From f423da270331b7226a6cdfb51a7a567b71a3ed8b Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Tue, 28 Oct 2025 17:50:07 -0400
Subject: [PATCH 01/10] add draft dimensionality reduction compute

---
 .../plugins/dimensionalityReduction.tsx       | 171 ++++++++++++++++++
 .../components/computations/plugins/index.ts  |   2 +
 2 files changed, 173 insertions(+)
 create mode 100644 packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
new file mode 100644
index 0000000000..566f7280ae
--- /dev/null
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
@@ -0,0 +1,171 @@
+import { useFindEntityAndVariableCollection } from '../../..';
+import { VariableCollectionDescriptor } from '../../../types/variable';
+import { scatterplotVisualization } from '../../visualizations/implementations/ScatterplotVisualization';
+import { ComputationConfigProps, ComputationPlugin } from '../Types';
+import { partial } from 'lodash';
+import {
+  useConfigChangeHandler,
+  assertComputationWithConfig,
+  isNotAbsoluteAbundanceVariableCollection,
+  partialToCompleteCodec,
+} from '../Utils';
+import * as t from 'io-ts';
+import { Computation } from '../../../types/visualization';
+import SingleSelect from '@veupathdb/coreui/lib/components/inputs/SingleSelect';
+import { useMemo } from 'react';
+import ScatterBetadivSVG from '../../visualizations/implementations/selectorIcons/ScatterBetadivSVG';
+import { ComputationStepContainer } from '../ComputationStepContainer';
+import './Plugins.scss';
+import { makeClassNameHelper } from '@veupathdb/wdk-client/lib/Utils/ComponentUtils';
+import { VariableCollectionSingleSelect } from '../../variableSelectors/VariableCollectionSingleSelect';
+import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
+import { entityTreeToArray } from '../../../utils/study-metadata';
+
+const cx = makeClassNameHelper('AppStepConfigurationContainer');
+
+export type DimensionalityReductionConfig = t.TypeOf<
+  typeof DimensionalityReductionConfig
+>;
+// eslint-disable-next-line @typescript-eslint/no-redeclare
+export const DimensionalityReductionConfig = t.partial({
+  collectionVariable: VariableCollectionDescriptor,
+});
+
+const CompleteDimensionalityReductionConfig = partialToCompleteCodec(
+  DimensionalityReductionConfig
+);
+
+export const plugin: ComputationPlugin = {
+  configurationComponent: DimensionalityReductionConfiguration,
+  configurationDescriptionComponent:
+    DimensionalityReductionConfigDescriptionComponent,
+  createDefaultConfiguration: () => ({}),
+  isConfigurationComplete: CompleteDimensionalityReductionConfig.is,
+  visualizationPlugins: {
+    scatterplot: scatterplotVisualization
+      .withOptions({
+        getComputedXAxisDetails(config) {
+          if (
+            DimensionalityReductionConfig.is(config) &&
+            config.collectionVariable
+          ) {
+            return {
+              entityId: config.collectionVariable.entityId,
+              placeholderDisplayName: 'PCA Axis 1',
+              variableId: 'Axis1',
+            };
+          }
+        },
+        getComputedYAxisDetails(config) {
+          if (
+            DimensionalityReductionConfig.is(config) &&
+            config.collectionVariable
+          ) {
+            return {
+              entityId: config.collectionVariable.entityId,
+              placeholderDisplayName: 'PCA Axis 2',
+              variableId: 'Axis2',
+            };
+          }
+        },
+        hideShowMissingnessToggle: true,
+        hideTrendlines: true,
+        hideFacetInputs: true,
+        hideLogScale: true,
+        returnPointIds: false,
+      })
+      .withSelectorIcon(ScatterBetadivSVG),
+  },
+  isEnabledInPicker: isEnabledInPicker,
+  studyRequirements:
+    'These visualizations are only available for studies with compatible assay data.',
+};
+
+function DimensionalityReductionConfigDescriptionComponent({
+  computation,
+}: {
+  computation: Computation;
+}) {
+  const findEntityAndVariableCollection = useFindEntityAndVariableCollection();
+  assertComputationWithConfig(computation, DimensionalityReductionConfig);
+  const { configuration } = computation.descriptor;
+  const collectionVariable =
+    'collectionVariable' in configuration
+      ? configuration.collectionVariable
+      : undefined;
+  const updatedCollectionVariable =
+    findEntityAndVariableCollection(collectionVariable);
+
+  return (
+    <div className="ConfigDescriptionContainer">
+      <h4>
+        Data:{' '}
+        <span>
+          {updatedCollectionVariable ? (
+            `${updatedCollectionVariable.entity.displayName} > ${updatedCollectionVariable.variableCollection.displayName}`
+          ) : (
+            <i>Not selected</i>
+          )}
+        </span>
+      </h4>
+    </div>
+  );
+}
+
+export function DimensionalityReductionConfiguration(
+  props: ComputationConfigProps
+) {
+  const {
+    computationAppOverview,
+    computation,
+    analysisState,
+    visualizationId,
+  } = props;
+  assertComputationWithConfig(computation, DimensionalityReductionConfig);
+  const configuration = computation.descriptor.configuration;
+
+  const changeConfigHandler = useConfigChangeHandler(
+    analysisState,
+    computation,
+    visualizationId
+  );
+
+  return (
+    <ComputationStepContainer
+      computationStepInfo={{
+        stepNumber: 1,
+        stepTitle: `Configure ${computationAppOverview.displayName}`,
+      }}
+    >
+      <div className={cx()}>
+        <div className={cx('-InputContainer')}>
+          <span>Data</span>
+          <VariableCollectionSingleSelect
+            value={configuration.collectionVariable}
+            onSelect={(value) => {
+              if (typeof value === 'string') return;
+              changeConfigHandler('collectionVariable', value);
+            }}
+            collectionPredicate={isNotAbsoluteAbundanceVariableCollection}
+          />
+        </div>
+      </div>
+    </ComputationStepContainer>
+  );
+}
+
+// Beta div's only requirement of the study is that it contains
+// at least one collection
+function isEnabledInPicker({
+  studyMetadata,
+}: IsEnabledInPickerParams): boolean {
+  if (!studyMetadata) return false;
+  const entities = entityTreeToArray(studyMetadata.rootEntity);
+
+  // Ensure there are collections in this study. Otherwise, disable app
+  const studyHasCollections = entities.some(
+    (entity) => !!entity.collections?.length
+  );
+
+  return studyHasCollections;
+}
diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts b/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
index 58053638d3..a3d3186995 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
@@ -11,10 +11,12 @@ import { plugin as correlationassayassay } from './correlationAssayAssay'; // mb
 import { plugin as correlation } from './correlation'; // genomics (- vb)
 import { plugin as selfcorrelation } from './selfCorrelation';
 import { plugin as xyrelationships } from './xyRelationships';
+import { plugin as dimensionalityreduction } from './dimensionalityReduction';
 export const plugins: Record<string, ComputationPlugin> = {
   abundance,
   alphadiv,
   betadiv,
+  dimensionalityreduction,
   differentialabundance,
   correlationassaymetadata,
   correlationassayassay,

From f844bbb7a75edd69ccc14586b4267c530c1974a3 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Wed, 29 Oct 2025 13:24:34 -0400
Subject: [PATCH 02/10] working pca plot

---
 .../computations/plugins/dimensionalityReduction.tsx        | 5 +++--
 .../implementations/ScatterplotVisualization.tsx            | 6 ++++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
index 566f7280ae..9c2daae0ce 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
@@ -20,6 +20,7 @@ import { makeClassNameHelper } from '@veupathdb/wdk-client/lib/Utils/ComponentUt
 import { VariableCollectionSingleSelect } from '../../variableSelectors/VariableCollectionSingleSelect';
 import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
 import { entityTreeToArray } from '../../../utils/study-metadata';
+import { InputSpec } from '../../visualizations/InputVariables';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -52,7 +53,7 @@ export const plugin: ComputationPlugin = {
             return {
               entityId: config.collectionVariable.entityId,
               placeholderDisplayName: 'PCA Axis 1',
-              variableId: 'Axis1',
+              variableId: 'PC1',
             };
           }
         },
@@ -64,7 +65,7 @@ export const plugin: ComputationPlugin = {
             return {
               entityId: config.collectionVariable.entityId,
               placeholderDisplayName: 'PCA Axis 2',
-              variableId: 'Axis2',
+              variableId: 'PC2',
             };
           }
         },
diff --git a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
index 668981259d..1455233613 100755
--- a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
+++ b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
@@ -354,6 +354,8 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
       }
     : null;
 
+  console.log('computedXAxisDescriptor:', computedXAxisDescriptor);
+
   // When we only have a computed y axis (and no provided overlay) then the y axis var
   // can have a "normal" variable descriptor. See abundance app for the funny case of handeling a computed overlay.
   const computedYAxisDescriptor = computedYAxisDetails
@@ -745,8 +747,8 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
         config: {
           outputEntityId: outputEntity.id,
           valueSpec: hideTrendlines ? undefined : valueSpecValue,
-          xAxisVariable: vizConfig.xAxisVariable,
-          yAxisVariable: vizConfig.yAxisVariable,
+          xAxisVariable: computedXAxisDescriptor ?? vizConfig.xAxisVariable,
+          yAxisVariable: computedYAxisDescriptor ?? vizConfig.yAxisVariable,
           overlayVariable: vizConfig.overlayVariable,
           facetVariable: vizConfig.facetVariable
             ? [vizConfig.facetVariable]

From eef9f722016dee886888d98ded0bfec316b659f2 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Mon, 3 Nov 2025 15:09:23 -0500
Subject: [PATCH 03/10] add sendComputedVariablesInRequest to Options

---
 .../computations/plugins/dimensionalityReduction.tsx  |  1 +
 .../implementations/ScatterplotVisualization.tsx      | 11 +++++++++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
index 9c2daae0ce..a19b266c22 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
@@ -74,6 +74,7 @@ export const plugin: ComputationPlugin = {
         hideFacetInputs: true,
         hideLogScale: true,
         returnPointIds: false,
+        sendComputedVariablesInRequest: true,
       })
       .withSelectorIcon(ScatterBetadivSVG),
   },
diff --git a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
index 1455233613..90e8d2f9be 100755
--- a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
+++ b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
@@ -286,6 +286,7 @@ interface Options
   hideTrendlines?: boolean;
   hideLogScale?: boolean;
   returnPointIds?: boolean; // Determines whether the backend should return the ids of each point in the scatterplot
+  sendComputedVariablesInRequest?: boolean; // Determines whether computed variable descriptors should be sent to the backend in the data request.
 }
 
 function ScatterplotViz(props: VisualizationProps<Options>) {
@@ -332,6 +333,7 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
     computedYAxisDetails,
     computedOverlayVariableDescriptor,
     providedOverlayVariableDescriptor,
+    sendComputedVariablesInRequest,
   ] = useMemo(
     () => [
       options?.getComputedXAxisDetails?.(computation.descriptor.configuration),
@@ -340,6 +342,7 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
         computation.descriptor.configuration
       ),
       options?.getOverlayVariable?.(computation.descriptor.configuration),
+      options?.sendComputedVariablesInRequest ?? false,
     ],
     [computation.descriptor.configuration, options]
   );
@@ -747,8 +750,12 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
         config: {
           outputEntityId: outputEntity.id,
           valueSpec: hideTrendlines ? undefined : valueSpecValue,
-          xAxisVariable: computedXAxisDescriptor ?? vizConfig.xAxisVariable,
-          yAxisVariable: computedYAxisDescriptor ?? vizConfig.yAxisVariable,
+          xAxisVariable:
+            (sendComputedVariablesInRequest && computedXAxisDescriptor) ||
+            vizConfig.xAxisVariable,
+          yAxisVariable:
+            (sendComputedVariablesInRequest && computedYAxisDescriptor) ||
+            vizConfig.yAxisVariable,
           overlayVariable: vizConfig.overlayVariable,
           facetVariable: vizConfig.facetVariable
             ? [vizConfig.facetVariable]

From 44517294c570b5c46d9a2d1dffecc89aba65a252 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Tue, 4 Nov 2025 18:18:37 -0500
Subject: [PATCH 04/10] cleanup

---
 .../visualizations/implementations/ScatterplotVisualization.tsx | 2 --
 1 file changed, 2 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
index 90e8d2f9be..3ed262469c 100755
--- a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
+++ b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
@@ -357,8 +357,6 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
       }
     : null;
 
-  console.log('computedXAxisDescriptor:', computedXAxisDescriptor);
-
   // When we only have a computed y axis (and no provided overlay) then the y axis var
   // can have a "normal" variable descriptor. See abundance app for the funny case of handeling a computed overlay.
   const computedYAxisDescriptor = computedYAxisDetails

From 730c393654dd77e25c61cd74ecb573770044b709 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Wed, 5 Nov 2025 10:24:23 -0500
Subject: [PATCH 05/10] cleanup

---
 .../computations/plugins/dimensionalityReduction.tsx   |  8 ++------
 .../implementations/ScatterplotVisualization.tsx       | 10 ++++++----
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
index a19b266c22..e7f5de413e 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
@@ -2,7 +2,6 @@ import { useFindEntityAndVariableCollection } from '../../..';
 import { VariableCollectionDescriptor } from '../../../types/variable';
 import { scatterplotVisualization } from '../../visualizations/implementations/ScatterplotVisualization';
 import { ComputationConfigProps, ComputationPlugin } from '../Types';
-import { partial } from 'lodash';
 import {
   useConfigChangeHandler,
   assertComputationWithConfig,
@@ -11,8 +10,6 @@ import {
 } from '../Utils';
 import * as t from 'io-ts';
 import { Computation } from '../../../types/visualization';
-import SingleSelect from '@veupathdb/coreui/lib/components/inputs/SingleSelect';
-import { useMemo } from 'react';
 import ScatterBetadivSVG from '../../visualizations/implementations/selectorIcons/ScatterBetadivSVG';
 import { ComputationStepContainer } from '../ComputationStepContainer';
 import './Plugins.scss';
@@ -20,7 +17,6 @@ import { makeClassNameHelper } from '@veupathdb/wdk-client/lib/Utils/ComponentUt
 import { VariableCollectionSingleSelect } from '../../variableSelectors/VariableCollectionSingleSelect';
 import { IsEnabledInPickerParams } from '../../visualizations/VisualizationTypes';
 import { entityTreeToArray } from '../../../utils/study-metadata';
-import { InputSpec } from '../../visualizations/InputVariables';
 
 const cx = makeClassNameHelper('AppStepConfigurationContainer');
 
@@ -156,8 +152,8 @@ export function DimensionalityReductionConfiguration(
   );
 }
 
-// Beta div's only requirement of the study is that it contains
-// at least one collection
+// Dimensionality reduction's only requirement of the study is that it contains
+// at least one collection.
 function isEnabledInPicker({
   studyMetadata,
 }: IsEnabledInPickerParams): boolean {
diff --git a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
index 3ed262469c..8ed978d7aa 100755
--- a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
+++ b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
@@ -749,11 +749,13 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
           outputEntityId: outputEntity.id,
           valueSpec: hideTrendlines ? undefined : valueSpecValue,
           xAxisVariable:
-            (sendComputedVariablesInRequest && computedXAxisDescriptor) ||
-            vizConfig.xAxisVariable,
+            sendComputedVariablesInRequest && computedXAxisDescriptor
+              ? computedXAxisDescriptor
+              : vizConfig.xAxisVariable,
           yAxisVariable:
-            (sendComputedVariablesInRequest && computedYAxisDescriptor) ||
-            vizConfig.yAxisVariable,
+            sendComputedVariablesInRequest && computedYAxisDescriptor
+              ? computedYAxisDescriptor
+              : vizConfig.yAxisVariable,
           overlayVariable: vizConfig.overlayVariable,
           facetVariable: vizConfig.facetVariable
             ? [vizConfig.facetVariable]

From e079883ae27bcfd4444e6af41f1c5fd4a021cfc9 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Tue, 11 Nov 2025 16:56:38 -0500
Subject: [PATCH 06/10] dual compute notebook success

---
 .../plugins/dimensionalityReduction.tsx            |  7 ++++++-
 .../eda/src/lib/notebook/ComputeNotebookCell.tsx   | 14 ++++++++++++--
 .../eda/src/lib/notebook/EdaNotebookAnalysis.tsx   |  3 +++
 .../libs/eda/src/lib/notebook/NotebookPresets.tsx  | 14 ++++++++++++++
 .../libs/eda/src/lib/notebook/NotebookRoute.tsx    |  2 +-
 5 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
index e7f5de413e..351e6c6e0a 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
@@ -118,16 +118,21 @@ export function DimensionalityReductionConfiguration(
     computation,
     analysisState,
     visualizationId,
+    changeConfigHandlerOverride,
   } = props;
   assertComputationWithConfig(computation, DimensionalityReductionConfig);
   const configuration = computation.descriptor.configuration;
 
-  const changeConfigHandler = useConfigChangeHandler(
+  const workspaceChangeConfigHandler = useConfigChangeHandler(
     analysisState,
     computation,
     visualizationId
   );
 
+  const changeConfigHandler = changeConfigHandlerOverride
+    ? changeConfigHandlerOverride
+    : workspaceChangeConfigHandler;
+
   return (
     <ComputationStepContainer
       computationStepInfo={{
diff --git a/packages/libs/eda/src/lib/notebook/ComputeNotebookCell.tsx b/packages/libs/eda/src/lib/notebook/ComputeNotebookCell.tsx
index 059aabd431..dc93b01ada 100644
--- a/packages/libs/eda/src/lib/notebook/ComputeNotebookCell.tsx
+++ b/packages/libs/eda/src/lib/notebook/ComputeNotebookCell.tsx
@@ -15,6 +15,7 @@ export function ComputeNotebookCell(
   const { analysisState, cell, isDisabled, wdkState, projectId } = props;
   const { analysis } = analysisState;
   if (analysis == null) throw new Error('Cannot find analysis.');
+  console.log('compute name', cell.computationName);
 
   const {
     computationName,
@@ -48,6 +49,7 @@ export function ComputeNotebookCell(
   // Ideally it should also use the functional update form of setComputations.
   //
   // We'll use a special, simple changeConfigHandler for the computation configuration
+  console.log('analysis', analysis.descriptor.computations);
   const changeConfigHandler = (propertyName: string, value?: any) => {
     if (!computation || !analysis.descriptor.computations[0]) return;
 
@@ -61,7 +63,9 @@ export function ComputeNotebookCell(
 
     const existingComputation =
       analysisState.analysis?.descriptor.computations.find(
-        (comp) => isEqual(comp.descriptor.configuration, updatedConfiguration) //&&
+        (comp) =>
+          isEqual(comp.computationId, computationId) &&
+          isEqual(comp.descriptor.configuration, updatedConfiguration)
       );
 
     if (existingComputation) return;
@@ -74,7 +78,13 @@ export function ComputeNotebookCell(
       },
     };
 
-    analysisState.setComputations([updatedComputation]);
+    analysisState.setComputations((computations) => {
+      return computations.map((comp) =>
+        comp.computationId === computation.computationId
+          ? updatedComputation
+          : comp
+      );
+    });
   };
 
   const { jobStatus, createJob } = useComputeJobStatus(
diff --git a/packages/libs/eda/src/lib/notebook/EdaNotebookAnalysis.tsx b/packages/libs/eda/src/lib/notebook/EdaNotebookAnalysis.tsx
index a1292bd74b..8b94fac591 100644
--- a/packages/libs/eda/src/lib/notebook/EdaNotebookAnalysis.tsx
+++ b/packages/libs/eda/src/lib/notebook/EdaNotebookAnalysis.tsx
@@ -118,8 +118,11 @@ export function EdaNotebookAnalysis(props: Props) {
     // This ensures that updates are queued and applied in order, even across
     // multiple recursive calls.
     notebookPreset.cells.forEach((cell) => processCell(cell));
+    console.log('createdcells');
   }, [analysis, setComputations, addVisualization, notebookPreset]);
 
+  console.log('notebookpreset', notebookPreset);
+
   //
   // Now we render the notebook directly from the read-only `notebookPreset`,
   // fetching computations and visualizations from analysisState.analysis where needed.
diff --git a/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx b/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
index f2c5f3731b..9649149d9a 100644
--- a/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
+++ b/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
@@ -81,6 +81,20 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
     displayName: 'Differential Abundance Notebook',
     projects: ['MicrobiomeDB'],
     cells: [
+      {
+        type: 'compute',
+        title: 'PCA',
+        computationName: 'dimensionalityreduction',
+        computationId: 'pca_1',
+        cells: [
+          {
+            type: 'visualization',
+            title: 'PCA Plot',
+            visualizationName: 'scatterplot',
+            visualizationId: 'pca_1',
+          },
+        ],
+      },
       {
         type: 'compute',
         title: 'Differential Abundance',
diff --git a/packages/libs/eda/src/lib/notebook/NotebookRoute.tsx b/packages/libs/eda/src/lib/notebook/NotebookRoute.tsx
index a99ab74dd2..62398ff1fd 100644
--- a/packages/libs/eda/src/lib/notebook/NotebookRoute.tsx
+++ b/packages/libs/eda/src/lib/notebook/NotebookRoute.tsx
@@ -70,7 +70,7 @@ export default function NotebookRoute(props: Props) {
               >
                 <EdaNotebookAnalysis
                   analysisState={analysisState}
-                  notebookType="wgcnaCorrelationNotebook"
+                  notebookType="differentialAbundanceNotebook"
                   wdkState={{}}
                 />
               </EDAWorkspaceContainer>

From 6082e20ed17c0e808620a611e44ef8954ecb9d4b Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Wed, 12 Nov 2025 09:35:11 -0500
Subject: [PATCH 07/10] show step number and helper text for pca

---
 .../computations/plugins/dimensionalityReduction.tsx  |  2 ++
 .../libs/eda/src/lib/notebook/NotebookPresets.tsx     | 11 ++++++++++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
index 351e6c6e0a..71ed6b531f 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx
@@ -119,6 +119,7 @@ export function DimensionalityReductionConfiguration(
     analysisState,
     visualizationId,
     changeConfigHandlerOverride,
+    showStepNumber = true,
   } = props;
   assertComputationWithConfig(computation, DimensionalityReductionConfig);
   const configuration = computation.descriptor.configuration;
@@ -139,6 +140,7 @@ export function DimensionalityReductionConfiguration(
         stepNumber: 1,
         stepTitle: `Configure ${computationAppOverview.displayName}`,
       }}
+      showStepNumber={showStepNumber}
     >
       <div className={cx()}>
         <div className={cx('-InputContainer')}>
diff --git a/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx b/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
index 9649149d9a..7cdc1145f6 100644
--- a/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
+++ b/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
@@ -83,9 +83,18 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
     cells: [
       {
         type: 'compute',
-        title: 'PCA',
+        title: 'Configure PCA',
         computationName: 'dimensionalityreduction',
         computationId: 'pca_1',
+        helperText: (
+          <NumberedHeader
+            number={1}
+            text={
+              'Use PCA to investigate possible sources of variation in the dataset.'
+            }
+            color={colors.grey[800]}
+          />
+        ),
         cells: [
           {
             type: 'visualization',

From 749db05d9e594f9a076927195869cea03d9dcb61 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Thu, 4 Dec 2025 18:44:49 -0500
Subject: [PATCH 08/10] update differential expression notebook to include pca

---
 .../components/computations/plugins/index.ts   |  4 ++--
 .../eda/src/lib/notebook/NotebookPresets.tsx   | 18 +++++++++---------
 .../eda/src/lib/notebook/TextNotebookCell.tsx  |  8 +++++++-
 3 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts b/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
index 6ab384e7e2..9ba9bd4f22 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
@@ -6,7 +6,7 @@ import { plugin as distributions } from './distributions';
 import { plugin as countsandproportions } from './countsAndProportions';
 import { plugin as abundance } from './abundance';
 import { plugin as differentialabundance } from './differentialabundance';
-// import { plugin as differentialexpression } from './differentialExpression';
+import { plugin as differentialexpression } from './differentialExpression';
 import { plugin as correlationassaymetadata } from './correlationAssayMetadata'; // mbio
 import { plugin as correlationassayassay } from './correlationAssayAssay'; // mbio
 import { plugin as correlation } from './correlation'; // genomics (- vb)
@@ -19,7 +19,7 @@ export const plugins: Record<string, ComputationPlugin> = {
   betadiv,
   dimensionalityreduction,
   differentialabundance,
-  // differentialexpression,
+  differentialexpression,
   correlationassaymetadata,
   correlationassayassay,
   correlation,
diff --git a/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx b/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
index 30bc4ac306..5aed8168c1 100644
--- a/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
+++ b/packages/libs/eda/src/lib/notebook/NotebookPresets.tsx
@@ -129,7 +129,7 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
           <NumberedHeader
             number={2}
             text={
-              'Run a differential expression analysis using DESeq2.Please choose the metadata variable for comparison, and then set up the reference and comparison groups. When all selections have been made, we can run the computation.'
+              'Run a differential expression analysis using DESeq2. Please choose the metadata variable for comparison, and then set up the reference and comparison groups. When all selections have been made, we can run the computation.'
             }
             color={colors.grey[800]}
           />
@@ -177,7 +177,7 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
             },
             helperText: (
               <NumberedHeader
-                number={2}
+                number={3}
                 text={
                   'Once the DESeq2 results are ready, a volcano plot will appear below. Set the threshold lines to color the genes based on their significance and fold change.'
                 }
@@ -190,7 +190,7 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
             title: 'Review and run search',
             helperText: (
               <NumberedHeader
-                number={3}
+                number={4}
                 text={
                   'After identifying genes of interest from the volcano plot, run a gene search to review the genes in the Gene Search Results table.'
                 }
@@ -216,15 +216,15 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
               if (!analysisState.analysis?.descriptor?.computations?.length) {
                 return <div>No analysis configuration available</div>;
               }
-              const computation =
-                analysisState.analysis.descriptor.computations[0];
-              if (!computation?.visualizations?.length) {
+              const differentialExpressionComputation =
+                analysisState.analysis.descriptor.computations[1];
+              if (!differentialExpressionComputation?.visualizations?.length) {
                 return <div>No visualization configuration available</div>;
               }
 
               const volcanoPlotConfig =
-                analysisState.analysis?.descriptor.computations[0]
-                  .visualizations[0].descriptor.configuration;
+                differentialExpressionComputation.visualizations[0].descriptor
+                  .configuration;
 
               if (
                 !volcanoPlotConfig ||
@@ -262,7 +262,7 @@ export const presetNotebooks: Record<string, PresetNotebook> = {
                     }}
                   >
                     To make adjustments, update the volcano plot settings in
-                    step 2.
+                    step 3.
                   </span>
                 </div>
               );
diff --git a/packages/libs/eda/src/lib/notebook/TextNotebookCell.tsx b/packages/libs/eda/src/lib/notebook/TextNotebookCell.tsx
index 1413484c70..123c0343f2 100644
--- a/packages/libs/eda/src/lib/notebook/TextNotebookCell.tsx
+++ b/packages/libs/eda/src/lib/notebook/TextNotebookCell.tsx
@@ -1,12 +1,18 @@
 import ExpandablePanel from '@veupathdb/coreui/lib/components/containers/ExpandablePanel';
 import { NotebookCellProps } from './NotebookCell';
 import { TextCellDescriptor } from './NotebookPresets';
+import { useMemo } from 'react';
 
 export function TextNotebookCell(props: NotebookCellProps<TextCellDescriptor>) {
   const { cell, isDisabled, analysisState } = props;
 
   const { text, title, getDynamicContent } = cell;
 
+  const dynamicContent = useMemo(
+    () => getDynamicContent?.(analysisState),
+    [getDynamicContent, analysisState]
+  );
+
   return (
     <>
       {cell.helperText && (
@@ -24,7 +30,7 @@ export function TextNotebookCell(props: NotebookCellProps<TextCellDescriptor>) {
           className={'NotebookCellContent' + (isDisabled ? ' disabled' : '')}
         >
           {text}
-          {getDynamicContent && getDynamicContent(analysisState)}
+          {dynamicContent}
         </div>
       </ExpandablePanel>
     </>

From 931bfe82c6be2441608fdb6245fe828b190287b1 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Mon, 8 Dec 2025 12:16:27 -0500
Subject: [PATCH 09/10] ensure consistent calculation of axis variables

---
 .../computations/plugins/differentialExpression.tsx    |  3 +--
 .../implementations/ScatterplotVisualization.tsx       | 10 ++++++++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/differentialExpression.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/differentialExpression.tsx
index cf08770928..a4e0ef1765 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/differentialExpression.tsx
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/differentialExpression.tsx
@@ -2,7 +2,6 @@ import {
   ContinuousVariableDataShape,
   DistributionResponse,
   LabeledRange,
-  usePromise,
   useStudyMetadata,
 } from '../../..';
 import {
@@ -25,7 +24,7 @@ import {
   useFindEntityAndVariableCollection,
   useSubsettingClient,
 } from '../../../hooks/workspace';
-import { ReactNode, useCallback, useEffect, useMemo, useRef } from 'react';
+import { ReactNode, useEffect, useMemo, useRef } from 'react';
 import { ComputationStepContainer } from '../ComputationStepContainer';
 import VariableTreeDropdown from '../../variableSelectors/VariableTreeDropdown';
 import { ValuePicker } from '../../visualizations/implementations/ValuePicker';
diff --git a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
index 8ed978d7aa..2a728dd982 100755
--- a/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
+++ b/packages/libs/eda/src/lib/core/components/visualizations/implementations/ScatterplotVisualization.tsx
@@ -379,8 +379,14 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
   // variables within a viz. Computed overlay was left out intentionally to retain
   // desired behavior (see PR #38).
   const variablesForConstraints = useDeepValue({
-    xAxisVariable: computedXAxisDescriptor ?? vizConfig.xAxisVariable,
-    yAxisVariable: computedYAxisDescriptor ?? vizConfig.yAxisVariable,
+    xAxisVariable:
+      sendComputedVariablesInRequest && computedXAxisDescriptor
+        ? computedXAxisDescriptor
+        : vizConfig.xAxisVariable,
+    yAxisVariable:
+      sendComputedVariablesInRequest && computedYAxisDescriptor
+        ? computedYAxisDescriptor
+        : vizConfig.yAxisVariable,
     overlayVariable:
       vizConfig.overlayVariable &&
       (providedOverlayVariableDescriptor ?? vizConfig.overlayVariable),

From 955831643cd7306694d4e331846e80006d265e5e Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Mon, 8 Dec 2025 12:17:05 -0500
Subject: [PATCH 10/10] temporarily turn off differentialexpression

---
 .../eda/src/lib/core/components/computations/plugins/index.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts b/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
index 9ba9bd4f22..6ab384e7e2 100644
--- a/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
+++ b/packages/libs/eda/src/lib/core/components/computations/plugins/index.ts
@@ -6,7 +6,7 @@ import { plugin as distributions } from './distributions';
 import { plugin as countsandproportions } from './countsAndProportions';
 import { plugin as abundance } from './abundance';
 import { plugin as differentialabundance } from './differentialabundance';
-import { plugin as differentialexpression } from './differentialExpression';
+// import { plugin as differentialexpression } from './differentialExpression';
 import { plugin as correlationassaymetadata } from './correlationAssayMetadata'; // mbio
 import { plugin as correlationassayassay } from './correlationAssayAssay'; // mbio
 import { plugin as correlation } from './correlation'; // genomics (- vb)
@@ -19,7 +19,7 @@ export const plugins: Record<string, ComputationPlugin> = {
   betadiv,
   dimensionalityreduction,
   differentialabundance,
-  differentialexpression,
+  // differentialexpression,
   correlationassaymetadata,
   correlationassayassay,
   correlation,