cy2.edge.names: cy2.edge.names

In tmuetze/Bioconductor_RCy3_the_new_RCytoscape: Display and manipulate graphs in Cytoscape >= 3.3.0

Description

Bioconductor graph edges are named, i.e., A~B. The same edge in the Cytoscape domain would be 'A (<edgeType>) B', where '<edgeType>' might be 'phosphorylates' or 'represses'.

Usage

cy2.edge.names(graph, R.edge.names=NA)

Arguments

graph	An R graph
R.edge.names	one or more R graph-style edge names. default NA, in which case all edges in the graph are translated to cy2-style.

Value

A named list, in with Cytoscape edges names are the content, and bioc graph edge names are their names.

Author(s)

Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

  ## Not run: 
  # first, delete existing windows to save memory:
  deleteAllWindows(CytoscapeConnection())

  g <- makeSimpleGraph ()
  cy2.edge.names (g)
    #                      A~B                      B~C                      C~A 
    #    "A (phosphorylates) B" "B (synthetic lethal) C"        "C   (undefined) A" 
  cy2.edge.names (g, R.edge.names="B~C")
    #                      B~C 
    # "B (synthetic lethal) C" 


## End(Not run)

tmuetze/Bioconductor_RCy3_the_new_RCytoscape documentation built on May 31, 2019, 4:39 p.m.