R/LCC_Bipartide.R

In NetSci: Calculates Basic Network Measures Commonly Used in Network Medicine

#' LCC_Bipartide
#' @description LCC size for Rewire Bipartide Network
#' @param g Bipartide Graph to be rewired
#' @param N Number of resamples
#' @importFrom magrittr `%>%` `%<>%`
#' @importFrom igraph components graph_from_data_frame bipartite_mapping degree V E as_incidence_matrix induced_subgraph
#'
#'
#' @return a list with the LCC
#' - $LCCZ all values from the randomizations
#' - $mean the average LCC of the randomizations
#' - $sd the sd LCC of the randomizations
#' - $Z The Z-score
#' - $LCC the LCC of the original network
#' - $emp\_p the empirical p-value for the LCC
#' @export
#'
#' @examples
#' nodes = data.frame(c("D1", "D2", "D3", "D4", "D5",
#'                      "G1", "G2", "G3", "G4", "G6"),
#'                    type = c(TRUE, TRUE, TRUE, TRUE, TRUE,
#'                             FALSE, FALSE, FALSE, FALSE, FALSE))
#'
#' g = data.frame(from = c("D1", "D2", "D2", "D3", "D4", "D5", "D5", "D3"),
#'                to =   c("G1", "G1", "G2", "G3", "G4", "G4", "G1", "G6"))
#'
#' g = igraph::graph_from_data_frame(g, directed = FALSE, vertices = nodes)
#'
#' plot(g, layout = igraph::layout.bipartite)
#'
#' igraph::components(g)
#'
#'   # if (!require("BiocManager", quietly = TRUE))
#'   # install.packages("BiocManager")
#'  # BiocManager::install("BiRewire")
#'
#' # LCC_BIP = LCC_Component(g)
#' # Histogram_LCC(LCC_BIP)
#'
# LCC_Component = function(g, N = 1000){
#
#   original =  igraph::components(g)
#   cmp_o = original$csize %>% max
#   LCC = list()
#
#   for(i in 1:N){
#     cmp = birewire.rewire.bipartite(g, verbose = FALSE) %>%
#       igraph::components()
#     LCC[[i]] = cmp$csize %>% max()
#   }
#   LCC %<>% unlist()
#
#   muC = mean(LCC)
#   sdC = sd(LCC)
#   Z = (cmp_o-muC)/sdC
#   p = pvals(x = LCC, val = cmp_o )
#
#   out = list(LCC = cmp_o,
#     LCCZ = LCC,
#              mean = mean(LCC),
#              sd = sd(LCC),
#              Z = Z,
#     emp_p = p$p_gt
#                )
#   return(out)
# }