R/box_fun.R

In HallLab/clarite: CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures

#' box_fun
#'
#' Create boxplots and choose number to display per page
#' Note: Call quatrz() prior to plottting in RStudio\cr
#' Dependencies: ggplot2, gridExtra
#' @param d data frame
#' @param i column index
#' @param annotate optional data frame with annotation information in the following format (order is important): Variable, Norm_min, Norm_max, Min, Max
#' @return png image(s)

box_fun <- function(d, i, annotate) {
  if (!requireNamespace(c("ggplot2", "gridExtra"), quietly = TRUE)==TRUE) {
    stop("Please install ggplot2 and gridExtra to create visualization.", call. = FALSE)
  } #else {
    #packages = c("ggplot2", "gridExtra")
    #lapply(packages, library, character.only = TRUE)
  #}

  if(!missing(annotate)){
    #Add clinical lab information
    c <- stats::setNames(data.frame(t(annotate[,-1])), annotate[,1])
  } else {
    print("No annotations available")
  }

  v <- names(d[i])
  smpls <- length(d[[v]][!is.na(d[[v]])])
  std <- stats::sd(d[[i]], na.rm=TRUE)
  avg <- mean(d[[i]], na.rm=TRUE)
  sumstr <- paste("Sample Size = ", smpls, ", Std.Dev. = ", format(std, digits=4), sep="")

  #Explicitly set aes to look in local environment due to bug in ggplot
  b <- ggplot2::ggplot(data=d, aes(x=factor(0), y=d[[v]]), environment=environment()) + ggplot2::geom_boxplot(width=0.5, outlier.shape=1, outlier.colour="red", fill="cadetblue4")
  b <- b + ggplot2::labs(y="Value") + ggplot2::theme(axis.text.x=ggplot2::element_blank(), axis.title.x=ggplot2::element_blank(), axis.ticks.x=ggplot2::element_blank(), plot.title=ggplot2::element_text(size=9), axis.title=ggplot2::element_text(size=8))
  b <- b + ggplot2::stat_summary(fun.y=mean,geom="point", shape=18, colour="yellow") + ggplot2::guides(fill=FALSE) + ggplot2::ggtitle(bquote(atop(.(v), atop(.(sumstr), ""))))

  if(!missing(annotate)){
    if(v %in% names(c)){
      #[1,] = normal min, [2,] = normal max, [3,] = physiological min, [4,] = physiological max
      if(!is.na(c[v][1,])){
        b <- b + ggplot2::geom_hline(yintercept=c[v][1,], colour="grey12", linetype="dashed")
      }
      if(!is.na(c[v][2,])){
        b <- b + ggplot2::geom_hline(yintercept=c[v][2,], colour="grey12", linetype="dashed")
      }
      if(!is.na(c[v][3,])){
        b <- b + ggplot2::geom_hline(yintercept=c[v][3,], colour="red")
      }
      if(!is.na(c[v][4,])){
        b <- b + ggplot2::geom_hline(yintercept=c[v][4,], colour="red")
      }
    }
  }

  print(b)
  return(b)
}