1\name{cluster_mat} 2\alias{cluster_mat} 3\title{Cluster Matrix Rows in Annotated Heatmaps} 4\usage{ 5 cluster_mat(mat, param, distfun, hclustfun, reorderfun, 6 na.rm = TRUE, subset = NULL, verbose = FALSE) 7} 8\arguments{ 9 \item{mat}{original input matrix that has already been 10 appropriately subset in the caller function 11 (\code{aheatmap})} 12 13 \item{param}{clustering specifications} 14 15 \item{distfun}{Default distance method/function} 16 17 \item{hclustfun}{Default clustering (linkage) 18 method/function} 19 20 \item{reorderfun}{Default reordering function} 21 22 \item{na.rm}{Logical that specifies if NA values should 23 be removed} 24 25 \item{subset}{index (integer) vector specifying the 26 subset indexes used to subset mat. This is required to be 27 able to return the original indexes.} 28} 29\description{ 30 Cluster Matrix Rows in Annotated Heatmaps 31} 32\keyword{internal} 33 34