diff --git a/R/plotPrevalence.R b/R/plotPrevalence.R index a67ea4b3..a1491022 100644 --- a/R/plotPrevalence.R +++ b/R/plotPrevalence.R @@ -30,7 +30,7 @@ #' #' @param as_relative logical scalar: Should the detection threshold be applied #' on compositional (relative) abundances? Passed onto -#' \code{\link[mia:getPrevalence]{getPrevalence}}. (default: \code{TRUE}) +#' \code{\link[mia:addPrevalence]{addPrevalence}}. (default: \code{TRUE}) #' #' @param colour_by Specification of a feature to colour points by, see the #' \code{by} argument in @@ -86,8 +86,8 @@ #' \code{prevalences} was defined. #' #' @seealso -#' \code{\link[mia:getPrevalence]{getPrevalence}}, -#' \code{\link[mia:getPrevalence]{agglomerateByPrevalence}}, +#' \code{\link[mia:addPrevalence]{addPrevalence}}, +#' \code{\link[mia:addPrevalence]{agglomerateByPrevalence}}, #' \code{\link[mia:agglomerate-methods]{agglomerateByRank}} #' #' @name plotPrevalence diff --git a/man/plotPrevalence.Rd b/man/plotPrevalence.Rd index 0884ae88..ab06b9d1 100644 --- a/man/plotPrevalence.Rd +++ b/man/plotPrevalence.Rd @@ -83,7 +83,7 @@ will be disabled.)} \item{as_relative}{logical scalar: Should the detection threshold be applied on compositional (relative) abundances? Passed onto -\code{\link[mia:getPrevalence]{getPrevalence}}. (default: \code{TRUE})} +\code{\link[mia:addPrevalence]{addPrevalence}}. (default: \code{TRUE})} \item{rank, ...}{additional arguments \itemize{ @@ -177,7 +177,7 @@ plotPrevalentAbundance(GlobalPatterns, rank = "Family", scale_x_log10() } \seealso{ -\code{\link[mia:getPrevalence]{getPrevalence}}, -\code{\link[mia:getPrevalence]{agglomerateByPrevalence}}, +\code{\link[mia:addPrevalence]{addPrevalence}}, +\code{\link[mia:addPrevalence]{agglomerateByPrevalence}}, \code{\link[mia:agglomerate-methods]{agglomerateByRank}} }