R/customCnet2Cytoscape.R

In fpsanz/enrichGene:

customCnet2Cytoscape <- function(kgg, category=NULL, nPath=NULL, byDE=FALSE){
    if(! "ggraph" %in% .packages()) require("ggraph")
    if(! "igraph" %in% .packages()) require("igraph")
    if(! "RCy3" %in% .packages()) require("RCy3")
    if(! "dplyr" %in% .packages()) require("dplyr")
    if(! "tidyr" %in% .packages()) require("tidyr")
    ## check if cytoscape is running
    a <- tryCatch( expr= { cytoscapePing() },
                   error = function(e){print("Error!! Cytoscape must be running")}
                   )
    ## define palette
    color_palette <- function(colors) colorRampPalette(colors)(n = 299)
    if(byDE){
        kgg <- kgg %>% arrange(-DE)
    }
    ## check parameters
    if(!is.null(category)){
        if(is.numeric(category)){
            tmp <- kgg[category, c(1,6)]
        } else{
            tmp <- kgg[kgg$Pathway %in% category, c(1,6)]
        }
    } else{
        tmp <- kgg[,c(1,6)]
    }
    if(!is.null(nPath)){
        if(is.numeric(nPath)){
            tmp <- tmp[1:nPath, ]
        } else{ stop("nPath must be numeric or NULL")}
    }
    # prepare data
    tmp2 <- tmp %>%  separate_rows( genes, convert=TRUE)
    g <- igraph::graph.data.frame(tmp2, directed=FALSE)
    size <- tmp2 %>% dplyr::select(Pathway) %>% group_by(Pathway) %>%  summarise(n=n())
    size <- left_join(tmp, size, by=c("Pathway"))
    size <- size$n
    V(g)$size <- min(size)/2
    n <- dim(tmp)[1]
    V(g)$size[1:n] <- size
    V(g)$pval <- NA
    V(g)$pval[1:n] <- kgg$P.DE[1:n]
    edge_layer <- geom_edge_link(alpha=.8, colour='darkgrey')
    fc <- V(g)$pval
    V(g)$color <- fc
    createNetworkFromIgraph(g, "customIgraph")
}