riches: Strucutral and Functional Enrichment Analyses

##' @importFrom FELLA generateResultsGraph
##' @importFrom tidygraph activate
##' @importFrom ggthemes ptol_pal
##' @importFrom dplyr mutate
##' @importFrom stringr str_split_fixed coll
##' @importFrom ggraph create_layout ggraph geom_edge_link geom_node_point geom_node_text theme_graph
##' @importFrom tibble tibble
##' @importFrom ggplot2 aes scale_colour_manual coord_fixed labs

# setGeneric('plotGraph',function(x,comparison,type = 'diffusion'){
#   standardGeneric('plotGraph')
# })
# 
# setMethod('plotGraph',signature = 'FunctionalEnrichment',
#           function(x,comparison,type = 'diffusion'){
#             en <- x@results[[comparison]]
#             
#             FELLA <- x@network
#             
#             pg <- generateResultsGraph(method = type,object = en,data = FELLA,nlimit = 1000,LabelLengthAtPlot = 100) %>%
#               as_tbl_graph() %>%
#               activate(nodes)
#             
#             types <- pg %>%
#               nodes() %>%
#               .$com
#             
#             types[types == 1] <- 'Pathway'
#             types[types == 2] <- 'Module'
#             types[types == 3] <- 'Enzyme'
#             types[types == 4] <- 'Reaction'
#             types[types == 5] <- 'Compound'
#             
#             pg <- pg %>%
#               mutate(Type = factor(types,levels = c('Compound','Reaction','Enzyme','Module','Pathway')),
#                      label = str_split_fixed(label,coll(' - '),2)[,1])
#             
#             pageLayout <- pg %>%
#               create_layout('nicely') 
#             
#             pagePathways <- pageLayout %>%
#               filter(Type == 'Pathway')
#             
#             pageCompounds <- pageLayout %>%
#               filter(Type == 'Compound')
#             
#             nudgey <- ({pageLayout$y %>% max()} - {pageLayout$y %>% min()}) / 25
#             
#             colours <- tibble(Type = c('Compound','Reaction','Enzyme','Module','Pathway'),
#                               Colour = ptol_pal()(5))
#             
#             ggraph(pageLayout) +
#               geom_edge_link(alpha = 0.4) +
#               geom_node_point(aes(colour = Type),size = 3,alpha = 0.5) +
#               geom_node_text(data = pagePathways,aes(label = label),nudge_y = nudgey,size = 3,colour = 'black') +
#               geom_node_text(data = pageCompounds,aes(label = label),nudge_y = nudgey,size = 3,colour = 'black') +
#               scale_colour_manual(values = colours %>% filter(Type %in% unique(pg %>% nodes() %>% .$Type)) %>% .$Colour) +
#               theme_graph(base_size = 11,base_family = '') +
#               coord_fixed() +
#               labs(title = comparison) 
#           }
# )