R/plotBlandAltman.R

In nwisn/blandPower: Tools for Bland-Altman Analysis

#' Bland-Altman plot
#'
#' @param x measurement vector from device 1
#' @param y measurement vector from device 2
#' @param gamma alpha level for calculating limits of agreement
#' @param alpha alpha level for calculating limits of agreement confidence intervals
#' @param sigfigs number of significant digits to display
#' @return a ggplot2 object
#' @importFrom magrittr "%>%"
#' @export
#' @examples 
#'   plotBlandAltman(1:20, rnorm(20))
plotBlandAltman <- function(x, y, gamma = 0.05, alpha = 0.05, sigfigs = 2){
  
  df <- data.frame(mean = (x+y)/2, difference = (x - y)) %>%
    na.omit
  
  n  <- nrow(df)
  mu <- mean(df$difference)
  SD <- stats::sd(df$difference)

  CI <- estimateLimitsOfAgreement(mu = mu, SD = SD, gamma = gamma) %>%
    estimateConfidenceIntervals(n = n, alpha = alpha)

  df %>%
    ggplot2::ggplot() +
    ggplot2::aes(x = mean, y = difference) +
    ggplot2::xlab("mean") +
    ggplot2::ylab("difference") +
    ggplot2::geom_point() +

    # zero
    ggplot2::geom_hline(yintercept = 0,
               lty = 3, col = "black") +

    # mean
    ggplot2::geom_hline(yintercept = c(CI$LOA$mu),
               lty = 1, col = "blue") +
    ggplot2::geom_hline(yintercept = c(CI$CI$mu_lowerCI, CI$CI$mu_upperCI),
               lty = 2, col = "blue") +

    # upper LOA
    ggplot2::geom_hline(yintercept = c(CI$LOA$upperLOA),
               lty = 1, col = "red") +
    ggplot2::geom_hline(yintercept = c(CI$CI$upperLOA_lowerCI, CI$CI$upperLOA_upperCI),
               lty = 2, col = "red") +

    # lower LOA
    ggplot2::geom_hline(yintercept = c(CI$LOA$lowerLOA),
               lty = 1, col = "green3") +
    ggplot2::geom_hline(yintercept = c(CI$CI$lowerLOA_upperCI, CI$CI$lowerLOA_lowerCI),
               lty = 2, col = "green3") +

    ggplot2::scale_y_continuous(breaks = signif(c(CI$LOA$mu, CI$CI$mu_lowerCI, CI$CI$mu_upperCI,
                                  CI$LOA$upperLOA, CI$LOA$lowerLOA,
                                  CI$CI$lowerLOA_upperCI, CI$CI$upperLOA_lowerCI,
                                  CI$CI$lowerLOA_lowerCI, CI$CI$upperLOA_upperCI), sigfigs)) +
    ggplot2::ggtitle("Bland-Altman plot") +
    ggplot2::theme_classic()
}