#' List concatamers of selected sites for all working_swarm sequences in swarmset.
#'
#' @param x swarmset
#' @param ... not currently used by could and should be soon
#' @seealso \code{\link{swarmset}}
#'
#' @family swarmset methods
#'
#' @export
print.swarmset <- function(x, ...) {
dots <- list(...)
# output the TF concatamer sequence first
i <- min(which(x$working_swarm$is_included == T))
if (!is.null(x$tf_index) & x$working_swarm$is_included[x$tf_index] &
x$tf_index != i)
i <- x$tf_index
cat(paste(names(x$working_swarm$seq_concatamer[i]),
x$working_swarm$seq_concatamer[i], sep='\t'), '\n')
ins <- which(x$working_swarm$is_included == T)
for (i in 2:length(ins))
cat(paste(names(x$working_swarm$dotseq_concatamer[ins[i]]),
x$working_swarm$dotseq_concatamer[ins[i]], sep='\t'), '\n')
message(paste0("Number of mutations to be represented was initially ",
x$working_swarm$initial_n_variants, "."))
if (length(which(c(x$working_swarm$variant_counts) > 0)) == 0) {
message("Number of mutations to be represented is now 0.")
} else {
message("Missed:")
pos.counts <- apply(x$working_swarm$variant_counts, 2, max)
r=1
for (i in which(pos.counts > 0)) {
for (j in which(x$working_swarm$variant_counts[, i] > 0)) {
message(paste(r, "\t",
paste(colnames(x$working_swarm$dot_concatamer)[i],
rownames(x$working_swarm$variant_counts)[j], sep='')))
r=r+1
}
}
}
}
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