Merge branch 'main' into junction_record_id

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

@@ -90,7 +90,13 @@ export const plugin: ComputationPlugin = {
   createDefaultConfiguration: () => undefined,
   isConfigurationValid: isCompleteDifferentialAbundanceConfig,
   visualizationPlugins: {
-    volcanoplot: volcanoPlotVisualization, // Must match name in data service and in visualization.tsx
+    volcanoplot: volcanoPlotVisualization.withOptions({
+      getPlotSubtitle(config) {
+        if (DifferentialAbundanceConfig.is(config)) {
+          return `Differential abundance computed using ${config.differentialAbundanceMethod} with default parameters.`;
+        }
+      },
+    }), // Must match name in data service and in visualization.tsx
   },
 };
 
@@ -117,10 +123,6 @@ function DifferentialAbundanceConfigDescriptionComponent({
     'comparator' in configuration
       ? findEntityAndVariable(configuration.comparator.variable)
       : undefined;
-  const differentialAbundanceMethod =
-    'differentialAbundanceMethod' in configuration
-      ? configuration.differentialAbundanceMethod
-      : undefined;
 
   const updatedCollectionVariable = collections.find((collectionVar) =>
     isEqual(
@@ -154,22 +156,14 @@ function DifferentialAbundanceConfigDescriptionComponent({
           )}
         </span>
       </h4>
-      <h4>
-        Method:{' '}
-        <span>
-          {differentialAbundanceMethod ? (
-            differentialAbundanceMethod
-          ) : (
-            <i>Not selected</i>
-          )}
-        </span>
-      </h4>
     </div>
   );
 }
 
 // Include available methods in this array.
-const DIFFERENTIAL_ABUNDANCE_METHODS = ['DESeq', 'Maaslin'];
+// 10/10/23 - decided to only release Maaslin for the first roll-out. DESeq is still available
+// and we're poised to release it in the future.
+const DIFFERENTIAL_ABUNDANCE_METHODS = ['Maaslin']; // + 'DESeq' in the future
 
 export function DifferentialAbundanceConfiguration(
   props: ComputationConfigProps
@@ -189,6 +183,11 @@ export function DifferentialAbundanceConfiguration(
   const filters = analysisState.analysis?.descriptor.subset.descriptor;
   const findEntityAndVariable = useFindEntityAndVariable(filters);
 
+  // Only releasing Maaslin for b66
+  if (configuration)
+    configuration.differentialAbundanceMethod =
+      DIFFERENTIAL_ABUNDANCE_METHODS[0];
+
   // Include known collection variables in this array.
   const collections = useCollectionVariables(studyMetadata.rootEntity);
   if (collections.length === 0)
@@ -207,13 +206,14 @@ export function DifferentialAbundanceConfiguration(
     );
 
   const collectionVarItems = useMemo(() => {
+    // Show all collections except for absolute abundance. Eventually this will be performed by
+    // the backend, similar to how we do visualization input var constraints.
     return collections
       .filter((collectionVar) => {
-        return collectionVar.normalizationMethod // i guess diy stuff doesnt have this prop?
-          ? //  !collectionVar.isProportion &&
-            //  collectionVar.normalizationMethod === 'NULL' &&
-            !collectionVar.displayName?.includes('pathway')
-          : true;
+        return collectionVar.normalizationMethod
+          ? collectionVar.normalizationMethod !== 'NULL' ||
+              collectionVar.displayName?.includes('pathway')
+          : true; // DIY may not have the normalizationMethod annotations, but we still want those datasets to pass.
       })
       .map((collectionVar) => ({
         value: {
@@ -225,7 +225,6 @@ export function DifferentialAbundanceConfiguration(
       }));
   }, [collections]);
 
-  // TODO presumably to keep the saved analyses from breaking, we need to maintain support for a variableId
   const selectedCollectionVar = useMemo(() => {
     if (configuration && 'collectionVariable' in configuration) {
       const selectedItem = collectionVarItems.find((item) =>
@@ -298,12 +297,6 @@ export function DifferentialAbundanceConfiguration(
         }
       );
 
-  const differentialAbundanceMethod = useMemo(() => {
-    if (configuration && 'differentialAbundanceMethod' in configuration) {
-      return configuration.differentialAbundanceMethod;
-    }
-  }, [configuration]);
-
   return (
     <ComputationStepContainer
       computationStepInfo={{
@@ -465,24 +458,6 @@ export function DifferentialAbundanceConfiguration(
             </Tooltip>
           </div>
         </div>
-
-        <div className={cx('-InputContainer')}>
-          <span>Method</span>
-          <SingleSelect
-            value={differentialAbundanceMethod ?? 'Select a method'}
-            buttonDisplayContent={
-              differentialAbundanceMethod ?? 'Select a method'
-            }
-            onSelect={partial(
-              changeConfigHandler,
-              'differentialAbundanceMethod'
-            )}
-            items={DIFFERENTIAL_ABUNDANCE_METHODS.map((method) => ({
-              value: method,
-              display: method,
-            }))}
-          />
-        </div>
       </div>
     </ComputationStepContainer>
   );

packages/libs/eda/src/lib/core/components/visualizations/implementations/VolcanoPlotVisualization.tsx

@@ -25,7 +25,7 @@ import { createVisualizationPlugin } from '../VisualizationPlugin';
 import LabelledGroup from '@veupathdb/components/lib/components/widgets/LabelledGroup';
 import { NumberInput } from '@veupathdb/components/lib/components/widgets/NumberAndDateInputs';
 
-import { LayoutOptions } from '../../layouts/types';
+import { LayoutOptions, TitleOptions } from '../../layouts/types';
 import { RequestOptions } from '../options/types';
 
 // Volcano plot imports
@@ -34,7 +34,6 @@ import DataClient, {
   VolcanoPlotResponse,
 } from '../../../api/DataClient';
 import {
-  VolcanoPlotData,
   VolcanoPlotDataPoint,
   VolcanoPlotStats,
 } from '@veupathdb/components/lib/types/plots/volcanoplot';
@@ -54,6 +53,7 @@ import SliderWidget, {
 import { ResetButtonCoreUI } from '../../ResetButton';
 import AxisRangeControl from '@veupathdb/components/lib/components/plotControls/AxisRangeControl';
 import { fixVarIdLabel } from '../../../utils/visualization';
+import { OutputEntityTitle } from '../OutputEntityTitle';
 // end imports
 
 const DEFAULT_SIG_THRESHOLD = 0.05;
@@ -106,6 +106,7 @@ export const VolcanoPlotConfig = t.partial({
 
 interface Options
   extends LayoutOptions,
+    TitleOptions,
     RequestOptions<VolcanoPlotConfig, {}, VolcanoPlotRequestParams> {}
 
 // Volcano Plot Visualization
@@ -120,8 +121,6 @@ function VolcanoPlotViz(props: VisualizationProps<Options>) {
     updateConfiguration,
     updateThumbnail,
     filters,
-    dataElementConstraints,
-    dataElementDependencyOrder,
     filteredCounts,
     computeJobStatus,
   } = props;
@@ -384,6 +383,11 @@ function VolcanoPlotViz(props: VisualizationProps<Options>) {
     ]
   );
 
+  // plot subtitle
+  const plotSubtitle = options?.getPlotSubtitle?.(
+    computation.descriptor.configuration
+  );
+
   // Add labels to the extremes of the x axis. These may change in the future based on the type
   // of data. For example, for genes we may want to say Up regulated in...
   const comparisonLabels =
@@ -627,12 +631,7 @@ function VolcanoPlotViz(props: VisualizationProps<Options>) {
         />
       </LabelledGroup>
 
-      {/* This should be populated with info from the colections var. So like "Showing 1000 taxa blah". Waiting on collections annotations. */}
-      {/* <OutputEntityTitle
-        entity={outputEntity}
-        outputSize={outputSize}
-        subtitle={plotSubtitle}
-      /> */}
+      <OutputEntityTitle subtitle={plotSubtitle} />
       <LayoutComponent
         isFaceted={false}
         legendNode={legendNode}