +77,6 @@ function createModelTF() {
   colors: state.colors,
   pointDilation: state.pointDilation,
   genesets: state.genesets.genesets,
-  differential: state.differential,
 }))
 class Graph extends React.Component {
   static createReglState(canvas) {
@@ -785,17 +784,11 @@ class Graph extends React.Component {
   }
 
   createColorByQuery(colors) {
-    const { annoMatrix, genesets, differential } = this.props;
+    const { annoMatrix, genesets } = this.props;
     const { schema } = annoMatrix;
     const { colorMode, colorAccessor } = colors;
 
-    return createColorQuery(
+    return createColorQuery(colorMode, colorAccessor, schema, genesets);
-      colorMode,
-      colorAccessor,
-      schema,
-      genesets,
-      differential.diffExp
-    );
   }
 
   renderPoints(

client/src/components/graph/overlays/centroidLabels.js

@@ -15,7 +15,6 @@ export default
   categoricalSelection: state.categoricalSelection,
   showLabels: state.centroidLabels?.showLabels,
   genesets: state.genesets.genesets,
-  differential: state.differential,
 }))
 class CentroidLabels extends PureComponent {
   static watchAsync(props, prevProps) {
@@ -76,16 +75,10 @@ class CentroidLabels extends PureComponent {
   };
 
   colorByQuery() {
-    const { annoMatrix, colors, genesets, differential } = this.props;
+    const { annoMatrix, colors, genesets } = this.props;
     const { schema } = annoMatrix;
     const { colorMode, colorAccessor } = colors;
-    return createColorQuery(
+    return createColorQuery(colorMode, colorAccessor, schema, genesets);
-      colorMode,
-      colorAccessor,
-      schema,
-      genesets,
-      differential.diffExp
-    );
   }
 
   async fetchData() {

client/src/components/menubar/cellSetButtons.js

@@ -9,12 +9,9 @@ import actions from "../../actions";
 }))
 class CellSetButton extends React.PureComponent {
   set() {
-    const { differential, dispatch, eitherCellSetOneOrTwo } = this.props;
+    const { dispatch, eitherCellSetOneOrTwo } = this.props;
 
-    if (!differential.diffExp) {
+    dispatch(actions.setCellSetFromSelection(eitherCellSetOneOrTwo));
-      // disallow this action if the user has active differential expression results
-      dispatch(actions.setCellSetFromSelection(eitherCellSetOneOrTwo));
-    }
   }
 
   render() {
@@ -31,7 +28,6 @@ class CellSetButton extends React.PureComponent {
       >
         <AnchorButton
           type="button"
-          disabled={differential.diffExp}
           onClick={() => {
             this.set();
           }}

client/src/components/menubar/diffexpButtons.js

@@ -1,6 +1,6 @@
 import React from "react";
 import { connect } from "react-redux";
-import { Button, ButtonGroup, AnchorButton, Tooltip } from "@blueprintjs/core";
+import { ButtonGroup, AnchorButton, Tooltip } from "@blueprintjs/core";
 import * as globals from "../../globals";
 import styles from "./menubar.css";
 import actions from "../../actions";
@@ -8,8 +8,6 @@ import CellSetButton from "./cellSetButtons";
 
 @connect((state) => ({
   differential: state.differential,
-  celllist1: state.differential?.celllist1,
-  celllist2: state.differential?.celllist2,
   diffexpMayBeSlow: state.config?.parameters?.["diffexp-may-be-slow"] ?? false,
   diffexpCellcountMax: state.config?.limits?.diffexp_cellcount_max,
 }))
@@ -26,17 +24,6 @@ class DiffexpButtons extends React.PureComponent {
     }
   };
 
-  clearDifferentialExpression = () => {
-    const { dispatch, differential } = this.props;
-    dispatch({
-      type: "clear differential expression",
-      diffExp: differential.diffExp,
-    });
-    dispatch({
-      type: "clear scatterplot",
-    });
-  };
-
   render() {
     /* diffexp-related buttons may be disabled */
     const { differential, diffexpMayBeSlow, diffexpCellcountMax } = this.props;
@@ -65,41 +52,22 @@ class DiffexpButtons extends React.PureComponent {
       <ButtonGroup className={styles.menubarButton}>
         <CellSetButton eitherCellSetOneOrTwo={1} />
         <CellSetButton eitherCellSetOneOrTwo={2} />
-        {!differential.diffExp ? (
+        <Tooltip
-          <Tooltip
+          content={warnMaxSizeExceeded ? tipMessageWarn : tipMessage}
-            content={warnMaxSizeExceeded ? tipMessageWarn : tipMessage}
+          position="bottom"
-            position="bottom"
+          hoverOpenDelay={globals.tooltipHoverOpenDelayQuick}
-            hoverOpenDelay={globals.tooltipHoverOpenDelayQuick}
+          intent={warnMaxSizeExceeded ? "danger" : "none"}
-            intent={warnMaxSizeExceeded ? "danger" : "none"}
+        >
-          >
+          <AnchorButton
-            <AnchorButton
+            disabled={!haveBothCellSets || warnMaxSizeExceeded}
-              disabled={!haveBothCellSets || warnMaxSizeExceeded}
+            intent={warnMaxSizeExceeded ? "danger" : "primary"}
-              intent={warnMaxSizeExceeded ? "danger" : "primary"}
+            data-testid="diffexp-button"
-              data-testid="diffexp-button"
+            loading={differential.loading}
-              loading={differential.loading}
+            icon="left-join"
-              icon="left-join"
+            fill
-              fill
+            onClick={this.computeDiffExp}
-              onClick={this.computeDiffExp}
+          />
-            />
+        </Tooltip>
-          </Tooltip>
-        ) : null}
-
-        {differential.diffExp ? (
-          <Tooltip
-            content="Remove differentially expressed gene list and clear cell selections"
-            position="bottom"
-            hoverOpenDelay={globals.tooltipHoverOpenDelayQuick}
-          >
-            <Button
-              type="button"
-              fill
-              intent="warning"
-              onClick={this.clearDifferentialExpression}
-            >
-              Clear Differential Expression
-            </Button>
-          </Tooltip>
-        ) : null}
       </ButtonGroup>
     );
   }

client/src/components/menubar/index.js

@@ -29,17 +29,13 @@ import { getEmbSubsetView } from "../../util/stateManager/viewStackHelpers";
   return {
     subsetPossible,
     subsetResetPossible,
-    differential: state.differential,
     graphInteractionMode: state.controls.graphInteractionMode,
     clipPercentileMin: Math.round(100 * (annoMatrix?.clipRange?.[0] ?? 0)),
     clipPercentileMax: Math.round(100 * (annoMatrix?.clipRange?.[1] ?? 1)),
     userDefinedGenes: state.controls.userDefinedGenes,
-    diffexpGenes: state.controls.diffexpGenes,
     colorAccessor: state.colors.colorAccessor,
     scatterplotXXaccessor: state.controls.scatterplotXXaccessor,
     scatterplotYYaccessor: state.controls.scatterplotYYaccessor,
-    celllist1: state.differential.celllist1,
-    celllist2: state.differential.celllist2,
     libraryVersions: state.config?.library_versions,
     auth: state.config?.authentication,
     userInfo: state.userInfo,

client/src/components/scatterplot/scatterplot.js

@@ -51,7 +51,6 @@ const getYScale = memoize(getScale);
     scatterplotXXaccessor,
     scatterplotYYaccessor,
 
-    differential: state.differential,
     crossfilter,
     genesets: state.genesets.genesets,
   };
@@ -314,16 +313,10 @@ class Scatterplot extends React.PureComponent {
   }
 
   createColorByQuery(colors) {
-    const { annoMatrix, genesets, differential } = this.props;
+    const { annoMatrix, genesets } = this.props;
     const { schema } = annoMatrix;
     const { colorMode, colorAccessor } = colors;
-    return createColorQuery(
+    return createColorQuery(colorMode, colorAccessor, schema, genesets);
-      colorMode,
-      colorAccessor,
-      schema,
-      genesets,
-      differential
-    );
   }
 
   updateColorTable(colors, colorDf) {

client/src/reducers/colors.js

@@ -7,9 +7,7 @@ const ColorsReducer = (
     colorMode: null /* by continuous, by expression */,
     colorAccessor: null /* tissue, Apod */,
   },
-  action,
+  action
-  nextSharedState,
-  prevSharedState
 ) => {
   switch (action.type) {
     case "universe: user color load success": {
@@ -20,19 +18,6 @@ const ColorsReducer = (
       };
     }
 
-    case "clear differential expression":
-    case "set clip quantiles":
-    case "subset to selection": {
-      const { controls: prevControls } = prevSharedState;
-      if (prevControls.diffexpGenes.includes(state.colorAccessor)) {
-        return {
-          colorMode: null,
-          colorAccessor: null,
-        };
-      }
-      return state;
-    }
-
     case "annotation: category edited": {
       const { colorAccessor } = state;
       if (action.metadataField !== colorAccessor) {

client/src/reducers/controls.js

@@ -1,6 +1,5 @@
 import uniq from "lodash.uniq";
 import filter from "lodash.filter";
-import { subsetAndResetGeneLists } from "../util/stateManager/controlsHelpers";
 
 const Controls = (
   state = {
@@ -11,7 +10,6 @@ const Controls = (
     // all of the data + selection state
     userDefinedGenes: [],
     userDefinedGenesLoading: false,
-    diffexpGenes: [],
 
     resettingInterface: false,
     graphInteractionMode: "select",
@@ -45,26 +43,16 @@ const Controls = (
       };
     }
     case "reset subset": {
-      const [newUserDefinedGenes, newDiffExpGenes] = subsetAndResetGeneLists(
-        state
-      );
       return {
         ...state,
         resettingInterface: false,
-        userDefinedGenes: newUserDefinedGenes,
-        diffexpGenes: newDiffExpGenes,
       };
     }
     case "subset to selection": {
-      const [newUserDefinedGenes, newDiffExpGenes] = subsetAndResetGeneLists(
-        state
-      );
       return {
         ...state,
         loading: false,
         error: null,
-        userDefinedGenes: newUserDefinedGenes,
-        diffexpGenes: newDiffExpGenes,
       };
     }
     case "request user defined gene started": {
@@ -90,19 +78,6 @@ const Controls = (
         userDefinedGenesLoading: false,
       };
     }
-    case "request differential expression success": {
-      const diffexpGenes = action.data.map((v) => v[0]);
-      return {
-        ...state,
-        diffexpGenes,
-      };
-    }
-    case "clear differential expression": {
-      return {
-        ...state,
-        diffexpGenes: [],
-      };
-    }
     case "clear user defined gene": {
       const { userDefinedGenes } = state;
       const newUserDefinedGenes = filter(

client/src/reducers/differential.js

@@ -1,6 +1,5 @@
 const Differential = (
   state = {
-    diffExp: null,
     loading: null,
     error: null,
     celllist1: null,
@@ -20,7 +19,6 @@ const Differential = (
         ...state,
         error: null,
         loading: false,
-        diffExp: action.data,
       };
     case "request differential expression error":
       return {
@@ -38,18 +36,10 @@ const Differential = (
         ...state,
         celllist2: action.data,
       };
-    case "clear differential expression":
-      return {
-        ...state,
-        diffExp: null,
-        celllist1: null,
-        celllist2: null,
-      };
     case "reset subset":
     case "subset to selection":
       return {
         ...state,
-        diffExp: null,
         celllist1: null,
         celllist2: null,
       };

client/src/reducers/genesets.js

@@ -69,6 +69,7 @@ const GeneSets = (
       }
 
       return {
+        ...state,
         initialized: true,
         lastTid,
         genesets,
@@ -353,6 +354,33 @@ const GeneSets = (
       };
     }
 
+    case "request differential expression success": {
+      const { data } = action;
+
+      const genes = new Map(
+        data.map((diffExpGene) => [
+          diffExpGene[0],
+          {
+            geneSymbol: diffExpGene[0],
+          },
+        ])
+      );
+
+      const genesetName = `DiffExp Set (${new Date().toLocaleString()})`;
+
+      const genesets = new Map(state.genesets); // clone
+      genesets.set(genesetName, {
+        genesetName,
+        genesetDescription: "",
+        genes,
+      });
+
+      return {
+        ...state,
+        genesets,
+      };
+    }
+
     default:
       return state;
   }

client/src/reducers/undoableFsm.js

@@ -185,20 +185,6 @@ const createFsmTransitions = (
       action: applyPending,
     },
 
-    /* Clear Differential Expression button user action */
-    {
-      event: "clear differential expression",
-      from: "init",
-      to: "CDE Button in progress",
-      action: stashPending,
-    },
-    {
-      event: "clear scatterplot",
-      from: "CDE Button in progress",
-      to: "done",
-      action: applyPending,
-    },
-
     /* clear scatter plot button (eg, on scatterplot view) */
     {
       event: "clear scatterplot",

client/src/util/stateManager/colorHelpers.js

@@ -12,13 +12,7 @@ import { range } from "../range";
 given a color mode & accessor, generate an annoMatrix query that will
 fulfill it
 */
-export function createColorQuery(
+export function createColorQuery(colorMode, colorByAccessor, schema, genesets) {
-  colorMode,
-  colorByAccessor,
-  schema,
-  genesets,
-  diffExp
-) {
   if (!colorMode || !colorByAccessor || !schema || !genesets) return null;
 
   switch (colorMode) {
@@ -46,19 +40,8 @@ export function createColorQuery(
       if (!varIndex) return null;
       if (!genesets) return null;
 
-      let _geneset;
+      const _geneset = genesets.get(colorByAccessor);
-      let _setGenes;
+      const _setGenes = [..._geneset.genes.keys()];
-
-      if (colorByAccessor === "Temp DiffExp Set") {
-        _geneset = diffExp;
-        _setGenes = _geneset.map((diffexpResultItem) => {
-          const geneName = diffexpResultItem[0];
-          return geneName;
-        });
-      } else {
-        _geneset = genesets.get(colorByAccessor);
-        _setGenes = [..._geneset.genes.keys()];
-      }
 
       return [
         "X",

client/src/util/stateManager/controlsHelpers.js

@@ -2,7 +2,6 @@
 Helper functions for the controls reducer
 */
 
-import uniq from "lodash.uniq";
 import difference from "lodash.difference";
 
 import * as globals from "../../globals";
@@ -158,12 +157,3 @@ export function pruneVarDataCache(varData, needed) {
   }
   return varData;
 }
-
-export function subsetAndResetGeneLists(state) {
-  const { userDefinedGenes, diffexpGenes } = state;
-  const newUserDefinedGenes = uniq(
-    [].concat(userDefinedGenes, diffexpGenes)
-  ).slice(0, globals.maxGenes);
-  const newDiffExpGenes = [];
-  return [newUserDefinedGenes, newDiffExpGenes];
-}