cyto_vis {KEGGlincs} | R Documentation

## Send graph to Cytoscape via CyREST

### 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)

[Package KEGGlincs version 1.12.0 Index]