Add PCA (dimensionality reduction) compute and plot

packages/libs/eda/src/lib/core/components/computations/plugins/dimensionalityReduction.tsx

@@ -0,0 +1,169 @@
+import { useFindEntityAndVariableCollection } from '../../..';
+import { VariableCollectionDescriptor } from '../../../types/variable';
+import { scatterplotVisualization } from '../../visualizations/implementations/ScatterplotVisualization';
+import { ComputationConfigProps, ComputationPlugin } from '../Types';
+import {
+  useConfigChangeHandler,
+  assertComputationWithConfig,
+  isNotAbsoluteAbundanceVariableCollection,
+  partialToCompleteCodec,
+} from '../Utils';
+import * as t from 'io-ts';
+import { Computation } from '../../../types/visualization';
+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: 'PC1',
+            };
+          }
+        },
+        getComputedYAxisDetails(config) {
+          if (
+            DimensionalityReductionConfig.is(config) &&
+            config.collectionVariable
+          ) {
+            return {
+              entityId: config.collectionVariable.entityId,
+              placeholderDisplayName: 'PCA Axis 2',
+              variableId: 'PC2',
+            };
+          }
+        },
+        hideShowMissingnessToggle: true,
+        hideTrendlines: true,
+        hideFacetInputs: true,
+        hideLogScale: true,
+        returnPointIds: false,
+        sendComputedVariablesInRequest: true,
+      })
+      .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>
+  );
+}
+
+// Dimensionality reduction'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;
+}

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,

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]
   );
@@ -745,8 +748,14 @@ function ScatterplotViz(props: VisualizationProps<Options>) {
         config: {
           outputEntityId: outputEntity.id,
           valueSpec: hideTrendlines ? undefined : valueSpecValue,
-          xAxisVariable: vizConfig.xAxisVariable,
-          yAxisVariable: vizConfig.yAxisVariable,
+          xAxisVariable:
+            sendComputedVariablesInRequest && computedXAxisDescriptor
+              ? computedXAxisDescriptor
+              : vizConfig.xAxisVariable,
+          yAxisVariable:
+            sendComputedVariablesInRequest && computedYAxisDescriptor
+              ? computedYAxisDescriptor
+              : vizConfig.yAxisVariable,
           overlayVariable: vizConfig.overlayVariable,
           facetVariable: vizConfig.facetVariable
             ? [vizConfig.facetVariable]