R/extract_fpca_object.R

In mxfda: A Functional Data Analysis Package for Spatial Single Cell Data

#' Extract FPCA object
#'
#' Function that extracts the FPCA object created either by [run_fpca()] or [run_mfpca()] from the `mxFDA` object
#'
#' @param mxFDAobject object of class `mxFDA`
#' @param what what functional PCA data to extract, e.g. 'uni k'
#'
#' @details
#' `r lifecycle::badge('stable')`
#'
#' Output object can be visualized with [refund.shiny::plot_shiny()]
#'
#' @return `fpca` object created with [run_fcm()]
#'
#' @author Alex Soupir \email{`r alexsoupir_email`}
#'
#' @examples
#' #load ovarian mxFDA object
#' data('ovarian_FDA')
#'
#' #run the FPCA
#' ovarian_FDA = run_fpca(ovarian_FDA, metric = "uni g", r = "r", value = "fundiff",
#'                        lightweight = TRUE,
#'                        pve = .99)
#'
#' #extract the fpca object
#' obj = extract_fpca_object(ovarian_FDA, "uni g fpca")
#'
#' @export
extract_fpca_object = function(mxFDAobject, what){
  if(!inherits(mxFDAobject, "mxFDA")) stop("supply object of class `mxFDA`")
  #check if object is of class mxFDA
  what = unlist(strsplit(what, split = " "))
  if(length(what) < 3) stop("need to specify FPCA or mFPCA")

  dat = get_data(mxFDAobject, what[1:2], type = what[3])

  if(grepl("m", what[3]))
    return(dat$mfpc_object)
  return(dat$fpc_object)
}