get_graph_object {KEGGlincs} | R Documentation

## Generate graph object from nodes and edges

### Description

Obtain a graph object in the form of an igraph with KEGG-specific graphical information

### Usage

    get_graph_object(node_mapping_info, expanded_edges,
      layered_nodes = FALSE)

### Arguments

`node_mapping_info` | The data.frame object generated by the function node_mapping_info()
`expanded_edges` | The data.frame object generated by the function edge_mapping_info()
`layered_nodes` | A logical indicator; if set to TRUE will create a graph with 'stacked' nodes that the user can manipulate when multiple nodes are mapped to one location

### Value

A list object with the node and edge information from the graph required for mapping.

### Examples

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

    p53_node_mapping_info <- node_mapping_info(p53_KEGG_mappings)
    p53_edge_mapping_info <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)

    #Default graph object will have 'expanded edges':
    expanded_edges_graph_object <- get_graph_object(p53_node_mapping_info,
                                                    p53_edge_mapping_info)

    #Graph with layered nodes:
    layered_nodes_graph_object <- get_graph_object(p53_node_mapping_info,
                                                   p53_edge_mapping_info,
                                                   layered_nodes = TRUE)

[Package KEGGlincs version 1.18.0 Index]