tidy up ms final report

phenomecentre · Nov 20, 2024 · 69bb195 · 69bb195
1 parent 4914af6
commit 69bb195
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/nPYc/StudyDesigns/SOP/GenericMS.json b/nPYc/StudyDesigns/SOP/GenericMS.json
@@ -27,5 +27,5 @@
 	"featureMetadataNotExported":["mzmin", "mzmax", "rtmin", "rtmax", "npeaks", "ms_level", "Exclusion Details",
 		"User Excluded","blankFilter", "blankValue", "artifactualFilter", "rsdFilter", "rsdSP",
 		"correlationToDilution", "correlationToDilutionFilter", "varianceRatioFilter", "rsdSS/rsdSP"],
-	"samplesNotCorrected": {"SampleType" : ["StudyPool"], "AssayRole" : ["LinearityReference"]}
+	"samplesNotCorrected": {"SampleType" : ["StudyPool", "ProceduralBlank"], "AssayRole" : ["LinearityReference", "Blank"]}
 }
diff --git a/nPYc/reports/_finalReportPeakPantheR.py b/nPYc/reports/_finalReportPeakPantheR.py
@@ -73,8 +73,8 @@ def _finalReportPeakPantheR(dataset, destinationPath=None):
         dataset.saveFeatureMask()
 
 	# Use cpdName (targeted) to label RSD plot if available
-    if (hasattr(dataset.featureMetadata, 'cpdName')):
-        featureName = 'cpdName'
+    if (hasattr(dataset.featureMetadata, 'Compound Name')):
+        featureName = 'Compound Name'
         featName=True
         figureSize=(dataset.Attributes['figureSize'][0], dataset.Attributes['figureSize'][1] * (dataset.noFeatures / 35))
     else:
@@ -227,7 +227,7 @@ def _finalReportPeakPantheR(dataset, destinationPath=None):
             featureName=featureName,
             ratio=False,
             logx=True,
-            sortOrder=False,
+            #sortOrder=False,
             withExclusions=False,
             color='matchReport',
             featName=featName,

diff --git a/nPYc/reports/_generateReportMS.py b/nPYc/reports/_generateReportMS.py
@@ -149,8 +149,8 @@ def _finalReport(dataset, destinationPath=None, pcaModel=None, reportType='final
         saveAs = None
 
 	# TODO: change how this is done If targeted assay can use compound name to label RSD plots
-    if (hasattr(dataset.featureMetadata, 'cpdName')):
-        featureName = 'cpdName'
+    if (hasattr(dataset.featureMetadata, 'Compound Name')):
+        featureName = 'Compound Name'
         featName=True
         figureSize=(dataset.Attributes['figureSize'][0], dataset.Attributes['figureSize'][1] * (dataset.noFeatures / 35))
     else:
@@ -194,7 +194,7 @@ def _finalReport(dataset, destinationPath=None, pcaModel=None, reportType='final
 
     # Update 'All', 'Missing/Excluded' to only reflect sample types present in data
     sampleSummary['Acquired'].loc['All', 'Missing/Excluded'] = sum(sampleSummary['Acquired']['Missing/Excluded'][1:])
-    
+
     sampleSummary['isFinalReport'] = True
     if 'StudySamples Exclusion Details' in sampleSummary:
         sampleSummary['studySamplesExcluded'] = True