citrus.mapToClusterSpace: Map new data to existing clusters

In nolanlab/citrus: Citrus: Identification of stratifying subpopulations in Flow Cytometry Data.

Map new data to existing clusters

Description

Map new data to clusters defined by a clustering.

Usage

citrus.mapToClusterSpace(citrus.combinedFCSSet.new, citrus.combinedFCSSet.old,
  citrus.clustering, mappingColumns = NULL, ...)

Arguments

citrus.combinedFCSSet.new	A citrus.combinedFCSSet object containing new data to be mapped.
citrus.combinedFCSSet.old	A citrus.combinedFCSSet object containing new data that has been clustered.
citrus.clustering	A clustering of data in citrus.combinedFCSSet.old.
mappingColumns	Parameters to be used for mapping new data to existing cluster space. If NULL, then parameters used to cluster citrus.combinedFCSSet.old are used.
...	Additional arguments (ignored).

Value

A citrus.mapping object

clusterMembership	List of event indices, reporting which events in citrus.combinedFCSSet.new belong to each cluster in citrus.clustering.
mappingColumns	Columns used to match new data events with existing clustered data.

Author(s)

Robert Bruggner

Examples

# Where the data lives
dataDirectory = file.path(system.file(package = "citrus"),"extdata","example1")

# List of files to be clustered
fileList1 = data.frame("unstim"=list.files(dataDirectory,pattern=".fcs")[seq(from=2,to=20,by=2)])

# List of files to be mapped
fileList2 = data.frame("unstim"=list.files(dataDirectory,pattern=".fcs")[seq(from=1,to=19,by=2)])

# Read the data
citrus.combinedFCSSet1 = citrus.readFCSSet(dataDirectory,fileList1)
citrus.combinedFCSSet2 = citrus.readFCSSet(dataDirectory,fileList2)

# List of columns to be used for clustering
clusteringColumns = c("Red","Blue")

# Cluster first dataset
citrus.clustering = citrus.cluster(citrus.combinedFCSSet1,clusteringColumns)

# Map new data to exsting clustering
citrus.mapping = citrus.mapToClusterSpace(citrus.combinedFCSSet.new=citrus.combinedFCSSet1,citrus.combinedFCSSet.old=citrus.combinedFCSSet2,citrus.clustering)

nolanlab/citrus documentation built on April 19, 2024, 6:49 p.m.