edge_mapping_info: Prepare edges for mapping

In uc-bd2k/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data [option]

Description

Modify the mapping information for desired look when graphed in Cytoscape

Usage

edge_mapping_info(expanded_edges, data_added = FALSE,
  significance_markup = FALSE, tidy_edge = TRUE)

Arguments

expanded_edges	The data frame object generated via the function expand_KEGG_edges() OR has been modified by the function add_edge_data()
data_added	A logical indicator; must be set to TRUE if user data has been added (i.e. edges modified by function add_edge_data())
significance_markup	A logical indicator; if set to TRUE will color edges based on direction and significance of correlation (as determined by user-data-analysis)
tidy_edge	A logical indicator; must be set to FALSE for expanded edges

Value

A data.frame object for edges that will be passed on to the function get_graph_object

Examples

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

#Default; no data added to edges:

p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
p53_edge_mapping_info <- edge_mapping_info(p53_edges) 

#If data is added to edges as additional attribute[s]:

p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 
                               "HA1E", data_type = "100_bing")

p53_edges_HA1E_data_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, 
                                            p53_HA1E_data, 
                                            data_column_no = c(3, 10,12),
                                            only_mapped = TRUE)
                                               
p53_edge_mapping_HA1E <- edge_mapping_info(p53_edges_HA1E_data_MAPPED, 
                                                      data_added = TRUE)
                                                      

uc-bd2k/KEGGlincs documentation built on May 3, 2019, 2:13 p.m.