R/toolsNet.R

In belleau/subnetsim: Validating that a specific subnetwork has significantly more interactions than expected by randomness

# library(hash)
#
#
# readNetworkWithSub <- function(netFileName, subNetFileName){
#     netFile <- read.table(netFileName, header = FALSE, stringsAsFactors = FALSE,fill = TRUE, na.strings = "")
#     subNet <- read.table(subNetFileName, header = FALSE, stringsAsFactors = FALSE,fill = TRUE, na.strings = "")
#     netAll <- hash()
#     netLinks <- data.frame(n1 = rep(NA, length(netFile[!(is.na(netFile[,3])),1])),
#                           n2 = rep(NA, length(netFile[!(is.na(netFile[,3])),1])))
#
#
#     l <- 1
#     for( i in seq_len(length(netFile[,1]))){
#         if(!(is.na(netFile[i,3]))){
#             if(!(has.key(key = netFile[i,1], hash = netAll))){
#                 netAll[[netFile[i,1]]] <- hash()
#             }
#             netAll[[netFile[i,1]]][[netFile[i,3]]] <- l
#
#             if(!(has.key(key = netFile[i,3], hash = netAll))){
#                 netAll[[netFile[i,3]]] <- hash()
#             }
#             netAll[[netFile[i,3]]][[netFile[i,1]]] <- l
#
#             l <- l+1
#         }
#
#     }
#
#
#     nodesAll <- keys(netAll)
#
#     nodesAll <- nodesAll[order(nodesAll)]
#
#     nodesAllSub <- unique(c(subNet[,1], subNet[!is.na(subNet[,3]),3]))
#     nodesSubNet <- intersect(nodesAllSub, nodesAll)
#
#     nodesSubNet <- nodesSubNet[order(nodesSubNet)]
#     if(length(nodesSubNet) != length(nodesAllSub)){
#         warning("Subnetwork  not include in the network, keep only the intersection")
#     }
#     network <- list(netAll=netAll, nodesAll=nodesAll, nodesSubNet=nodesSubNet)
# }
#
#
# simuleSubNet <- function(netAll, nodesAll, nbIter, nbNodes, seedV){
#     set.seed(seedV)
#     pastSub <- hash()
#
#     distSubNet <- data.frame(nbNodes=rep(NA,nbIter), nbLink=rep(NA,nbIter), nbLinkSub=rep(NA,nbIter))
#
#     for(i in seq_len(nbIter)){
#         nodesSub <-sample(length(nodesAll), nbNodes, replace = FALSE)
#         nodesSub <- nodesSub[order(nodesSub)]
#         string_node <- paste(unlist(as.character(nodesSub)),sep="_", collapse = '_')
#
#
#         if(!(has.key(string_node, pastSub))){
#             pastSub[[string_node]] <- 1
#             distSubNet[i, 1:2] <- getOneLink(netAll, nodesAll[nodesSub])
#             distSubNet[i, 3] <- getSubNet(netAll, nodesAll[nodesSub])
#         }
#     }
#
#     return(distSubNet)
# }
#
# getOneLink <- function(netAll, nodesSel){
#
#     nodesFirst <- hash()
#     linkFirst <- hash()
#     cptNodes <- 0
#     cptLink <- 0
#     for(i in seq_len(length(nodesSel))){
#         listNodLink <- keys(netAll[[ nodesSel[i] ]])
#         if(!(has.key( nodesSel[i], nodesFirst))){
#             nodesFirst[[nodesSel[i]]] <- 1
#             cptNodes <- cptNodes + 1
#         }
#         for(j in seq_len(length(listNodLink))){
#             if(!(has.key( listNodLink[j], nodesFirst))){
#                 nodesFirst[[listNodLink[j]]] <- 1
#                 cptNodes <- cptNodes + 1
#             }
#
#             if(!(has.key(key = as.character(netAll[[nodesSel[i]]][[listNodLink[j]]]), hash = linkFirst))){
#                 linkFirst[[as.character(netAll[[nodesSel[i]]][[listNodLink[j]]]) ]] <- 1
#                 cptLink <- cptLink + 1
#             }
#         }
#     }
#     return(c(cptNodes, cptLink))
# }
#
# getSubNet <- function(netAll, nodesSel){
#
#     nodesSub <- hash()
#
#     for(i in seq_len(length(nodesSel))){
#         nodesSub[[nodesSel[i]]] <- 1
#     }
#
#     linkFirst <- hash()
#     cptNodes <- 0
#     cptLink <- 0
#     for(i in seq_len(length(nodesSel))){
#         listNodLink <- keys(netAll[[ nodesSel[i] ]])
#         for(j in seq_len(length(listNodLink))){
#
#             if(has.key(key = listNodLink[j], hash = nodesSub)){
#                 if(!(has.key(key = as.character(netAll[[nodesSel[i]]][[listNodLink[j]]]), hash = linkFirst))){
#                     linkFirst[[as.character(netAll[[nodesSel[i]]][[listNodLink[j]]]) ]] <- 1
#                     cptLink <- cptLink + 1
#                 }
#             }
#         }
#     }
#     return(cptLink)
# }
#
#
#
#
#
# ##############################################
# ##############################################
# ##############################################
#
#
# library(hash)
#
#
# IRGEN_all <- read.table("data/IRGEN_all.sif", header = FALSE, stringsAsFactors = FALSE,fill = TRUE, na.strings = "")
# IRGEN_can <- read.table("data/IRGEN_Diabetes_candidats.sif", header = FALSE, stringsAsFactors = FALSE,fill = TRUE, na.strings = "")
# colnames(IRGEN_all) <- c("N1", "L", "N2")
# head(IRGEN_all)
#
# netAll <- hash()
# netLink <- data.frame(n1 = rep(NA, length(IRGEN_all[!(is.na(IRGEN_all[,3])),1])),
#                       n2 = rep(NA, length(IRGEN_all[!(is.na(IRGEN_all[,3])),1])))
# l <- 1
# for( i in seq_len(length(IRGEN_all[,1]))){
#     if(!(is.na(IRGEN_all[i,3]))){
#         if(!(has.key(key = IRGEN_all[i,1], hash = netAll))){
#             netAll[[IRGEN_all[i,1]]] <- hash()
#         }
#         netAll[[IRGEN_all[i,1]]][[IRGEN_all[i,3]]] <- l
#
#         if(!(has.key(key = IRGEN_all[i,3], hash = netAll))){
#             netAll[[IRGEN_all[i,3]]] <- hash()
#         }
#         netAll[[IRGEN_all[i,3]]][[IRGEN_all[i,1]]] <- l
#         netLink[l,1] <- IRGEN_all[i,1]
#         netLink[l,2] <- IRGEN_all[i,3]
#         l <- l+1
#     }
#
# }
#
# nodesAll <- keys(netAll)
#
# nodesOrder <- order(nodesAll)
# nodesAll <- nodesAll[nodesOrder]
#
#
#
#
#
# res <- simuleSubNet(netAll, nodesAll, 10000, 94,32)
#
# library(ggplot2)
# breaks <- quantile(res$nbNodes,seq(0,1,by=0.01))
#
# ggplot(res, aes(x=nbNodes)) +
#     geom_histogram(breaks=breaks,aes(y=..density..),colour="black",fill=c("black"))
#
# colnames(res) <- c('nbNodes','nbLinks', 'nbLinksSub')
# df <-data.frame(nbNodes=272)
#
# gp1 <- ggplot(res, aes(x=nbNodes)) +
#     geom_histogram(colour="black",fill=c("black")) +
#     geom_vline(data = df,
#                aes(xintercept = nbNodes,
#                    color="observed"), linetype="longdash",
#                show.legend=TRUE)
# print(gp1)
# ggsave(paste0("data/nodesOneLink.pdf"), gp1, width=7,height=5)
#
# df <-data.frame(nbLinks=1070)
# gp2 <- ggplot(res, aes(x=nbLinks)) +
#     geom_histogram(colour="black",fill=c("black")) +
#     geom_vline(data = df,
#                aes(xintercept = nbLinks,
#                    color="observed"), linetype="longdash",
#                show.legend=TRUE)
# ggsave(paste0("data/linkssOneLink.pdf"), gp2, width=7,height=5)
# df <-data.frame(nbLinks=330)
# gp3 <- ggplot(res, aes(x=nbLinksSub)) +
#     geom_histogram(colour="black",fill=c("black")) +
#     geom_vline(data = df,
#                aes(xintercept = nbLinks,
#                    color="observed"), linetype="longdash",
#                show.legend=TRUE)
# ggsave(paste0("data/nodesSubNet.pdf"), gp3, width=7,height=5)
#
#
# netAll <- hash()
# if(!(is.na(IRGEN_all[i,3]))){
#     if(!(has.key(key = IRGEN_all[i,1], hash = netAll))){
#         netAll[[IRGEN_all[i,1]]] <- hash()
#     }
#     netAll[[IRGEN_all[i,1]]][[IRGEN_all[i,3]]] <- l
#
#     if(!(has.key(key = IRGEN_all[i,3], hash = netAll))){
#         netAll[[IRGEN_all[i,3]]] <- hash()
#     }
#     netAll[[IRGEN_all[i,3]]][[IRGEN_all[i,1]]] <- l
#     netLink[l,1] <- IRGEN_all[i,1]
#     netLink[l,2] <- IRGEN_all[i,3]
#     l <- l+1
# }
#
# inserLink <- function(x,netAll, netLink){
#     if(!(is.na(x[3]))){
#         if(!(has.key(key = x[1], hash = netAll))){
#             netAll[[x[1]]] <- hash()
#         }
#         l <- length(netLink[!(is.na(netLink[,1])), 1])
#         netAll[[x[1]]][[x[3]]] <- l + 1
#         if(!(has.key(key = x[3], hash = netAll))){
#             netAll[[x[3]]] <- hash()
#         }
#         netAll[[x[3]]][[x[1]]] <- l + 1
#         netLink[l+1,1] <- x[1]
#         netLink[l+1,2] <- x[3]
#
#     }else{
#         if(!(has.key(key = x[1], hash = netAll))){
#             netAll[[x[1]]] <- hash()
#         }
#     }
#     return(c(x[1], x[3]))
# }
# netAll <- hash()
# netLink <- data.frame(n1 = rep(NA, length(IRGEN_all[!(is.na(netFile[,3])),1])),
#                       n2 = rep(NA, length(IRGEN_all[!(is.na(netFile[,3])),1])))
#
# bla <- createNetwork("data/IRGEN_all.sif", "data/IRGEN_Diabetes_candidats.sif")
# getOneLink(bla$netAll, bla$nodesSubNet)
#
#
# res <- simuleSubNet(bla$netAll, bla$nodesAll, 10000, 94,32)