SPADE -- An analysis and visualization tool for Flow Cytometry

Documentation for package ‘spade’ version 1.8.0

SPADE.addClusterToFCS	Annotate observations in FCS file with cluster assignment
SPADE.addDensityToFCS	Annotate FCS file with local density of each observation
SPADE.annotateGraph	Add attributes to graph
SPADE.annotateMarkers	Compute marker medians, coefficient of variations and counts for clusters
SPADE.density	Annotate FCS file with local density of each observation
SPADE.downsampleFCS	Downsample observcations in a FCS file according to density parameter
SPADE.driver	SPADE workflow driver
SPADE.FCSToTree	Cluster and build minimum spanning tree from data in FCS files
SPADE.flattenAnnotations	Flatten list of annotations to matrix
SPADE.installPlugin	Install CytoSPADE Cytoscape plugin
SPADE.layout.arch	Generate coordinates for plotting graphs
SPADE.markerMedians	Compute marker medians, coefficient of variations and counts for clusters
SPADE.plot.trees	Plot trees with annotated vertices
SPADE.read.FCS	Read an FCS File
SPADE.transform.FCS	Annotate FCS file with local density of each observation
SPADE.write.graph	Writing the graph to a file in some format