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.
a vertex.sort object generated by applying the
export.to.cytoscape() function returns a list of two data frames:
a data frame that contains the edges of a graph that
has been sorted using the Vertex Sort algorithm by the
a data frame that contains the node attributes
of a graph that has been sorted using the Vertex Sort algorithm by the
Diala Abd-Rabbo email@example.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.
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## 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)
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