GENOME <- "panTro1"
ORGANISM <- "Pan troglodytes"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:23, "X", "Y", "M"))
CIRC_SEQS <- "chrM"
.order_seqlevels <- function(seqlevels)
{
random <- paste0("chr", c(1:23, "X", "Y", "Un"), "_random")
ordered_seqlevels <- c(ASSEMBLED_MOLECULES, random)
stopifnot(length(seqlevels) == length(ordered_seqlevels))
idx <- match(ordered_seqlevels, seqlevels)
stopifnot(!anyNA(idx))
idx
}
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)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.