edge_mapping_info {KEGGlincs} | R Documentation |
Modify the mapping information for desired look when graphed in Cytoscape
edge_mapping_info(expanded_edges, data_added = FALSE, significance_markup = FALSE, tidy_edge = TRUE)
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 |
A data.frame object for edges that will be passed on to the function get_graph_object
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)