R/cAMARETTO_modulenetwork.R

In broadinstitute/CommunityAMARETTO: CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

#' @title cAMARETTO_ModuleNetwork
#' 
#' Creates a module network.
#'
#' @param cAMARETTOresults cAMARETTOresults object
#' @param pvalue pvalue cut-off for each gene set
#' @param inter minimal overlap between two gene sets
#' @param color_list An optional list with colors
#' @param edge_method Define edge weights based 
#' p-values or overlap between the gene sets.
#' @param plot_network If TRUE, plots the Community Network at the end.
#'
#' @return a list with the module network, layout for the network,
#'  used p-value, used overlap en colors
#' @importFrom utils globalVariables
#' @importFrom randomcoloR randomColor
#' @importFrom igraph as_data_frame degree E graph_from_data_frame 
#' layout_with_fr V graph.data.frame norm_coords edge.betweenness.community
#' @importFrom dplyr filter mutate select
#' 
#' @examples 
#' try(
#' cAMARETTOnetworkM<-cAMARETTO_ModuleNetwork(cAMARETTOresults,0.10,5)
#' )
#' @export
cAMARETTO_ModuleNetwork<-function(cAMARETTOresults,
                                    pvalue = 0.05,
                                    inter = 5,
                                    color_list = NULL,
                                    edge_method = "pvalue",
                                    plot_network = TRUE){

    ############################################################
    #if(getRversion() >= "2.15.1")  utils::globalVariables(c("."))
    ############################################################
    padj<-n_Overlapping<-modulenames<-NULL
    RunName1<-RunName2<-NULL
    output_hgt_allcombinations_filtered <- cAMARETTOresults$hgt_modules %>% 
    dplyr::filter(padj<=pvalue & n_Overlapping>=inter)
    node_information <- as.data.frame(unique(
        c(output_hgt_allcombinations_filtered$Geneset1,
        output_hgt_allcombinations_filtered$Geneset2)
        ))
    colnames(node_information) <- c("modulenames")
    node_information <- node_information %>%
        dplyr::mutate(run=sub("\\|.*$","",modulenames))
    module_network <- graph_from_data_frame(
        d=output_hgt_allcombinations_filtered%>%
            dplyr::select(-RunName1,-RunName2),
        vertices=node_information, directed=FALSE)
    if (is.null(color_list)){
        color_list <- randomcoloR::randomColor(length(c(
        cAMARETTOresults$runnames,cAMARETTOresults$gmtnames)),
        luminosity="dark")
        names(color_list) <- c(cAMARETTOresults$runnames,
                                cAMARETTOresults$gmtnames)
    } else {
    c(cAMARETTOresults$runnames,
        cAMARETTOresults$gmtnames) %in% names(color_list)
    }
    igraph::V(module_network)$color <- color_list[igraph::V(module_network)$run]
    igraph::V(module_network)$size <- 2*sqrt(igraph::degree(module_network,
                                        mode="all"))
    if (edge_method=="pvalue"){
        igraph::E(module_network)$width <-
        -(log10(igraph::E(module_network)$p_value))*0.2
    } else if (edge_method=="overlap"){
        igraph::E(module_network)$width <- igraph::E(
            module_network)$n_Overlapping/8
    } else {
        stop("The edge method is not properly defined.")
    }
    layoutMN <- layout_with_fr(module_network)
    if(plot_network){
        plot(module_network, vertex.frame.color=NA,
            layout=layoutMN, vertex.label=NA, main="Module network",
            edge.color="gray80")
        legendMN <- legend(x = -1.5,
                        y = -1.1+0.05*length(color_list),
                        legend = names(color_list),
                        col = color_list,
                        pch=19,
                        bty="n",
                        ncol=ceiling(length(color_list)/5))
        legendMN
    }
    return(list(module_network=module_network,
            layoutMN=layoutMN, pvalue=pvalue,
            inter=inter, colMN=color_list))
}