R/assign.value.R

In sclero: Measure Growth Patterns and Align Sampling Spots in Photographs

#' @title Assign values to 'rawDist' objects for plotting.
#'
#' @description Assigns values to \code{\link[=convert.ijdata]{rawDist}} objects for \link[=plot.rawDist]{spatial density plotting}.
#' 
#' @param rawDist \code{\link[=convert.ijdata]{rawDist}} object to which the values should be assigned.
#' @param value a \code{\link{data.frame}} or list of data.frames of the same length than spot spequences (\code{\link[=read.ijdata]{spots}}). Each \code{data.frame} has to have identical length to spots. First column specifies the order. Second column containing the values (see Details).
#' @details This function can be used to plot values as color-densities on \link[=plot.rawDist]{sample maps}. The function is useful e.g. for examining the spatial distribution of geochemical data, such as element ratios or isotope ratios, along sample materials. If the \code{\link[=convert.ijdata]{rawDist}} object contains only one sample spot sequence, the \code{value} parameter should be expressed as a data.frame with two columns. If the \code{rawDist} object consists of several sample spot sequences, the \code{value} parameter should be a list of data.frames with length equivalent to number of spot sequences. The first column in all \code{value} data.frames represents spot number and should be equivalent to \code{$spots} marks in the \code{rawDist} object. The second column represents the values to be assigned. Column names are ignored.
#' @param value.name a character or function defining the name for the assigned value. Can be \code{\link[base]{expression}}
#' @return Returns a list of class \code{\link[=convert.ijdata]{rawDist}} containing spot value information.
#' @author Mikko Vihtakari
#' @seealso \code{\link{read.ijdata}} \code{\link{spot.dist}} \code{\link{assign.size}} \code{\link{plot.rawDist}}
#' @examples data(barium)
#' data(shellsizes)
#' 
#' ## rawDist
#' shellvalues <- assign.value(shellsizes, barium, value.name = "Ba/Ca")
#' plot(shellvalues, spot.size = "actual", spot.type = "value", main.type = "none")
#' 
#' ## spotDist
#' shellvalues.aligned <- spot.dist(shellvalues)
#' plot(shellvalues.aligned, spot.size = "actual", spot.type = "idvalue", 
#' spot.color = "darkgrey", highlight.gbs = c("WG_start", "WG_end"))
#' @export
#' 

assign.value <- function(rawDist, value, value.name = NULL){

if(class(value) == "data.frame" & length(rawDist$spots) == 1) {
  value <- list(value)
  names(value) <- names(rawDist$spots)
}  
  
TMP <- lapply(seq_along(rawDist$spots), function(k){
  tmp.s <- rawDist$spots[[k]]
  tmp.v <- value[[names(rawDist$spots[k])]]
  if(is.null(tmp.v)) {
    tmp.ret <- data.frame(spot.marks = marks(tmp.s), value = rep(NA, npoints(tmp.s)))} else {
    if(class(tmp.v) == "data.frame") {
      if(ncol(tmp.v) != 2) 
        stop("Each data.frame has to have 2 columns. First column defines the spot number, second the value ot be added") else {
          tmp.ret <- merge(data.frame(spot.marks = marks(tmp.s)), tmp.v, by = 1, sort = FALSE, all = TRUE)
        }
      }
    }
  return(tmp.ret)})
  
  names(TMP) <- names(rawDist$spots)
  X <- rawDist
  X$values <- TMP
  X$value.name <- value.name
  return(X)
}