GENOME <- "apiMel1"
ORGANISM <- "Apis mellifera"
ASSEMBLED_MOLECULES <- character(0)
CIRC_SEQS <- character(0)
.order_seqlevels <- function(seqlevels)
{
tmp <- IRanges::CharacterList(strsplit(seqlevels, ".", fixed=TRUE))
npart <- lengths(tmp)
stopifnot(all(npart == 2L))
m2 <- matrix(unlist(tmp), ncol=2L, byrow=TRUE)
groups <- paste0("Group", c(1:16, "Un"))
m21 <- match(m2[, 1L], groups)
stopifnot(!anyNA(m21))
m22 <- as.integer(m2[, 2L])
stopifnot(!anyNA(m22))
order(m21, m22)
}
FETCH_ORDERED_CHROM_SIZES <-
function(goldenPath.url=getOption("UCSC.goldenPath.url"))
{
chrom_sizes <- GenomeInfoDb:::fetch_chrom_sizes_from_UCSC(GENOME,
goldenPath.url=goldenPath.url)
oo <- .order_seqlevels(chrom_sizes[ , "chrom"])
S4Vectors:::extract_data_frame_rows(chrom_sizes, oo)
}
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