Merge pull request #103 from nolanlab/naDscrpt

Attempting to explicitly handle NA's in FCS parameter descriptions.
nolanlab · Oct 17, 2016 · a0ab57a · a0ab57a
2 parents 05b0b62 + 13cdc27
commit a0ab57a
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Showing 3 changed files with 43 additions and 12 deletions.
diff --git a/R/citrus.launchUI.R b/R/citrus.launchUI.R
@@ -54,9 +54,18 @@ citrus.getFileParameters = function(fileName,dataDir,...){
   cat(paste0("Reading parameters in ",fileName,"\n"));
   fcsFile = citrus.readFCS(file.path(dataDir,fileName),which.lines=1)
   parameterNames = flowCore::colnames(fcsFile)
-  pnames = as.vector(pData(flowCore::parameters(fcsFile))$desc)
-  pnames[sapply(pnames,nchar)<3] = parameterNames[sapply(pnames,nchar)<3]
-  names(parameterNames)=pnames
+
+  # This really should be done as part of citrus.readFCS
+  # Same in citrus.readFCSSet
+  parameterDescriptions = as.vector(pData(flowCore::parameters(fcsFile))$desc)
+  invalidDescriptions = unname(which(sapply(parameterDescriptions,nchar)<3 | is.na(parameterDescriptions)))
+  parameterDescriptions[invalidDescriptions] = parameterNames[invalidDescriptions]
+  names(parameterNames)=parameterDescriptions
+
+  #pnames = as.vector(pData(flowCore::parameters(fcsFile))$desc)
+  #pnames[sapply(pnames,nchar)<3] = parameterNames[sapply(pnames,nchar)<3]
+  #names(parameterNames)=pnames
+
   return(parameterNames)
 }
 

diff --git a/R/citrus.plot.R b/R/citrus.plot.R
@@ -11,14 +11,29 @@
 }
 
 .getDisplayNames=function(citrus.combinedFCSSet,clusteringColumns){
-  colLabels = citrus.combinedFCSSet$fileChannelNames[[1]][[1]]
-  reagentNames = citrus.combinedFCSSet$fileReagentNames[[1]][[1]]
-  displayNames = colLabels
-  displayNames[nchar(reagentNames)>2] = reagentNames[nchar(reagentNames)>2]
+
+  # Get channel names
+  #colLabels = citrus.combinedFCSSet$fileChannelNames[[1]][[1]]
+
+  # Get reagent names
+  #reagentNames = citrus.combinedFCSSet$fileReagentNames[[1]][[1]]
+
+  # Set display names to channel names
+  #displayNames = colLabels
+
+  # update display names to equal reagent names where reagent names > 2
+  #displayNames[nchar(reagentNames)>2] = reagentNames[nchar(reagentNames)>2]
+
+  displayNames = citrus.combinedFCSSet$fileReagentNames[[1]][[1]]
+
   if (all(is.numeric(clusteringColumns))){
+    # If clustering columns is numeric, pass back the indices
     return(displayNames[clusteringColumns])
   } else {
-    names(displayNames) = colLabels
+    # Otherwise, set the names of display names to be the channel names
+    #names(displayNames) = colLabels
+    names(displayNames) = citrus.combinedFCSSet$fileChannelNames[[1]][[1]]
+    # and return the display names from the corresponding clustering columns
     return(as.vector(displayNames[clusteringColumns]))
   }
 

diff --git a/R/citrus.util.R b/R/citrus.util.R
@@ -66,17 +66,24 @@ citrus.readFCSSet = function(dataDirectory,fileList,fileSampleSize=1000,transfor
 
       fcsData=exprs(fcsFile)
 
+      # Note - this should be done as part of citrus.readFCS. See citrus.getFileParameters too.
+      parameterDescriptions = as.vector(pData(flowCore::parameters(fcsFile))$desc)
+      parameterNames = flowCore::colnames(fcsFile)
+      invalidDescriptions = unname(which(sapply(parameterDescriptions,nchar)<3 | is.na(parameterDescriptions)))
+      parameterDescriptions[invalidDescriptions] = parameterNames[invalidDescriptions]
+
       if (useChannelDescriptions){
-       channelDescriptions = as.vector(pData(parameters(fcsFile))$desc)
-       colnames(fcsData)[nchar(channelDescriptions)>2] = channelDescriptions[nchar(channelDescriptions)>2]
+        #channelDescriptions = as.vector(pData(parameters(fcsFile))$desc)
+        #colnames(fcsData)[nchar(channelDescriptions)>2] = channelDescriptions[nchar(channelDescriptions)>2]
+        colnames(fcsData)=parameterDescriptions
       }
 
       if (!is.null(readParameters)){
         fcsData = fcsData[,readParameters]
       }
 
-      fileChannelNames[[conditions[i]]][[fileName]]=as.vector(pData(parameters(fcsFile))$name)
-      fileReagentNames[[conditions[i]]][[fileName]]=as.vector(pData(parameters(fcsFile))$desc)
+      fileChannelNames[[conditions[i]]][[fileName]]=parameterNames
+      fileReagentNames[[conditions[i]]][[fileName]]=parameterDescriptions
       fcsData = cbind(fcsData,fileEventNumber=1:nrow(fcsData),fileId=fileCounter);
       fileCounter=fileCounter+1;