citrus.plotClusters: Plot cluster histograms

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

Plot cluster histograms

Description

Plot expression of markers in cluster cells relative to all cells

Usage

citrus.plotClusters(clusterIds, clusterAssignments, citrus.combinedFCSSet,
  clusteringColumns, conditions = NULL, outputFile = NULL, ...)

Arguments

clusterIds	Vector of cluster IDs to plot
clusterAssignments	List containing indicies of cells assigned to each cluster.
citrus.combinedFCSSet	Combined FCS data that was clustered.
clusteringColumns	Columns for which to plot distributions
conditions	Vector of conditions clustering was performed on.
outputFile	If not NULL, plot is written to outputFile.
...	Other parameters (ignored).

Author(s)

Robert Bruggner

Examples

# 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)

# Plot clusters
citrus.plotClusters(clusterIds=c(19998,19997),clusterAssignments=citrus.clustering$clusterMembership,citrus.combinedFCSSet,clusteringColumns)

nolanlab/citrus documentation built on April 30, 2022, 3:24 a.m.