Change cluster assignment step from cbind to $ for minor speedup

angelolab · Apr 22, 2021 · 9c11720 · 9c11720
1 parent bbe6f63
commit 9c11720
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/ark/phenotyping/consensus_cluster.R b/ark/phenotyping/consensus_cluster.R
@@ -55,15 +55,15 @@ hClust <- consensusClusterResults[[maxK]]$consensusClass
 names(hClust) <- clusterAvgs$cluster
 
 # append hClust to each fov's data
-print('Writing consensus clustering results')
+print("Writing consensus clustering results")
 for (i in 1:length(fovs)) {
     # read in pixel data, we'll need the cluster column for mapping
     fileName <- file.path(fovs[i], "feather", fsep=".")
     matPath <- file.path(pixelClusterDir, fileName)
     fovPixelData <- arrow::read_feather(matPath)
 
     # assign hierarchical cluster labels
-    fovPixelData <- cbind(fovPixelData, hCluster_cap=hClust[as.character(fovPixelData$cluster)])
+    fovPixelData$hCluster_cap <- hClust[as.character(fovPixelData$cluster)]
 
     # write consensus clustered data
     clusterPath <- file.path(pixelMatConsensus, fileName)

diff --git a/ark/phenotyping/run_trained_som.R b/ark/phenotyping/run_trained_som.R
@@ -60,7 +60,7 @@ for (i in 1:length(fovs)) {
     clusters <- FlowSOM:::MapDataToCodes(somWeights, as.matrix(fovPixelData[, markers]))
 
     # assign cluster labels column to pixel data
-    fovPixelData <- cbind(fovPixelData, cluster=clusters[,1])
+    fovPixelData$cluster <- clusters[,1]
 
     # write to feather
     clusterPath <- file.path(pixelClusterDir, fileName)