R/cAMARETTO_ColorOneModule.R

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

#' @title cAMARETTO_ColorOneModule
#'
#' Creates a network with one (or none) colored modules
#'
#' @param cAMARETTOnetworkM The output of the Module Network function.
#' @param cAMARETTOnetworkC The output of the Identify Communities function.
#' @param ModuleNr The module number that you want to highlight.
#'
#' @return None
#' 
#' @importFrom igraph as_data_frame degree E graph_from_data_frame
#'  layout_with_fr V graph.data.frame norm_coords edge.betweenness.community
#' @importFrom graphics legend plot
#' @importFrom tibble add_row tibble column_to_rownames rownames_to_column
#' @examples
#' try(
#' cAMARETTO_ColorOneModule(cAMARETTOnetworkM, cAMARETTOnetworkC, 2)
#' )
#' @export
cAMARETTO_ColorOneModule <- function(cAMARETTOnetworkM,
    cAMARETTOnetworkC, ModuleNr) {

    selected_group <- cAMARETTOnetworkC$community_list[
    names(cAMARETTOnetworkC$community_list)==ModuleNr]

    color_group <- cAMARETTOnetworkC$color_list[
    names(cAMARETTOnetworkC$color_list)==ModuleNr]
    
    Nodes_Mnetwork <- igraph::as_data_frame(cAMARETTOnetworkM$module_network,
        what="vertices")

    plot(cAMARETTOnetworkC$CommGraph,layout=cAMARETTOnetworkM$layoutMN,
        vertex.color=as.character(Nodes_Mnetwork$color),
        vertex.label=NA,
        vertex.frame.color=NA,
        edge.color="gray80",
        mark.groups = selected_group,
        mark.col=color_group,
        mark.border=NA,
        main=NA)

    legend(x = -1.5,
        y = -1.1+0.05*length(cAMARETTOnetworkM$colMN),
        legend = names(cAMARETTOnetworkM$colMN),
        col = cAMARETTOnetworkM$colMN,
        pch=19,
        bty="n",
        ncol=ceiling(length(cAMARETTOnetworkM$colMN)/5))
}