delete make_cluster

#' Reorder matrix_data by hierarchical cluster

#' @title Hierarchical Clustering

#' @param md a matrix_data object.

#' @param index a integer or character index, specifying which matrix to cluster by.

#' @param cluster one of "all", "row", "col" or "none".

#' @param cluster_method the clustering agglomeration method to be used.

#' @param row_dist,col_dist NULL (default) or \code{dist_func()}.

#' @return a modified matrix_data object.

#' @rdname make_cluster

#' @author Hou Yun

#' @export

make_cluster <- function(md,

                         index = 1,

                         cluster = "none",

                         cluster_method = "complete",

                         row_dist = NULL,

                         col_dist = NULL)

{

  if (is_grouped_matrix_data(md)) {

    return(md)

  }

  stopifnot(is_matrix_data(md))

  cluster <- match.arg(cluster, c("all", "row", "col", "none"))

  if (cluster == "none") {

    return(md)

  }

  x <- md[[index]]

  attrs <- attributes(md)

  if(is.null(row_dist)) {

    row_dist <- dist_func()

  }

  if(is.null(col_dist)) {

    col_dist <- dist_func()

  }

  if (cluster == "all") {

    row_hc <- hclust(row_dist(x), method = cluster_method)

    col_hc <- hclust(gdist(t(x)), method = cluster_method)

    md <- lapply(md, function(.md) {

      .md[get_order(row_hc), get_order(col_hc)]

    })

  } else if (cluster == "row") {

    row_hc <- hclust(row_dist(x), method = cluster_method)

    md <- lapply(md, function(.md) {

      .md[get_order(row_hc), , drop = FALSE]

    })

  } else {

    col_hc <- hclust(gdist(t(x)), method = cluster_method)

    md <- lapply(md, function(.md) {

      .md[get_order(row_hc), , drop = FALSE]

    })

  }

  structure(.Data = md,

            type = attrs$type,

            diag = attrs$diag,

            class = "matrix_data")

}

% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/cluster-and-reorder.R

\name{make_cluster}

\alias{make_cluster}

\title{Hierarchical Clustering}

\usage{

make_cluster(

  md,

  index = 1,

  cluster = "none",

  cluster_method = "complete",

  row_dist = NULL,

  col_dist = NULL

)

}

\arguments{

\item{md}{a matrix_data object.}

\item{index}{a integer or character index, specifying which matrix to cluster by.}

\item{cluster}{one of "all", "row", "col" or "none".}

\item{cluster_method}{the clustering agglomeration method to be used.}

\item{row_dist, col_dist}{NULL (default) or \code{dist_func()}.}

}

\value{

a modified matrix_data object.

}

\description{

Reorder matrix_data by hierarchical cluster

}

\author{

Hou Yun

}