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
2026-09-15 12:47:56 +08:00 · 2021-05-25 10:51:31 -07:00
parent 6f6634a4d9
commit a4050f10e1
23 changed files with 21894 additions and 355 deletions
--- a/client/tests/util/stateManager/controlsHelpers.test.js
+++ b/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", () => {
-    const geneList = [];
-    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([]);
-  });
+  // TODO #2227 test: improve test coverage on control helper functions
+  // (`topNCategories()`, `isSelectableCategoryName()`, `selectableCategoryNames()`, `createCategorySummaryFromDfCol()`, `createCategoricalSelection()`, )
 });
--- a/client/package-lock.json
+++ b/client/package-lock.json
--- a/client/src/components/brushableHistogram/footer.js
+++ b/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 
-    differential expression info.
-  
+    Footer of each histogram.  Will render range and title.
+
    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>
    );
  }
--- a/client/src/components/brushableHistogram/index.js
+++ b/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
-                    ? "histogram-diffexp"
-                    : isUserDefined
+                  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>
--- a/client/src/components/categorical/category/index.js
+++ b/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,
-        differential.diffExp
+        genesets
      );
      if (query) colorDataPromise = annoMatrix.fetch(...query);
    }
--- a/client/src/components/continuousLegend/index.js
+++ b/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,
-        differential.diffExp
+        genesets
      );

      const colorDf = colorQuery ? await annoMatrix.fetch(...colorQuery) : null;
--- a/client/src/components/geneExpression/gene.js
+++ b/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 isDiffExp field={gene} mini />
-              ) : (
-                <HistogramBrush isUserDefined field={gene} mini />
-              )
+              <HistogramBrush isUserDefined field={gene} mini />
            ) : null}
          </div>
          <div style={{ flexShrink: 0, marginLeft: 2 }}>
-            {!isDiffExp ? (
-              <AnchorButton
-                minimal
-                small
-                data-testid={`delete-from-geneset-${gene}`}
-                onClick={this.handleDeleteGeneFromSet}
-                intent="none"
-                style={{ fontWeight: 700, marginRight: 2 }}
-                icon={<Icon icon="trash" iconSize={10} />}
-              />
-            ) : null}
+            <AnchorButton
+              minimal
+              small
+              data-testid={`delete-from-geneset-${gene}`}
+              onClick={this.handleDeleteGeneFromSet}
+              intent="none"
+              style={{ fontWeight: 700, marginRight: 2 }}
+              icon={<Icon icon="trash" iconSize={10} />}
+            />
+            )
            <AnchorButton
              minimal
              small
@@ -184,17 +176,7 @@ class Gene extends React.Component {
            />
          </div>
        </div>
-        {geneIsExpanded &&
-          (isDiffExp ? (
-            <HistogramBrush
-              isDiffExp
-              field={gene}
-              pvalAdj={pvalAdj}
-              logFoldChange={logFoldChange}
-            />
-          ) : (
-            <HistogramBrush isUserDefined field={gene} />
-          ))}
+        {geneIsExpanded && <HistogramBrush isUserDefined field={gene} />}
      </div>
    );
  }
--- a/client/src/components/geneExpression/geneSet.js
+++ b/client/src/components/geneExpression/geneSet.js
@@ -79,33 +79,8 @@ class GeneSet extends React.Component {
  };

  renderGenes() {
-    const {
-      setName,
-      setGenes,
-      setGenesWithDescriptions,
-      isDiffExp,
-      diffExp,
-    } = this.props;
+    const { setName, setGenes, setGenesWithDescriptions } = 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);

--- a/client/src/components/geneExpression/index.js
+++ b/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>
    );
--- a/client/src/components/geneExpression/menus/addGenes.js
+++ b/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 {
--- a/client/src/components/graph/graph.js
+++ b/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(
-      colorMode,
-      colorAccessor,
-      schema,
-      genesets,
-      differential.diffExp
-    );
+    return createColorQuery(colorMode, colorAccessor, schema, genesets);
  }

  renderPoints(
--- a/client/src/components/graph/overlays/centroidLabels.js
+++ b/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(
-      colorMode,
-      colorAccessor,
-      schema,
-      genesets,
-      differential.diffExp
-    );
+    return createColorQuery(colorMode, colorAccessor, schema, genesets);
  }

  async fetchData() {
--- a/client/src/components/menubar/cellSetButtons.js
+++ b/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) {
-      // disallow this action if the user has active differential expression results
-      dispatch(actions.setCellSetFromSelection(eitherCellSetOneOrTwo));
-    }
+    dispatch(actions.setCellSetFromSelection(eitherCellSetOneOrTwo));
  }

  render() {
@@ -31,7 +28,6 @@ class CellSetButton extends React.PureComponent {
      >
        <AnchorButton
          type="button"
-          disabled={differential.diffExp}
          onClick={() => {
            this.set();
          }}
--- a/client/src/components/menubar/diffexpButtons.js
+++ b/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
-            content={warnMaxSizeExceeded ? tipMessageWarn : tipMessage}
-            position="bottom"
-            hoverOpenDelay={globals.tooltipHoverOpenDelayQuick}
-            intent={warnMaxSizeExceeded ? "danger" : "none"}
-          >
-            <AnchorButton
-              disabled={!haveBothCellSets || warnMaxSizeExceeded}
-              intent={warnMaxSizeExceeded ? "danger" : "primary"}
-              data-testid="diffexp-button"
-              loading={differential.loading}
-              icon="left-join"
-              fill
-              onClick={this.computeDiffExp}
-            />
-          </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}
+        <Tooltip
+          content={warnMaxSizeExceeded ? tipMessageWarn : tipMessage}
+          position="bottom"
+          hoverOpenDelay={globals.tooltipHoverOpenDelayQuick}
+          intent={warnMaxSizeExceeded ? "danger" : "none"}
+        >
+          <AnchorButton
+            disabled={!haveBothCellSets || warnMaxSizeExceeded}
+            intent={warnMaxSizeExceeded ? "danger" : "primary"}
+            data-testid="diffexp-button"
+            loading={differential.loading}
+            icon="left-join"
+            fill
+            onClick={this.computeDiffExp}
+          />
+        </Tooltip>
      </ButtonGroup>
    );
  }
--- a/client/src/components/menubar/index.js
+++ b/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,
--- a/client/src/components/scatterplot/scatterplot.js
+++ b/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(
-      colorMode,
-      colorAccessor,
-      schema,
-      genesets,
-      differential
-    );
+    return createColorQuery(colorMode, colorAccessor, schema, genesets);
  }

  updateColorTable(colors, colorDf) {
--- a/client/src/reducers/colors.js
+++ b/client/src/reducers/colors.js
@@ -7,9 +7,7 @@ const ColorsReducer = (
    colorMode: null /* by continuous, by expression */,
    colorAccessor: null /* tissue, Apod */,
  },
-  action,
-  nextSharedState,
-  prevSharedState
+  action
 ) => {
  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) {
--- a/client/src/reducers/controls.js
+++ b/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(
--- a/client/src/reducers/differential.js
+++ b/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,
      };
--- a/client/src/reducers/genesets.js
+++ b/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;
  }
--- a/client/src/reducers/undoableFsm.js
+++ b/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",
--- a/client/src/util/stateManager/colorHelpers.js
+++ b/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(
-  colorMode,
-  colorByAccessor,
-  schema,
-  genesets,
-  diffExp
-) {
+export function createColorQuery(colorMode, colorByAccessor, schema, genesets) {
  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;
-      let _setGenes;
-
-      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()];
-      }
+      const _geneset = genesets.get(colorByAccessor);
+      const _setGenes = [..._geneset.genes.keys()];

      return [
        "X",
--- a/client/src/util/stateManager/controlsHelpers.js
+++ b/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];
-}