Suppress consensus cluster output barf

angelolab · May 13, 2022 · 4192c09 · 4192c09
1 parent 1e60432
commit 4192c09
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Showing 2 changed files with 2 additions and 4 deletions.
diff --git a/ark/phenotyping/cell_consensus_cluster.R b/ark/phenotyping/cell_consensus_cluster.R
@@ -59,9 +59,8 @@ clusterAvgsScale <- sapply(as.data.frame(clusterAvgsScale), pmin, cap)
 clusterAvgsScale <- sapply(as.data.frame(clusterAvgsScale), pmax, -cap)
 
 # run the consensus clustering
-# TODO: also look into invisible() function here (not urgent, just to prevent printout)
 print("Running consensus clustering")
-consensusClusterResults <- ConsensusClusterPlus(t(clusterAvgsScale), maxK=maxK, seed=seed)
+suppressMessages(consensusClusterResults <- ConsensusClusterPlus(t(clusterAvgsScale), maxK=maxK, seed=seed))
 som_to_meta_map <- consensusClusterResults[[maxK]]$consensusClass
 names(som_to_meta_map) <- clusterAvgs$cell_som_cluster
 

diff --git a/ark/phenotyping/pixel_consensus_cluster.R b/ark/phenotyping/pixel_consensus_cluster.R
@@ -60,9 +60,8 @@ clusterAvgsScale <- sapply(as.data.frame(clusterAvgsScale), pmin, cap)
 clusterAvgsScale <- sapply(as.data.frame(clusterAvgsScale), pmax, -cap)
 
 # run the consensus clustering
-# TODO: look into suppressing output for Rs (invisible), not urgent
 print("Running consensus clustering")
-consensusClusterResults <- ConsensusClusterPlus(t(clusterAvgsScale), maxK=maxK, seed=seed)
+suppressMessages(consensusClusterResults <- ConsensusClusterPlus(t(clusterAvgsScale), maxK=maxK, seed=seed))
 som_to_meta_map <- consensusClusterResults[[maxK]]$consensusClass
 names(som_to_meta_map) <- clusterAvgs$pixel_som_cluster