R/plot-ggclust.R

In xiangpin/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

#' @title plot the result of hierarchical cluster analysis for the samples
#' @param obj R object, treedata object.
#' @param layout character, the layout of tree, see also \code{\link[ggtree]{ggtree}}.
#' @param factorNames character, default is NULL.
#' @param factorLevels list, default is NULL.
#' @param pointsize numeric, the size of point, default is 2.
#' @param fontsize numeric, the size of text of tiplabel, default is 2.6.
#' @param hjust numeric, default is -0.1
#' @param ..., additional params, see also \code{\link[ggtree]{geom_tippoint}}
#' @return the figures of hierarchical cluster.
#' @author Shuangbin Xu
#' @export
#' @examples
#' \dontrun{
#' library(phyloseq)
#' library(ggtree)
#' library(ggplot2)
#' data(GlobalPatterns)
#' subGlobal <- subset_samples(GlobalPatterns,
#'          SampleType %in% c("Feces", "Mock", "Ocean", "Skin"))
#' hcsample <- get_clust(subGlobal, distmethod="jaccard",
#'                   method="hellinger", hclustmethod="average")
#' hc_p <- ggclust(hcsample, layout = "rectangular",
#'                 pointsize=1, fontsize=0,
#'                 factorNames=c("SampleType")) +
#'         theme_tree2(legend.position="right",
#'                     plot.title = element_text(face="bold", lineheight=25,hjust=0.5))
#' }
ggclust <- function(obj,...){
    UseMethod("ggclust")
}

#' @method ggclust treedata
#' @rdname ggclust
#' @importFrom ggtree ggtree geom_tippoint geom_tiplab
#' @importFrom ggplot2 labs element_text
#' @export
ggclust.treedata <- function(obj, 
                             layout="rectangular",
                             factorNames=NULL,
                             factorLevels=NULL,
                             pointsize=2,
                             fontsize=2.6,
                             hjust=-0.1,
                             ...){
    tippoint <- NULL
    if (!all(dim(obj@data)==0)){
        if(!is.null(factorNames)){
            tmpfactormap <- set_factormap(factorNames)
        }else{
            tmpfactormap <- set_factormap(colnames(obj@data)[-1])
        }
        if(!is.null(factorLevels)){
            obj@data <- setfactorlevels(obj@data, factorLevels)
        }
        tippoint <- geom_tippoint(tmpfactormap, size=pointsize)
    }
    samplehcp <- ggtree(obj, layout=layout)
    if (!is.null(tippoint)){
        samplehcp <- samplehcp + tippoint
    }
    samplehcp <- samplehcp + 
                 geom_tiplab(size=fontsize, hjust=hjust, ...) 
    if (!is.null(attr(obj, "distmethod"))){
        samplehcp <- samplehcp + labs(title=paste0("Hierarchical Cluster of Samples ", "(", attr(obj, "distmethod"), ")"))
    }
    samplehcp <- samplehcp + 
                 theme(plot.title = element_text(face="bold", lineheight=25, hjust=0.5))
    return(samplehcp)
}

#' @importFrom ggplot2 aes_string
#' @keywords internal
set_factormap <- function(namelist){
    if (length(namelist)==1){
        tmpfactormap <- aes_string(color=namelist[1])
    }else{
        tmpfactormap <- aes_string(color=namelist[1],
                                   shape=namelist[2])
    }
    return(tmpfactormap)
}