SPADE -- An analysis and visualization tool for Flow Cytometry


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Documentation for package ‘spade’ version 1.14.0

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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.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.write.graph Writing the graph to a file in some format