cyto_vis: Send graph to Cytoscape via CyREST

Description Usage Arguments Value Examples

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

1
2
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
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.