% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/cyto_vis.R
\title{Send graph to Cytoscape via CyREST}
cyto_vis(graph_object, title = "Cytoscape Graph Window",
  edge_width_attribute = "summary_score", port.number = 1234)
\item{graph_object}{An igraph object such as the one generated by the 
function \code{\link{get_graph_object}}}

\item{title}{An optional title for the graph when it is in Cytoscape}

\item{edge_width_attribute}{The attribute that will be used for edge width; 
if data is not added or the attribute is not part of the graphing 
information, the edge width will default to 1.}

\item{port.number}{The port address for Cytoscape}
A dynamic map in Cytoscape automatically formatted for convenient 
View the KEGG pathway in Cytoscape. With either the 
'expanded edges' or 'stacked nodes' layout, users can visualize and interact 
with the graphs [strictly] as they are documented in the most recent KGML
available from KEGG.  
This function is a modified version of the function send2cy(),
 which is part of the cyREST utility functions.
p53_KGML <- get_KGML("hsa04115")
p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML, FALSE)
nodes <- node_mapping_info(p53_KEGG_mappings)

p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
edges <- edge_mapping_info(p53_edges) 

p53_graph_object <- get_graph_object(nodes, edges)
cyto_vis(p53_graph_object, "Default p53 Graph [no data added]")

#Workflow to visualize graph with data-dependent attributes:

p53_KGML <- get_KGML("hsa04115")
p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)
nodes <- node_mapping_info(p53_KEGG_mappings)

p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)

p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, "HA1E", 
                               data_type = "100_bing")
p53_edges_plus_data <- add_edge_data(p53_edges, p53_KEGG_mappings, 
                                      p53_HA1E_data, c(3, 10,12),
                                      only_mapped = TRUE)

edges <- edge_mapping_info(p53_edges_plus_data, data_added = TRUE)
p53_plus_data_graph_object <- get_graph_object(nodes, edges)
cyto_vis(p53_plus_data_graph_object, "p53 Graph: Mapped Edges + HA1E Data",
         edge_width_attribute = "UP")