R/cAMARETTO_heatmap.R

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

#' @title cAMARETTO_heatmap
#'
#' Constructs a heatmap with the comparison between
#'  modules of two runs based on a hyper geometric test
#' 
#' @param cAMARETTOresults cAMARETTO_Run output
#' @param run1 name of run 1
#' @param run2 name of run 2
#'
#' @return None
#' @importFrom ComplexHeatmap Heatmap
#' @importFrom circlize colorRamp2
#' @importFrom tidyr spread
#' @importFrom tibble add_row tibble column_to_rownames rownames_to_column
#' @importFrom grid gpar
#' @importFrom dplyr select filter
#' @examples 
#' try(
#' cAMARETTO_heatmap(cAMARETTOresults, "LIHC", "GBM")
#' )
#' @export
cAMARETTO_heatmap<-function(cAMARETTOresults,run1,run2){
        Geneset2<-Geneset1<-p_value<-NULL

        results_filtered<-cAMARETTOresults$hgt_modules %>%
        dplyr::filter((grepl(run1,Geneset2)|grepl(run2,Geneset2))&
                (grepl(run1,Geneset1)|grepl(run2,Geneset1)))
        pvalue_matrix<-tidyr::spread(results_filtered %>%
            dplyr::select(Geneset2,
                            Geneset1,
                            p_value),key=Geneset1,value=p_value)
        pvalue_matrix<-tibble::column_to_rownames(pvalue_matrix,"Geneset2")
        pvalue_matrix<--log10(pvalue_matrix)
        Heatmap(pvalue_matrix,
                name = "Pvalues Compare Modules",
                column_title = "Regulator Genes\nExpression",
                show_column_names = TRUE,
                column_names_gp = gpar(fontsize = 8),
                row_names_gp = gpar(fontsize = 8),
                column_title_gp = grid::gpar(fontsize = 12, fontface = "bold"),
                col=colorRamp2(c(0, max(pvalue_matrix,na.rm = TRUE)),
                                c("white","darkred"))
        )
}