update log labels for metric table

broadinstitute · Sep 9, 2024 · 3bf322c · 3bf322c
1 parent f8785b2
commit 3bf322c
Showing 1 changed file with 26 additions and 19 deletions.
diff --git a/browser/src/VariantPage/VariantSiteQualityMetrics.tsx b/browser/src/VariantPage/VariantSiteQualityMetrics.tsx
@@ -626,13 +626,10 @@ const SiteQualityMetricsHistogram = ({
   height,
   width,
 }: SiteQualityMetricsHistogramProps) => {
-  const isLogScale = metric === 'SiteQuality' || metric === 'AS_QUALapprox' || metric === 'DP'
+  const logScaleMetrics = ['SiteQuality', 'AS_QUALapprox', 'QUALapprox', 'DP', 'AS_VarDP']
+  const isLogScale = logScaleMetrics.includes(metric)
 
-  const logLabels = ['AS_VarDP', 'QUALapprox', 'AS_QUALapprox']
-
-  const isLogMetrics = logLabels.includes(xLabel)
-
-  const xLabelRenamed = isLogMetrics ? `log(${xLabel})` : xLabel
+  const xLabelRenamed = isLogScale ? `log(${xLabel})` : xLabel
 
   const primaryValues = exomeBinValues || genomeBinValues
   const secondaryValues = exomeBinValues ? genomeBinValues : null
@@ -641,14 +638,14 @@ const SiteQualityMetricsHistogram = ({
     exomeMetricValue !== null ? exomeMetricValue : genomeMetricValue
 
   const primaryMetricValue =
-    isLogMetrics && originalPrimaryMetricValue > 0
+    isLogScale && originalPrimaryMetricValue > 0
       ? Math.log10(originalPrimaryMetricValue)
       : originalPrimaryMetricValue
 
   const originalSecondaryMetricValue = exomeMetricValue !== null ? genomeMetricValue : null
 
   const secondaryMetricValue =
-    isLogMetrics && originalSecondaryMetricValue > 0
+    isLogScale && originalSecondaryMetricValue > 0
       ? Math.log10(originalSecondaryMetricValue)
       : originalSecondaryMetricValue
 
@@ -891,7 +888,7 @@ const SiteQualityMetricsHistogram = ({
               fontSize={12}
               textAnchor={secondaryLabelOnLeft ? 'end' : 'start'}
             >
-              {formatMetricValue(originalSecondaryMetricValue, metric, isLogMetrics)}
+              {formatMetricValue(originalSecondaryMetricValue, metric, isLogScale)}
             </text>
           </>
         )}
@@ -920,7 +917,7 @@ const SiteQualityMetricsHistogram = ({
               textAnchor={primaryLabelOnLeft ? 'end' : 'start'}
             >
               {/* {formattedLabel} */}
-              {formatMetricValue(originalPrimaryMetricValue, metric, logLabels.includes(xLabel))}
+              {formatMetricValue(originalPrimaryMetricValue, metric, isLogScale)}
             </text>
           </>
         )}
@@ -1038,32 +1035,31 @@ const VariantSiteQualityMetricsDistribution = ({
   const includeExomes = selectedSequencingType.includes('e')
   const includeGenomes = selectedSequencingType.includes('g')
 
-  const logLabels = ['AS_VarDP', 'QUALapprox', 'AS_QUALapprox']
-
-  const isLogMetrics = logLabels.includes(selectedMetric)
+  const logScaleMetrics = ['SiteQuality', 'AS_QUALapprox', 'QUALapprox', 'DP', 'AS_VarDP']
+  const isLogScale = logScaleMetrics.includes(selectedMetric)
 
   let values
   if (variant.exome && variant.genome) {
     values = `${
       exomeMetricValue === null
         ? '–'
-        : formatMetricValue(exomeMetricValue, selectedMetric, isLogMetrics)
+        : formatMetricValue(exomeMetricValue, selectedMetric, isLogScale)
     } (exome samples), ${
       genomeMetricValue === null
         ? '–'
-        : formatMetricValue(genomeMetricValue, selectedMetric, isLogMetrics)
+        : formatMetricValue(genomeMetricValue, selectedMetric, isLogScale)
     } (genome samples)`
   } else if (variant.exome) {
     values = `${
       exomeMetricValue === null
         ? '–'
-        : formatMetricValue(exomeMetricValue, selectedMetric, isLogMetrics)
+        : formatMetricValue(exomeMetricValue, selectedMetric, isLogScale)
     } (exome samples)`
   } else {
     values = `${
       genomeMetricValue === null
         ? '–'
-        : formatMetricValue(genomeMetricValue, selectedMetric, isLogMetrics)
+        : formatMetricValue(genomeMetricValue, selectedMetric, isLogScale)
     } (genome samples)`
   }
 
@@ -1154,6 +1150,7 @@ const TooltipHint = styled.span`
 
 const renderMetric = (metric: any, datasetId: any) => {
   let description
+  console.log(metric)
   if (metric === 'SiteQuality') {
     description = getSiteQualityMetricDescription(datasetId)
   } else if (metric.startsWith('AS_')) {
@@ -1208,6 +1205,8 @@ const VariantSiteQualityMetricsTable = ({
 
   const availableMetrics = getAvailableMetrics(datasetId)
 
+  const logScaleMetrics = ['SiteQuality', 'AS_QUALapprox', 'QUALapprox', 'DP', 'AS_VarDP']
+
   return (
     // @ts-expect-error TS(2769) FIXME: No overload matches this call.
     <BaseTable style={{ width: '100%' }}>
@@ -1226,14 +1225,22 @@ const VariantSiteQualityMetricsTable = ({
               {exomeMetricValues && metric in exomeMetricValues && isVariantInExomes && (
                 <td>
                   {exomeMetricValues![metric] != null
-                    ? formatMetricValue(exomeMetricValues![metric], metric)
+                    ? formatMetricValue(
+                        exomeMetricValues![metric],
+                        metric,
+                        logScaleMetrics.includes(metric)
+                      )
                     : '–'}
                 </td>
               )}
               {genomeMetricValues && metric in genomeMetricValues && isVariantInGenomes && (
                 <td>
                   {genomeMetricValues && ![metric] != null
-                    ? formatMetricValue(genomeMetricValues![metric], metric)
+                    ? formatMetricValue(
+                        genomeMetricValues![metric],
+                        metric,
+                        logScaleMetrics.includes(metric)
+                      )
                     : '–'}
                 </td>
               )}