R/assignClusters.R

In plbaldoni/mikado: What the package does (short line)

#' Initializer for mikado
#'
#' Add description here
#'
#' @param object a mikadoDataSet
#' @param initializer the output of the function initializer
#' @param control list of control arguments from controlEM()
#'
#' @return
#' Add return here
#'
#' @author Pedro L. Baldoni, \email{pedrobaldoni@gmail.com}
#' @references
#' \url{https://github.com/plbaldoni/epigraHMM}
#'
#' @import data.table
#' @importFrom  stats rbinom dbinom glm quasibinomial
#' @rawNamespace import(SummarizedExperiment, except = shift)
#' @rawNamespace import(S4Vectors, except = c(first,second))
#' @importFrom foreach %dopar%
#' @importFrom magrittr %<>%
#'
#' @export
assignClusters <- function(object,initializer,control){
    
    # Creating control elements
    
    for(i in seq_along(control)){assign(names(control)[i],control[[i]])}
    
    # Running heatmaps
    
    if(is.null(clusters)){
        
        # Plotting without assignments
        
        pheatmap::pheatmap(as.matrix(initializer$dist),
                           color=viridis::magma(255),
                           cluster_rows=initializer$hclust,
                           cluster_cols=initializer$hclust,
                           border_color = NA,
                           show_rownames=FALSE, show_colnames=FALSE)
        
        # Getting input from the user
        
        clusters <- utils::menu(1:10, title="How many clusters you want to asssign?")
    } 
    
    # Updating assignments
    
    SummarizedExperiment::colData(object) <- cbind(SummarizedExperiment::colData(object),
                                                   assignedClusters = as.factor(stats::cutree(tree = initializer$hclust,k = clusters)))
    
    SummarizedExperiment::colData(object)$assignedClusters[which(unlist(lapply(initializer$par,function(x){all(is.na(x$pi))})))] <- NA
    
    # Plotting with assignments
    
    colClusters <- Polychrome::kelly.colors()[-c(1,2)][seq_len(clusters)]
    names(colClusters) <- seq_len(clusters)
    
    pheatmap::pheatmap(as.matrix(initializer$dist),
                       color=viridis::magma(255),
                       cluster_rows=initializer$hclust,
                       cluster_cols=initializer$hclust,
                       border_color = NA,
                       annotation_colors = list(Clusters = colClusters),
                       annotation_col=data.frame(Clusters = SummarizedExperiment::colData(object)[['assignedClusters']]),
                       show_rownames=FALSE, show_colnames=FALSE)
    
    return(object)
}