## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set( eval=FALSE ) ## ----------------------------------------------------------------------------- # if(!"RCy3" %in% installed.packages()){ # install.packages("BiocManager") # BiocManager::install("RCy3") # } # library(RCy3) # if(!"igraph" %in% installed.packages()){ # install.packages("igraph") # } # library(igraph) # if(!"plyr" %in% installed.packages()){ # install.packages("plyr") # } # library(plyr) ## ----------------------------------------------------------------------------- # cytoscapePing() ## ----------------------------------------------------------------------------- # lesmis <- system.file("extdata","lesmis.txt", package="RCy3") # dataSet <- read.table(lesmis, header = FALSE, sep = "\t") ## ----------------------------------------------------------------------------- # gD <- igraph::simplify(igraph::graph.data.frame(dataSet, directed=FALSE)) ## ----------------------------------------------------------------------------- # igraph::vcount(gD) # igraph::ecount(gD) ## ----------------------------------------------------------------------------- # degAll <- igraph::degree(gD, v = igraph::V(gD), mode = "all") ## ----------------------------------------------------------------------------- # betAll <- igraph::betweenness(gD, v = igraph::V(gD), directed = FALSE) / (((igraph::vcount(gD) - 1) * (igraph::vcount(gD)-2)) / 2) # betAll.norm <- (betAll - min(betAll))/(max(betAll) - min(betAll)) # rm(betAll) ## ----------------------------------------------------------------------------- # dsAll <- igraph::similarity.dice(gD, vids = igraph::V(gD), mode = "all") ## ----------------------------------------------------------------------------- # gD <- igraph::set.vertex.attribute(gD, "degree", index = igraph::V(gD), value = degAll) # gD <- igraph::set.vertex.attribute(gD, "betweenness", index = igraph::V(gD), value = betAll.norm) ## ----------------------------------------------------------------------------- # summary(gD) ## ----------------------------------------------------------------------------- # F1 <- function(x) {data.frame(V4 = dsAll[which(igraph::V(gD)$name == as.character(x$V1)), which(igraph::V(gD)$name == as.character(x$V2))])} # dataSet.ext <- plyr::ddply(dataSet, .variables=c("V1", "V2", "V3"), function(x) data.frame(F1(x))) # # gD <- igraph::set.edge.attribute(gD, "weight", index = igraph::E(gD), value = 0) # gD <- igraph::set.edge.attribute(gD, "similarity", index = igraph::E(gD), value = 0) ## ----------------------------------------------------------------------------- # for (i in 1:nrow(dataSet.ext)) # { # igraph::E(gD)[as.character(dataSet.ext$V1) %--% as.character(dataSet.ext$V2)]$weight <- as.numeric(dataSet.ext$V3) # igraph::E(gD)[as.character(dataSet.ext$V1) %--% as.character(dataSet.ext$V2)]$similarity <- as.numeric(dataSet.ext$V4) # } # rm(dataSet,dsAll, i, F1) ## ----------------------------------------------------------------------------- # summary(gD) ## ----------------------------------------------------------------------------- # createNetworkFromIgraph(gD,new.title='Les Miserables') ## ----------------------------------------------------------------------------- # getLayoutNames() ## ----------------------------------------------------------------------------- # getLayoutPropertyNames("fruchterman-rheingold") ## ----------------------------------------------------------------------------- # layoutNetwork('fruchterman-rheingold gravity_multiplier=1 nIterations=10') ## ----------------------------------------------------------------------------- # layoutNetwork('force-directed defaultSpringLength=70 defaultSpringCoefficient=0.000003') ## ----------------------------------------------------------------------------- # setNodeColorMapping('degree', c(min(degAll), mean(degAll), max(degAll)), c('#F5EDDD', '#F59777', '#F55333')) # lockNodeDimensions(TRUE) # setNodeSizeMapping('betweenness', c(min(betAll.norm), mean(betAll.norm), max(betAll.norm)), c(30, 60, 100)) ## ----------------------------------------------------------------------------- # setEdgeLineWidthMapping('weight', c(min(as.numeric(dataSet.ext$V3)), mean(as.numeric(dataSet.ext$V3)), max(as.numeric(dataSet.ext$V3))), c(1,3,5)) # setEdgeColorMapping('weight', c(min(as.numeric(dataSet.ext$V3)), mean(as.numeric(dataSet.ext$V3)), max(as.numeric(dataSet.ext$V3))), c('#BBEE00', '#77AA00', '#558800')) ## ----------------------------------------------------------------------------- # setBackgroundColorDefault('#D3D3D3') # setNodeBorderColorDefault('#000000') # setNodeBorderWidthDefault(3) # setNodeShapeDefault('ellipse') # setNodeFontSizeDefault(20) # setNodeLabelColorDefault('#000000') ## ----------------------------------------------------------------------------- # cytoscapeVersionInfo() ## ----------------------------------------------------------------------------- # sessionInfo()