calculate the centered log ratio (CLR) for a data matrix (for compositional data)

calculate_clr.R

#' Centered log-ratio transformation
#'
#' @param m Count matrix with features in rows and samples (cells) in columns
#' @return matrix
#' @export
clr <- function(m) {
  apply(m, 2, function(x) {
    log1p(x = x/(exp(x = sum(log1p(x = x[x > 0]), na.rm = TRUE)/length(x = x))))
  })
}