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(v0.7.0.9010) mo_synonyms, plot/barplot fixes

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dr. M.S. (Matthijs) Berends
2019-06-16 21:42:40 +02:00
parent 980be2b22d
commit 9c39c35f86
72 changed files with 595 additions and 802 deletions
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15
R/mo_property.R
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@ -73,6 +73,7 @@
#' mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
#' mo_rank("E. coli") # "species"
#' mo_url("E. coli") # get the direct url to the online database entry
#' mo_synonyms("E. coli") # get previously accepted taxonomic names
#'
#' ## scientific reference
#' mo_ref("E. coli") # "Castellani et al., 1919"
@ -312,12 +313,24 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
subspecies = mo_subspecies(x, language = language))
}
#' @rdname mo_property
#' @export
mo_synonyms <- function(x, ...) {
x <- AMR::as.mo(x, ...)
col_id <- AMR::microorganisms[which(AMR::microorganisms$mo == x), "col_id"]
if (is.na(col_id) | !col_id %in% AMR::microorganisms.old$col_id_new) {
return(NULL)
}
sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
}
#' @rdname mo_property
#' @export
mo_info <- function(x, language = get_locale(), ...) {
x <- AMR::as.mo(x, ...)
c(mo_taxonomy(x, language = language),
list(url = unname(mo_url(x, open = FALSE)),
list(synonyms = mo_synonyms(x),
url = unname(mo_url(x, open = FALSE)),
ref = mo_ref(x)))
}