R/extract_fpca_scores.R

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

#' Extract FPCA scores
#'
#' @param mxFDAobject object of class `mxFDA`
#' @param what what functional PCA data to extract, e.g. 'uni k'
#'
#' @details `r lifecycle::badge('stable')`
#'
#' @return fpca object
#'
#' @author Alex Soupir \email{`r alexsoupir_email`}
#'
#' @examples
#' #load ovarian mxFDA object
#' data('ovarian_FDA')
#'
#' #run ghe lfcm model
#' ovarian_FDA = run_fpca(ovarian_FDA, metric = "uni g", r = "r",
#'                        value = "fundiff",
#'                        analysis_vars = c("age", "survival_time"))
#'
#' #extract uni fpc scores
#' fpc = extract_fpca_scores(ovarian_FDA, 'uni g fpca')
#'
#' @export
extract_fpca_scores = function(mxFDAobject, what){
  #check if object is of class mxFDA
  if(!inherits(mxFDAobject, "mxFDA")) stop("supply object of class `mxFDA`")
  #get the right data
  if(length(what) != 1)
    stop("Please provide a single spatial metric to extract surface for")
  what = unlist(strsplit(what, split = " "))
  if(length(what) != 3)
    stop("Please provide either FPCA or mFPCA to extract")

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

  if(grepl("m", what[3]))
    return(dat[1:2])

  #combine metadata with the scores
  #need to have the same number of metadata as number of derived samples
  #pretty sure if the number of samples in metadata don't match the number of spatial samples this will not work
  #no alternatiave because score_df doesn't report sample ID with it.
  new_df = mxFDAobject@Metadata %>%
    dplyr::left_join(dat$score_df)
  return(new_df)
}