R/search_ghap.R

Defines functions search_ghap query_db

Documented in search_ghap

query_db <- function(pattern, field = "LABEL", df = ghap::meta_ghap, ...) {

  if (!field %in% names(df))
    stop(sprintf("field : '%s' not in %s : '%s'", field, class(df), deparse(substitute(df))))

  df[grepl(pattern = pattern, x = df[, field], ...), ]

}


#' @title api to search ghap respositories
#' @description use regular expression to search fields in ghap study meta data
#' @param query character, search expression
#' @param field character, column of meta data to search on, Default: 'LABEL'
#' @param complete boolean, only show complete cases of query result, Default: FALSE
#' @param ... parameters to pass to grepl
#' @return data.frame
#' @import dplyr
#' @importFrom DT datatable
#' @importFrom plyr ddply
#' @importFrom reshape2 dcast
#' @export
#' @examples
#' \donttest{search_ghap(c('^Birth','birth \\(days\\)$'),complete = FALSE)}
search_ghap <- function(query, field = "LABEL", complete = FALSE, ...) {
  y <- data.frame(query = query, stringsAsFactors = FALSE) %>%
    plyr::ddply(c("query"), .fun = query_db, ...)

  out <- y %>%
    dplyr::mutate_(COLS = paste0("sprintf(\"%s\n[%s]\",", field, ", variable)")) %>%
    reshape2::dcast(Study_Type + STUDYID + DOMAIN ~ COLS, value.var = "query")

  if (complete)
    out <- out %>%
    dplyr::filter_(~complete.cases(.))

  DT::datatable(out,
                extensions = c("Buttons", "Scroller", "ColReorder", "FixedColumns"),
                filter = "top",
                options = list(deferRender = TRUE,
                               scrollX = TRUE,
                               pageLength = 50,
                               scrollY = 500,
                               scroller = TRUE,
                               dom = "Bfrtip",
                               colReorder = TRUE,
                               fixedColumns = TRUE,
                               buttons = c("copy", "csv", "excel", "pdf", "print", "colvis")
                               )
                )

  #invisible(out)
}
HBGDki/ghap documentation built on Sept. 23, 2017, 8:45 a.m.