R/multi_plot.R

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

#' multi_plot
#'
#' Create multiple types of plots on the same page\cr
#' Note: Call quatrz() prior to plottting in RStudio\cr
#' Dependencies: gridExtra
#' @param d data frame
#' @param n number of variables to display per page
#' @param nrow number of variables per row
#' @param ncol number of variables per column
#' @param wi width of plot
#' @param hgt height of plot
#' @param res resolution of plot
#' @param type sepcify plot type 'hist-qq, box-qq, hist-box, hist-box-qq'
#' @param annotate optional data frame with clinical lab information
#' @param file filename of output
#' @return png image(s)
#' @export
#' @family plot functions
#' @family continuous variable functions
#' @examples
#' \dontrun{
#' multi_plot(d, n=6, file="plot", nrow=3, ncol=2, wi=13.5, hgt=9, res=210, type="hist-qq", annotate)
#' }

multi_plot <- function(d, n=6, file="plot", nrow=3, ncol=2, wi=13.5, hgt=9, res=300, type, annotate) {
  t1 <- Sys.time()

  if (!requireNamespace("gridExtra", quietly = TRUE)==TRUE) {
    stop("Please install gridExtra to create visualization.", call. = FALSE)
  } #else {
    #packages = c("ggplot2", "gridExtra")
    #lapply(packages, library, character.only = TRUE)
  #}


  if(is.element('ID', names(d))==FALSE){
    stop("Please add ID to dataframe as column 1")
  }

  d <- d[, -1]

  if(n > ncol(d)){
    stop("Number of plots per page (", n, ") is larger than number of variables to plot (", ncol(d), ")")
  }

  if(missing(type)){
    stop("Please specify plot type")
  }

  iter <- ceiling(ncol(d)/n)
  k <- 1
  inc <- n

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

  for(j in 1:iter){
    print(paste("Creating image", j, "of", iter, sep=" "))
    plots <- list()
    lst_indx <- 1
    for(i in k:inc){
      if(length(grep("hist", type))!=0){
        if(!missing(annotate)){
          h <- hist_fun(d=d, i=i, annotate=annotate)
        } else {
          h <- hist_fun(d=d, i=i)
	}
      }
      if(length(grep("box", type))!=0){
        if(!missing(annotate)){
          b <- box_fun(d=d, i=i, annotate=annotate)
	} else {
	  b <- box_fun(d=d, i=i)
	}
      }
      if(length(grep("qq", type))!=0){
	q <- qq_fun(d=d, i=i)
      }

      if(length(grep("hist-qq", type))!=0){
	plots[[lst_indx]] <- gridExtra::grid.arrange(h, q, ncol=2)
      }
      if(length(grep("hist-box", type))!=0){
	plots[[lst_indx]] <- gridExtra::grid.arrange(h, b, ncol=2)
      }
      if(length(grep("box-qq", type))!=0){
	plots[[lst_indx]] <- gridExtra::grid.arrange(b, q, ncol=2)
      }
      if(length(grep("hist-box-qq", type))!=0){
        plots[[lst_indx]] <- gridExtra::grid.arrange(h, b, q, ncol=3)
      }

      lst_indx <- lst_indx + 1
    }

    grDevices::png(paste(file, "_", type, "_", j, ".png", sep=""), width=wi, height=hgt, units="in", res=res, pointsize=4)
    do.call(eval(parse(text="gridExtra::grid.arrange")), c(plots, ncol=ncol))
    grDevices::dev.off()
    print(paste("Printing image", j, "of", iter, sep=" "))

    k <- inc + 1
    inc <- if(j==iter-1) ncol(d) else inc + n
    #Adjust height for last plot
    if(inc==ncol(d)){
	n_row <- ceiling(((inc-k)+1)/ncol)
	hgt <- (hgt/nrow)*n_row
    }
  }

  t2 <- Sys.time()
  print(paste("Finished in", round(as.numeric(difftime(t2,t1, units="secs")), 6), "secs", sep=" "))
}