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############################################################################
#' method extensions to show for dada2 objects.
#'
#' See the general documentation of \code{\link[methods]{show}} method for
#' expected behavior.
#'
#' @seealso \code{\link[methods]{show}}
#'
#' @inheritParams methods::show
#' @return NULL.
#' @importFrom stats median
#' @rdname show-methods
#' @include allClasses.R
#' # examples
setMethod("show", "derep", function(object){
cat("derep-class: R object describing dereplicated sequencing reads", fill=TRUE)
if( length(object$uniques) > 0 ){
cat("$uniques:", sum(object$uniques, na.rm = TRUE), "reads in",
length(names(object$uniques)), "unique sequences\n")
seqlens <- nchar(names(object$uniques))
cat(" Sequence lengths: min=", min(seqlens), ", median=", median(seqlens),
", max=", max(seqlens), sep="", fill=TRUE)
}
if( length(object$quals) > 0 & inherits(object$quals, "matrix")){
cat("$quals: Quality matrix dimension: ", dim(object$quals), fill = TRUE)
quals <- as.vector(object$quals)
cat(" Consensus quality scores: min=", min(quals, na.rm=TRUE), ", median=", median(quals, na.rm=TRUE),
", max=", max(quals, na.rm=TRUE), sep="", fill=TRUE)
}
if( length(object$map) > 0 ){
cat("$map: Map from reads to unique sequences: ", object$map[1L:5L], "...", fill = TRUE)
}
})
#' @inheritParams methods::show
#' @rdname show-methods
#' @include allClasses.R
setMethod("show", "dada", function(object){
cat("dada-class: object describing DADA2 denoising results", fill=TRUE)
if( length(object$denoised) > 0 && length(object$map) > 0 ) {
cat(length(object$denoised), "sequence variants were inferred from", length(object$map), "input unique sequences.", fill=TRUE)
}
cat("Key parameters: OMEGA_A = ", object$opts$OMEGA_A,
", OMEGA_C = ", object$opts$OMEGA_C,
", BAND_SIZE = ", object$opts$BAND_SIZE,
sep="", fill=TRUE)
})
############################################################################
#' Deactivate renaming of derep-class objects.
#'
#' @inheritParams base::`names<-`
#' @return NULL.
#' @include allClasses.R
#'
setMethod("names<-", "derep", function(x, value){
warning("derep-class objects cannot be renamed.")
return(x)
})
############################################################################
#' Deactivate renaming of dada-class objects.
#'
#' @inheritParams base::`names<-`
#' @return NULL.
#' @include allClasses.R
#'
setMethod("names<-", "dada", function(x, value){
warning("dada-class objects cannot be renamed.")
return(x)
})
############################################################################
#' Change concatenation of derep-class objects to list construction.
#'
#' @inheritParams base::c
#' @param x A derep-class object
#' @return list.
#' @include allClasses.R
#'
setMethod("c", signature("derep"), function(x,...,recursive=FALSE){
list(x,...)
})
############################################################################
#' Change concatenation of dada-class objects to list construction.
#'
#' @inheritParams base::c
#' @param x A dada-class object
#' @return list.
#' @include allClasses.R
#'
setMethod("c", signature("dada"), function(x,...,recursive=FALSE){
list(x,...)
})
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