R/plot_qq.r

In boxuancui/DataExplorer: Automate Data Exploration and Treatment

#' Plot QQ plot
#'
#' Plot quantile-quantile for each continuous feature
#' @param data input data
#' @param by feature name to be broken down by. If selecting a continuous feature, it will be grouped by 5 equal ranges, otherwise, all existing categories for a discrete feature. Default is \code{NULL}.
#' @param sampled_rows number of rows to sample if data has too many rows. Default is all rows, which means do not sample.
#' @param geom_qq_args a list of other arguments to \link{geom_qq}
#' @param geom_qq_line_args a list of other arguments to \link{geom_qq_line}
#' @param title plot title
#' @param ggtheme complete ggplot2 themes. Default is \link{theme_gray}.
#' @param theme_config a list of configurations to be passed to \link{theme}
#' @param nrow number of rows per page. Default is 3.
#' @param ncol number of columns per page. Default is 3.
#' @param parallel enable parallel? Default is \code{FALSE}.
#' @return invisibly return the named list of ggplot objects
#' @keywords plot_qq
#' @import data.table
#' @import ggplot2
#' @export
#' @examples
#' plot_qq(iris)
#' plot_qq(iris, by = "Species", ncol = 2L)
#'
#' plot_qq(
#'   data = airquality,
#'   geom_qq_args = list(na.rm = TRUE),
#'   geom_qq_line_args = list(na.rm = TRUE)
#' )

plot_qq <- function(data, by = NULL, sampled_rows = nrow(data),
                    geom_qq_args = list(), geom_qq_line_args = list(),
                    title = NULL,
                    ggtheme = theme_gray(), theme_config = list(),
                    nrow = 3L, ncol = 3L,
                    parallel = FALSE) {
  ## Declare variable first to pass R CMD check
  variable <- value <- group <- NULL
  ## Check if input is data.table
  if (!is.data.table(data)) data <- data.table(data)
  ## Sample data if necessary
  if (sampled_rows < nrow(data)) data <- data[sample.int(nrow(data), sampled_rows)]
  ## Stop if no continuous features
  split_obj <- split_columns(data)
  if (split_obj$num_continuous == 0) stop("No Continuous Features!")
  ## Get continuous features
  continuous <- split_obj$continuous
  ## Check feature to be broken down
  if (!is.null(by)) {
    by_feature <- data[[by]]
    if (is.null(by_feature)) stop(paste0("Feature \"", by, "\" not found!"))
    if (is.numeric(by_feature)) {
      dt <- suppressWarnings(melt.data.table(data.table(continuous, "group" = cut_interval(by_feature, 5)), id.vars = "group", variable.factor = FALSE))
    } else {
      dt <- suppressWarnings(melt.data.table(data.table(continuous, "group" = by_feature), id.vars = "group", variable.factor = FALSE))
    }
    dt2 <- dt[variable != by]
  } else {
    dt2 <- suppressWarnings(melt.data.table(data.table(continuous), measure.vars = names(continuous), variable.factor = FALSE))
  }
  feature_names <- unique(dt2[["variable"]])
  ## Calculate number of pages
  layout <- .getPageLayout(nrow, ncol, ncol(continuous))
  ## Create list of ggplot objects
  plot_list <- .lapply(
    parallel = parallel,
    X = layout,
    FUN = function(x) {
      if (is.null(by)) {
        ggplot(dt2[variable %in% feature_names[x]], aes(sample = value)) +
          do.call("geom_qq", geom_qq_args) +
          do.call("geom_qq_line", geom_qq_line_args)
      } else {
        ggplot(dt2[variable %in% feature_names[x]], aes(sample = value, color = group)) +
          do.call("geom_qq", geom_qq_args) +
          do.call("geom_qq_line", geom_qq_line_args)
      }
    }
  )
  ## Plot objects
  class(plot_list) <- c("multiple", class(plot_list))
  plotDataExplorer(
    plot_obj = plot_list,
    page_layout = layout,
    title = title,
    ggtheme = ggtheme,
    theme_config = theme_config,
    facet_wrap_args = list(
      "facet" = ~ variable,
      "nrow" = nrow,
      "ncol" = ncol,
      "scales" = "free_y"
    )
  )
}