R/boxplot_bw.R

In miriamMota/mmotaF: Primer paquet, funcions R habituals

#' A boxplot_bw Function
#'
#' Boxplot incluyendo puntos individuales
#' @param dat matrix or data frame containing the variables in the formula.
#' @param y name numeric vector of data values.
#' @param group name factor vector. Default value is NULL.
#' @param ylim.plot is vector which contains lower and upper limits which are to appear on the y axes.
#' @param title.plot a main title for the plot
#' @param sub.plot a sub title for the plot
#' @param do.test logical value si se quiere realizar test kruskall Wallis.
#' @param las numeric in {0,1,2,3}; the style of axis labels. 0: always parallel to the axis [default],
#' 1: always horizontal, 2:always perpendicular to the axis, 3: always vertical.
#' @param ylab a title for the y axis
#' @param xlab a title for the x axis.
#' @param cex.lab size of the axis label text with a numeric value.
#' @param cex.pval size of the p-value text with a numeric value.
#' @param cex.main expansion factor for main names (size main)
#' @param cex.n expansion factor for size n
#' @param bw logical value for beeswarm
#' @export boxplot_bw
#' @import beeswarm
#' @author Miriam Mota \email{mmota.foix@@gmail.com}
#' @examples
#' df <- data.frame(runif = c(runif(100, min = -3, max = 3),
#' rep(0,25)), rnorm = c(rnorm(100),rep(0,25)) )
#' boxplot_bw(dat = df, y = 'rnorm' )
#' boxplot_bw(dat = mtc_bis, y = 'qsec', title.plot = "Title" )
#' boxplot_bw(dat = mtc_bis, y = 'qsec', group = 'gear',
#' title.plot = "Boxplot per grup", do.test = TRUE, las = 2)
#' boxplot_bw(dat = df, y = 'rnorm', bw = FALSE )
#' boxplot_bw(dat = mtc_bis, y = 'qsec', title.plot = "Title", bw = FALSE )
#' boxplot_bw(dat = mtc_bis, y = 'qsec', group = 'gear',
#' title.plot = "Boxplot per grup", do.test = TRUE, las = 2, bw = FALSE)
#' @keywords plots descriptive boxplot

boxplot_bw <- function(y, group = NULL, dat,
                       las = 0,
                       title.plot = NULL,
                       sub.plot = NULL,
                       ylim.plot = NULL,
                       cex.lab = 1,
                       cex.main = 1,
                       cex.pval = 0.6,
                       cex.n = 0.5,
                       ylab = "",
                       xlab = NULL,
                       do.test = FALSE,
                       color = NULL,
                       bw = TRUE,
                       show.n = T) {

  # cex.dot <- ifelse(bw,1,0)
  if (is.null(ylim.plot))
    ylim.plot <- c(min(dat[, y], na.rm = T), max(dat[, y] + 0.2, na.rm = T))
  op <- par(cex.axis = cex.lab)

  ## univariant
  if (is.null(group)) {
    if (is.null(title.plot))
      title.plot <- y
    if (bw) {
      beeswarm(dat[, y],
               ylab = "",
               main = strwrap(title.plot,width = 40),
               sub = sub.plot,
               cex.main = cex.main,
               cex.sub = .7,
               ylim = ylim.plot,
               axes = F,
               pch = 20,
               col = gg_color(1),
               corral = "gutter")}

    boxplot(dat[, y],
            add = bw,
            col = makeTransparent("grey", alpha = 0.3),
            las = las)

    mtext(paste0("n = ", sum(complete.cases(dat[,y]))),side = 3, adj = 1,
          cex = cex.n)

    ## bivariant
  } else {
    if (is.null(title.plot))  {title.plot <- ""    }
    label_group <- Hmisc::label(dat[,group])
    xlab <- ifelse(is.null(xlab), ifelse(label_group == "", group, label_group), xlab)
    xlab <- strwrap(xlab,width = 40)
    if (!is.factor(dat[,group]))  dat[,group] <- factor_ueb(dat[,group])

    if (is.null(color))  color <- gg_color(length(levels(dat[, group])))

    if (is.factor(dat[,group]))  dat[,group] <- droplevels(dat[,group])
    if (bw) {
      beeswarm(dat[, y] ~ dat[, group],
               ylab = "", xlab = wrap.it(xlab,30),
               main = strwrap(title.plot,width = 40),
               ylim = ylim.plot,
               axes = F,
               cex.main = cex.main,
               cex.lab = 1,
               cex.axis = cex.lab,
               pch = 20,
               col = color)}
    boxplot(dat[, y] ~ dat[, group],
            add = bw,
            col = makeTransparent("grey", alpha = 0.3),
            las = las,
            cex.lab = 1,
            cex.axis = cex.lab,
            sub = sub.plot,
            cex.sub = .7,
            ylab = ylab,
            names = wrap.it(levels(dat[,group]),10))
    if (do.test) {
      KWpval <- kruskal.test(dat[, y] ~ dat[, group])$p.val
      mtext(paste("KW p-value: ", ifelse( round(KWpval,3) < 0.001, "<0.001", round(KWpval,3) )) ,
            adj = 0, side = 3,cex = cex.pval)
    }
    if (show.n) mtext(paste0("n = ",nrow(na.omit(dat[,c(group,y)]))),side = 3, adj = 1,
                     cex = cex.n)
  }
  par(op)
}