citrus.createHierarchyGraph | R Documentation |
Create a graph object from clustering hierarchy that may be used by other plotting functions.
citrus.createHierarchyGraph(citrus.clustering, selectedClusters)
citrus.foldFeatureSet |
A |
citrus.foldClustering |
A |
A graph
object and other properties for plotting.
graph |
An |
layout |
An |
plotSize |
Size of PDF for plotting (inches) calculated based on the number of clusters to be plotted. |
Robert Bruggner
# Where the data lives
dataDirectory = file.path(system.file(package = "citrus"),"extdata","example1")
# Create list of files to be analyzed
fileList = data.frame("unstim"=list.files(dataDirectory,pattern=".fcs"))
# Read the data
citrus.combinedFCSSet = citrus.readFCSSet(dataDirectory,fileList)
# List of columns to be used for clustering
clusteringColumns = c("Red","Blue")
# Cluster data
citrus.clustering = citrus.cluster(citrus.combinedFCSSet,clusteringColumns)
# Large enough clusters
largeEnoughClusters = citrus.selectClusters(citrus.clustering)
# Create graph for plotting
hierarchyGraphStuff = citrus.createHierarchyGraph(citrus.clustering,selectedClusters=largeEnoughClusters)
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