Nothing
###-----------------------------------------------------------------------------
###
### write.txt.long
###
###
##' @param object the \code{hyperSpec} object
##' @param order which columns should be \code{\link[base]{order}}ed?
##' \code{order} is used as index vector into a \code{data.frame} with
##' columns given by \code{cols}.
##' @param na.last handed to \code{\link[base]{order}} by
##' \code{write.txt.long}.
##' @param quote,sep,col.names,row.names have their usual meaning (see
##' \code{\link[utils]{read.table}} and \code{\link[utils]{write.table}}),
##' but different default values.
##'
##' For file import, \code{row.names} should usually be \code{NULL} so that the
##' first column becomes a extra data column (as opposed to row names of the extra data).
##' @param col.labels Should the column labels be used rather than the
##' colnames?
##' @param append Should the output be appended to an existing file?
##' @aliases write.txt.long
##' @rdname textio
##' @export
write.txt.long <- function (object,
file = "",
order = c (".rownames", ".wavelength"),
na.last = TRUE, decreasing = FALSE,
quote = FALSE, sep = "\t",
row.names = FALSE,
cols = NULL,
col.names = TRUE,
col.labels = FALSE, # use labels instead of column names?
append = FALSE,
...){
validObject (object)
col.spc <- match ("spc", colnames (object@data))
X <- as.long.df (object, rownames = TRUE)
if (!is.null (order)){
if (is.character (order)) {
tmp <- match (order, colnames (X))
if (any (is.na (tmp)))
stop ("write.txt.long: no such columns: ",
paste (order [is.na (tmp)], collapse = ", "))
order <- tmp
}
if (length (decreasing) < length (order))
decreasing <- rep (decreasing, length.out = length (order))
order.data <- as.list (X [, order, drop = FALSE])
for (i in seq_along (order)){
if (is.factor(order.data [[i]]))
order.data [[i]] <- rank (order.data [[i]], na.last = na.last | is.na (na.last))
if (decreasing [i])
order.data [[i]] <- - order.data [[i]]
}
X <- X[do.call ("order",
c (order.data, na.last = na.last | is.na (na.last), decreasing = FALSE)
), ]
}
if (is.na (na.last))
X <- X[! is.na (X$spc), ]
if (!is.null (cols))
X <- X [, cols, drop = FALSE]
if (!row.names)
X$.rownames <- NULL
else
cln [match (".rownames", cln)] <- "row"
if (col.names){
if (col.labels){
cln <- match (colnames (X), names (object@label))
cln[!is.na (cln)] <- object@label [cln[!is.na(cln)]]
cln[is.na (cln)] <- colnames (X) [is.na(cln)]
cln <- sapply (cln, as.character)
} else {
cln <- colnames (X)
}
write.table (matrix (cln, nrow = 1), file = file, append = append,
quote = quote, sep = sep, row.names = FALSE, col.names = FALSE)
append <- TRUE
}
write.table (X, file, append = append, quote = quote, sep = sep,
row.names = FALSE, col.names = FALSE, ...)
}
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