export.to.cytoscape: Facilitates export of results of the Vertex Sort algorithm to...
In VertexSort: Network Hierarchical Structure and Randomization

Description Usage Arguments Value Author(s) References See Also Examples

The export.to.cytoscape() function facilitates export of a graph that was sorted by the vertex sort algorithm to the Cytoscape. It creates a list of two data frames. The first data frame contains the edges of the graph and the second data frame contains node attributes of the graph. These data frames could be written to text files and could be imported to cytoscape to allow to query certain details of the results (e.g. layer of a node) and to also permit the visualization and customization of the graphic representation of the sorted graph in order to generate figures.

1	export.to.cytoscape(vs_object)

vs_object

a vertex.sort object generated by applying the vertex.sort() function.

The export.to.cytoscape() function returns a list of two data frames:

`edges`	a data frame that contains the edges of a graph that has been sorted using the Vertex Sort algorithm by the `vetex.sort()` function.
`node_attribute`	a data frame that contains the node attributes of a graph that has been sorted using the Vertex Sort algorithm by the `vetex.sort()` function. It includes the following columns: node identifier, node type, node layer and node level. For more details, see `vertex.sort()` function

Diala Abd-Rabbo diala.abd.rabbo@gmail.com

Jothi, R., Balaj, S., Wuster, A. et al. 2009 Molecular system biology 5, –294-309.

Abd-Rabbo, D. and Michnick, S.W. 2017 BMC Syst Biol 11.

vertex.sort.

  ## load the VertexSort library
  library(VertexSort)

  ## load interactions of the kinase-phosphatase network (kp-net)
  data("interactions")

  ## apply the vertex sort algorithm
  vs_kp_net <- vertex.sort(interactions)

  ## apply the export.to.cytoscape function
  df <- export.to.cytoscape(vs_kp_net)

  ## view the first 6 lines of each data frame
  head(df$edges)
  head(df$node_attribute)