cyto_vis: Send graph to Cytoscape via CyREST

In shanawhite-UC/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

Description

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.

Usage

cyto_vis(graph_object, title = "Cytoscape Graph Window",
  edge_width_attribute = "summary_score", port.number = 1234)

Arguments

graph_object	An igraph object such as the one generated by the function get_graph_object
title	An optional title for the graph when it is in Cytoscape
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.
port.number	The port address for Cytoscape

Value

A dynamic map in Cytoscape automatically formatted for convenient viewing.

Examples

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)
                                      
## Not run: 
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")
         
## End(Not run)

shanawhite-UC/KEGGlincs documentation built on May 29, 2019, 8:07 p.m.