R/plot.disease_expose.R

In npeters1322/hospEpi: Perform Basic Hospital Epidemiology Tasks

#' @title Plot a \code{disease_expose} Object
#'
#' @description Create grouped bar charts for each disease-exposure combination on one page
#'
#' @param x an object of class \code{disease_expose}, created with \code{\link{disease_expose}}
#' @param ... additional arguments to be passed to \code{\link{geom_bar}}, such as \code{position}
#'
#' @return A \code{\link{gtable}} object of grouped bar charts on one page
#' @export
#'
#' @importFrom ggplot2 ggplot aes geom_bar xlab ylab labs
#' @importFrom snakecase to_title_case
#' @importFrom gridExtra grid.arrange
#' @importFrom gtable gtable
#'
#' @examples
#' de_data <- disease_expose_data # use the example data in the package
#'
#' cleaned_de_data <- clean_disease_expose(data = de_data, disease = "disease", noDisease = "No", exposures = c("exposure1", "exposure2", "exposure3")) # clean the data using specific columns in the dataset
#'
#' \dontrun{
#' de_object <- disease_expose(cleaned_de_data) # the best way to create a disease_expose object is by using the helper and selecting your choices in the Shiny gadget
#' }
#'
#' de_object <- new_disease_expose(cleaned_de_data, disease = 1, exposures = 2:8) # another way to create a disease_expose object is to use the constructor and manually enter the information
#'
#' plot(x = de_object) # plot your disease_expose object
#'
#' plot(x = de_object, position = 'dodge') # provide an input to geom_bar using the ... argument to customize the plot a little more
#'
plot.disease_expose <- function(x, ...) {

  plots <- lapply(seq_along(x[,-1]), function(i){

    curr_col <- names(x[i+1])

    ggplot(data = x, aes(x = x[,curr_col], fill = as.factor(x[,1]))) +
      geom_bar(...) +
      xlab(to_title_case(curr_col)) +
      ylab("Count") +
      labs(fill = "Diseased")

  })

  if(length(plots) <= 12){

    num_plot_cols <- floor(sqrt(length(plots)))

    do.call("grid.arrange", c(plots, ncol = num_plot_cols))

  } else {

    warning("Only the first 12 plots were created. Subset the argument to the function to include the disease column and other exposure columns if wanted. Ex. plot(data[,c(1,13:20), where 1 is the disease column and 13:20 are the other exposures you want to plot. You can also use the character names of the columns to subset instead.")

    do.call("grid.arrange", c(plots[1:12], ncol = 3))

  }

}