@@ -8,6 +8,12 @@

 #'    Alternatively, a \linkS4class{SpatialExperiment} object.

 #'

 #' @param ... For the generic, arguments to pass to specific methods.

+#' @param coordinates A `data.frame` with sample coordinates. Each row is a

+#'   sample, the columns with coordinates should be named 'x' and 'y'.

+#'

+#'   For the *SpatialExperiment* method, coordinates are taken from

+#'   `spatialCoords(x)`.

+#'

 #' @param assay_type A `character` string specifying the assay from `x` to use

 #'   as input. Defaults to `"counts"`.

 #' @param verbose A `logical` controlling the display of a progress bar from the

@@ -32,7 +38,6 @@

 #'

 #' ## Run spatialDE

 #' de_results <- spatialDE(spe)

-#' head(de_results)

 #'

 #' @seealso

 #' The individual steps performed by this function: [stabilize()],

@@ -19,6 +19,12 @@ Alternatively, a \linkS4class{SpatialExperiment} object.}

 \item{...}{For the generic, arguments to pass to specific methods.}

+\item{coordinates}{A \code{data.frame} with sample coordinates. Each row is a

+sample, the columns with coordinates should be named 'x' and 'y'.

+

+For the \emph{SpatialExperiment} method, coordinates are taken from

+\code{spatialCoords(x)}.}

+

 \item{verbose}{A \code{logical} controlling the display of a progress bar from the

 Python package.}

@@ -50,7 +56,6 @@ spe <- mockSVG(size = 10, tot_genes = 200, de_genes = 20, return_SPE = TRUE)

 ## Run spatialDE

 de_results <- spatialDE(spe)

-head(de_results)

 }

 \references{