R/brain_join.R

In neuroconductor/ggseg: Plotting Tool for Brain Atlases

#' Join atlas and data
#'
#' Joins data frame with a brain-atlas
#' object.
#'
#' @param data data.frame
#' @param atlas atlas data
#' @param by optional character vector of column to join by
#'
#' @return either an sf-object or a tibble with merged atlas and data
#' @export
#' @importFrom dplyr is.grouped_df full_join as_tibble
#' @importFrom tidyr nest unnest
#' @importFrom sf st_as_sf
#' @examples
#' someData = data.frame(
#'     region = c("transverse temporal", "insula",
#'                 "precentral","superior parietal"),
#'     p = sample(seq(0,.5,.001), 4),
#'     stringsAsFactors = FALSE)
#'
#' brain_join(someData, dk)
#' brain_join(someData, dk, "region")
#'
brain_join <- function(data, atlas, by = NULL){
  atlas <- as.data.frame(atlas)

  if(is.null(by)){
    by <- names(data)[names(data) %in% names(atlas)]
    message(paste0("merging atlas and data by ",
                   paste(sapply(by, function(x) paste0("'", x, "'")),
                         collapse = ", ")))
  }

  if(is.grouped_df(data)){

    data2 <- nest(data)
    data2$data <- lapply(1:nrow(data2),
                         function(x) full_join(atlas,
                                               data2$data[[x]],
                                               by = by))

    dt <- unnest(data2, data)

  }else{
    dt <- full_join(atlas,
                    data,
                    by = by)
  }

  errs <- dt[is.na(dt$atlas),]

  if(nrow(errs) > 0){
    errs <- dplyr::select(errs, -starts_with("."))
    errs <- dplyr::as_tibble(errs)

    warning(paste("Some data not merged properly. Check for naming errors in data:",
                  paste0(capture.output(errs)[-1], collapse="\n"), sep="\n"),
            call. = FALSE)
  }

  if("geometry" %in% names(dt)){
    st_as_sf(dt)
  }else{
    as_tibble(dt)
  }
}