R/plot.R

In xRing: Identify and Measure Tree Rings on X-Ray Micro-Density Profiles

# helpers
years2xLim <- function(x, years) {
  years <- pmin(pmax(years, min(x$years) + 1), max(x$years))
  YEARmin <- which(x$years == min(years - 1))
  YEARmax <- which(x$years == max(years))
  c(range(x$limits[YEARmin:YEARmax])) + c(-1, 1)
}

#' @name plot
#' @title Plot xRing and xRingList Objects
#' @description Plot method for objects of class "xRing" and "xRingList".
#' @param x an object of class "xRing" or "xRingList".
#' @param years the years to be plotted, if \code{NULL} the whole time span is plotted.
#' @param EwLw logical. If \code{TRUE} the earlywood and latewood boundaries and width is plotted.
#' @param xlim vector of length 2 giving the x limits for the plot.
#' @param ylim the y limits of the plot.
#' @param ...	other arguments to be passed to plotRings function
#' @return None.
#' @seealso
#' \link{plotRings}
#' @export
#' @examples
#'
#' data(PaPiRaw)
#' data(PaPiSpan)
#'
#' PaPi <- detectRings(PaPiRaw, PaPiSpan)
#' class(PaPi)
#'
#' PaPiRings <- detectEwLw(PaPi, ew = 0.5)
#' plot(PaPiRings, series = "AFO1001a")
#'
#' PaPiRings1 <- detectEwLw(PaPi, ew = 0.35, lw = 0.55)
#' plot(PaPiRings1, series = "AFO1001a")
#'
#' plot(PaPiRings, series = "AFO1001a", years = c(1990, 2000))
#' plot(PaPiRings$AFO1001a)
#'
#' @name plot
#' @aliases plot.xRing
#' @export
#' @usage \method{plot}{xRing}(x, years = NULL, EwLw = TRUE,  xlim = NULL, ylim = NULL, ...)

plot.xRing <- function(x,
                       years = NULL,
                       EwLw = TRUE,
                       xlim = NULL,
                       ylim = NULL,
                       ...) {
  mar <- par("mar")
  on.exit(par("mar" = mar))
  if (!is.null(years)) {
    xlim <- years2xLim(x, years)
  }
  local(plotRings(
    x,
    EwLw = EwLw,
    xlim = xlim,
    ylim = ylim,
    ...
  ))
}


#' @name plot
#' @aliases plot.xRingList
#' @param series gives the name (or the index) of the series to be plotted, by default is 1 (i.e., the first series)
#' @export
#' @usage \method{plot}{xRingList}(x, series = 1, years = NULL, EwLw = TRUE,  xlim = NULL, ylim = NULL, ...)



plot.xRingList <- function(x,
                           series = 1,
                           years = NULL,
                           EwLw = TRUE,
                           xlim = NULL,
                           ylim = NULL,
                           ...) {
  if (series %in% as.character(1:length(x))) {
    series <- names(x)[as.integer(series)]
  }
  seriesID <- which(names(x) == series)
  if (length(seriesID) == 0) {
    return(message(
      paste("Please correct the series name or ID (ID <", length(x), ")")
    ))
  }
  x <- x[[seriesID]]
  
  if (!is.null(years)) {
    xlim <- years2xLim(x, years)
  }
  mar <- par("mar")
  on.exit(par("mar" = mar))
  local(plotRings(
    x,
    EwLw = EwLw,
    xlim = xlim,
    ylim = ylim,
    ...
  ))
}