Bit of cleanup

weng-lab · Nov 4, 2024 · 1637b00 · 1637b00
1 parent 39d92d8
commit 1637b00
Show file tree

Hide file tree

Showing 2 changed files with 17 additions and 17 deletions.
diff --git a/screen2.0/src/app/applets/gene-expression/MultiSelect.tsx b/screen2.0/src/app/applets/gene-expression/MultiSelect.tsx
@@ -90,12 +90,7 @@ const MultiSelect = ({
   })
 
   return (
-    /**
-     * Manually specify type arguments, since when overriding AutocompleteChangeDetails in TissueMultiSelectOnChange to be
-     * AutocompleteChangeDetails<string | string[]> (for select all compatibility), the type of option in renderOption was inferred to be string | string[]
-     * for some reason. Couldn't figure out why -JF 10/31/24
-     */
-    <Autocomplete<string, true, false, false, undefined>
+    <Autocomplete
       multiple
       limitTags={limitTags}
       size='small'
@@ -138,7 +133,7 @@ const MultiSelect = ({
       //Parent element of options contained within above {paperProps.children}
       ListboxComponent={ListboxComponent}
       //Each option
-      renderOption={(props, option, { selected }) => {
+      renderOption={(props, option: string, { selected }) => {
         const { key, ...optionProps } = props;
         return (
           <li key={key} {...optionProps}>

diff --git a/screen2.0/src/app/applets/gene-expression/geneexpression.tsx b/screen2.0/src/app/applets/gene-expression/geneexpression.tsx
@@ -129,29 +129,32 @@ export function GeneExpression(props: {
     }
   }, [scale])
 
+
   const plotData: BarData<GeneDataset>[] = useMemo(() => {
     if (dataExperiments && dataExperiments.gene_dataset.length > 0) {
+      //Filter data points
       const filteredData = dataExperiments.gene_dataset
-        .filter(d => biosamples.includes(d.biosample_type)) //filter by sample type
-        .filter((d) => tissues.includes(d.tissue)) //TODO put tissue filter here
-        .filter(d => RNAtype === "all" || d.assay_term_name === RNAtype) //filter by RNA type
-        .filter(d => sampleMatchesSearch(d))
+        .filter(d => biosamples.includes(d.biosample_type)) //biosample type
+        .filter(d => tissues.includes(d.tissue)) //tissue
+        .filter(d => RNAtype === "all" || d.assay_term_name === RNAtype) //RNA type
+        .filter(d => sampleMatchesSearch(d)) //search
+      //holder for plot data as replicates are parsed for each experiment
       let parsedReplicates: BarData<GeneDataset>[] = []
       filteredData.forEach((biosample) => {
-        if (replicates === "all") {
+        if (replicates === "all") { //push all replicates
           biosample.gene_quantification_files.forEach((exp) => {      
             parsedReplicates.push({
               category: biosample.tissue,
-              label: makeLabel(scaleData(exp.quantifications?.[0]?.tpm || 0), biosample.biosample, biosample.accession, exp.biorep),
-              value: scaleData(exp.quantifications?.[0]?.tpm || 0), //IMPORTANT casting empty quantifications array to 0 tpm. Maybe bad assumption
+              label: makeLabel(scaleData(exp.quantifications[0].tpm), biosample.biosample, biosample.accession, exp.biorep),
+              value: scaleData(exp.quantifications[0].tpm), //indexing into 0th position, only one gene so quantifications should always be length 1
               color: tissueColors[biosample.tissue] ?? tissueColors.missing,
               metadata: biosample as GeneDataset
             })
           })
         } else { //average replicates
           let sum = 0
           biosample.gene_quantification_files.forEach((exp) => {
-            sum += (exp.quantifications?.[0]?.tpm ?? 0) //using reduce had terrible readability so doing avg manually
+            sum += (exp.quantifications[0].tpm) //using reduce had terrible readability so doing avg manually
           })
           const avgTPM = sum / biosample.gene_quantification_files.length
           parsedReplicates.push({
@@ -164,10 +167,11 @@ export function GeneExpression(props: {
         }
       })
       switch (viewBy) {
-        case ("byExperimentTPM"):
+        case ("byExperimentTPM"):{
           //sort by value
           parsedReplicates.sort((a, b) => b.value - a.value);
           break;
+        }
         case ("byTissueTPM"): {
           //find max value for each tissue
           const maxValuesByTissue: {[key: string]: number} = parsedReplicates.reduce((acc, item) => {
@@ -183,11 +187,13 @@ export function GeneExpression(props: {
           break;
         }
         case ("byTissueMaxTPM"): {
+          //find max value for each tissue
           const maxValuesByTissue: {[key: string]: number} = parsedReplicates.reduce((acc, item) => {
             acc[item.category] = Math.max(acc[item.category] || -Infinity, item.value);
             return acc;
           }, {});
 
+          //filter out all but max value for each tissue, then sort descending
           parsedReplicates = parsedReplicates.filter(x => x.value === maxValuesByTissue[x.category])
           parsedReplicates.sort((a, b) => b.value - a.value);
         }
@@ -480,7 +486,6 @@ export function GeneExpression(props: {
             <ToggleButton sx={{ textTransform: "none" }} value="all">Show Replicates</ToggleButton>
           </ToggleButtonGroup>
         </FormControl>
-
         <FormControl>
           <FormLabel>{biosamples.length === biosampleTypes.length ? "Biosample Types" : <i>Biosample Types*</i>}</FormLabel>
           <MultiSelect