R/subset-COMPASSContainer.R

In COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells

##' Subset a COMPASSContainer
##'
##' Use this function to subset a \code{COMPASSContainer}.
##'
##' @param x A \code{COMPASSContainer}.
##' @param subset A logical expression, evaluated within the metadata,
##'   indicating which entries to keep.
##' @param ... other arguments passed to 'COMPASSContainer' call.
##' @export
##' @examples
##' subset(CC, iid == "iid_1")
subset.COMPASSContainer <- function(x, subset, ...) {

  call <- match.call()$subset

  keep <- eval(call, envir=x$meta)
  if (!is.logical(keep)) {
    stop("'subset' should evaluate to a logical result")
  }

  if (!length(keep)) {
    stop("Subsetting has removed all samples!")
  }

  good_samples <- unique(x$meta[[ x$sample_id ]][keep])

  ## subset everything
  output <- COMPASSContainer(
    data=x$data[good_samples],
    counts=x$counts[good_samples],
    meta=x$meta[keep, ],
    individual_id=x$individual_id,
    sample_id=x$sample_id
    , ...
  )
  setattr(output, "class", "COMPASSContainer")
  return(output)

}