Description Usage Arguments Details Value Author(s) See Also Examples
Performing "arch" layouts of graph vertices
1 | SPADE.layout.arch(mst_graph)
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mst_graph |
The graph to layout. Must be acyclic and undirected. |
These functions calculate the coordinates of the vertices for a graph.
layout.arch
lays out the longest chain of the graph, the "backbone", on an arch, and the "side chains" as trees normal to that backbone.
All these functions return a numeric matrix with at least two columns, x and y positions, and the same number of lines as the number of vertices.
Michael Linderman
1 2 3 4 5 6 7 8 9 10 11 | # Not run
## Load two-parameters sample data included in package
#data_file_path = paste(installed.packages()["spade","LibPath"],"spade","extdata","SimulatedRawData.fcs",sep=.Platform$file.sep)
## Run basic SPADE analyses, clustering on two parameters.
#output_dir <- tempdir()
#SPADE.driver(data_file_path, out_dir=output_dir, cluster_cols=c("marker1","marker2"))
## Generate PDFs of annotated graphs (into output_dir/pdf) using arch layout
#mst_graph <- igraph:::read.graph(paste(output_dir,"mst.gml",sep=.Platform$file.sep),format="gml")
#SPADE.plot.trees(mst_graph, output_dir, out_dir=paste(output_dir,"pdf",sep=.Platform$file.sep), layout=SPADE.layout.arch(mst_graph))
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