getJbrowseLink: Generate a url to TREW genome browser
In Marlin-Na/trewjb: Access TREW Genome Browser

Description Usage Arguments Value Examples

View source: R/trewjb.R

Generate a link to view desired range on the TREW browser according to the suppied arguments.

getJbrowseLink(genome, chromosome, range_start, range_end, hight_start,
  hight_end, tracks = c("DNA", "gene_model"),
  baseurl = "http://180.208.58.19/jbrowse", show_navagation = TRUE,
  show_tracklist = FALSE, show_overview = FALSE)

`genome`	Which genome to view, current supported values are "hg19", "mm10" and "dm6".
`chromosome`	Which chromosome, e.g. "chr1"
`range_start, range_end`	Length-one numeric vectors to indicate the start and end of the desired range.
`hight_start, hight_end`	Length-one numeric vectors to indicate the start and end of the hightlight range, if missing, highlight will be disabled.
`tracks`	Character vectors to indicate which tracks to show. In TREW database, they are also valid experiment id, other primary tracks include "DNA", "gene_model", "all_m6A", "all_m5C", "all_m1A" and "all_Psi". List of available tracks can be found at http://180.208.58.19/jbrowse/ .
`baseurl`	Default "http://180.208.58.19/jbrowse".
`show_navagation`	Logical, whether show the navagation parts of the Jbrowse UI?
`show_tracklist`	Logical, whether show the tracklist parts of the Jbrowse UI?
`show_overview`	Logical, whether show the overview parts of the Jbrowse UI?

A character as url.

if (interactive()) {
    url <- getJbrowseLink("hg19", "chr8", 92114847, 92231464,
        hight_start = 92150113, hight_end = 92152064,
        tracks = c("DNA", "gene_model", "all_m6A"),
        show_tracklist = TRUE, show_overview = TRUE)
    browseURL(url)
}