get_graph_object: Generate graph object from nodes and edges

In KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

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)

KEGGlincs documentation built on Nov. 8, 2020, 5:47 p.m.