From dbb240a52f291e98b468b7183e5436ebe191218e Mon Sep 17 00:00:00 2001
From: Elissa Alarmani <ealarman@broadinstitute.org>
Date: Fri, 6 Sep 2024 15:04:33 -0400
Subject: [PATCH] add log label for value

---
 .../VariantPage/VariantSiteQualityMetrics.tsx | 50 +++++++++++++++----
 1 file changed, 40 insertions(+), 10 deletions(-)

diff --git a/browser/src/VariantPage/VariantSiteQualityMetrics.tsx b/browser/src/VariantPage/VariantSiteQualityMetrics.tsx
index c11cf2df2..01da30005 100644
--- a/browser/src/VariantPage/VariantSiteQualityMetrics.tsx
+++ b/browser/src/VariantPage/VariantSiteQualityMetrics.tsx
@@ -571,7 +571,10 @@ const yTickFormat = (n: any) => {
   return `${n}`
 }
 
-const formatMetricValue = (value: any, metric: any) => {
+const formatMetricValue = (value: any, metric: any, isLog?: boolean) => {
+  if (isLog) {
+    return `log(${value})`
+  }
   if (value === 0) {
     return '0'
   }
@@ -627,13 +630,27 @@ const SiteQualityMetricsHistogram = ({
 
   const logLabels = ['AS_VarDP', 'QUALapprox', 'AS_QUALapprox']
 
-  const xLabelRenamed = logLabels.includes(xLabel) ? `log(${xLabel})` : xLabel
+  const isLogMetrics = logLabels.includes(xLabel)
+
+  const xLabelRenamed = isLogMetrics ? `log(${xLabel})` : xLabel
 
   const primaryValues = exomeBinValues || genomeBinValues
   const secondaryValues = exomeBinValues ? genomeBinValues : null
 
-  const primaryMetricValue = exomeMetricValue !== null ? exomeMetricValue : genomeMetricValue
-  const secondaryMetricValue = exomeMetricValue !== null ? genomeMetricValue : null
+  const originalPrimaryMetricValue =
+    exomeMetricValue !== null ? exomeMetricValue : genomeMetricValue
+
+  const primaryMetricValue =
+    isLogMetrics && originalPrimaryMetricValue > 0
+      ? Math.log(originalPrimaryMetricValue)
+      : originalPrimaryMetricValue
+
+  const originalSecondaryMetricValue = exomeMetricValue !== null ? genomeMetricValue : null
+
+  const secondaryMetricValue =
+    isLogMetrics && originalSecondaryMetricValue > 0
+      ? Math.log(originalSecondaryMetricValue)
+      : originalSecondaryMetricValue
 
   const primaryYLabel = exomeBinValues ? 'Exome variants' : 'Genome variants'
   const secondaryYLabel = 'Genome variants'
@@ -874,7 +891,7 @@ const SiteQualityMetricsHistogram = ({
               fontSize={12}
               textAnchor={secondaryLabelOnLeft ? 'end' : 'start'}
             >
-              {formatMetricValue(secondaryMetricValue, metric)}
+              {formatMetricValue(originalSecondaryMetricValue, metric, isLogMetrics)}
             </text>
           </>
         )}
@@ -902,7 +919,8 @@ const SiteQualityMetricsHistogram = ({
               fontSize={12}
               textAnchor={primaryLabelOnLeft ? 'end' : 'start'}
             >
-              {formatMetricValue(primaryMetricValue, metric)}
+              {/* {formattedLabel} */}
+              {formatMetricValue(originalPrimaryMetricValue, metric, logLabels.includes(xLabel))}
             </text>
           </>
         )}
@@ -1020,20 +1038,32 @@ const VariantSiteQualityMetricsDistribution = ({
   const includeExomes = selectedSequencingType.includes('e')
   const includeGenomes = selectedSequencingType.includes('g')
 
+  const logLabels = ['AS_VarDP', 'QUALapprox', 'AS_QUALapprox']
+
+  const isLogMetrics = logLabels.includes(selectedMetric)
+
   let values
   if (variant.exome && variant.genome) {
     values = `${
-      exomeMetricValue === null ? '–' : formatMetricValue(exomeMetricValue, selectedMetric)
+      exomeMetricValue === null
+        ? '–'
+        : formatMetricValue(exomeMetricValue, selectedMetric, isLogMetrics)
     } (exome samples), ${
-      genomeMetricValue === null ? '–' : formatMetricValue(genomeMetricValue, selectedMetric)
+      genomeMetricValue === null
+        ? '–'
+        : formatMetricValue(genomeMetricValue, selectedMetric, isLogMetrics)
     } (genome samples)`
   } else if (variant.exome) {
     values = `${
-      exomeMetricValue === null ? '–' : formatMetricValue(exomeMetricValue, selectedMetric)
+      exomeMetricValue === null
+        ? '–'
+        : formatMetricValue(exomeMetricValue, selectedMetric, isLogMetrics)
     } (exome samples)`
   } else {
     values = `${
-      genomeMetricValue === null ? '–' : formatMetricValue(genomeMetricValue, selectedMetric)
+      genomeMetricValue === null
+        ? '–'
+        : formatMetricValue(genomeMetricValue, selectedMetric, isLogMetrics)
     } (genome samples)`
   }