diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index ab6bc5a13..508f201c8 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -1099,7 +1099,7 @@ RunTSNE.Seurat <- function( add.iter = add.iter, dim.embed = dim.embed, reduction.key = reduction.key, - is_distance = TRUE, + is_distance = TRUE, ... ) } else if (!is.null(x = dims)) { @@ -1501,6 +1501,10 @@ ScoreJackStraw.Seurat <- function( return(object) } +#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +# Methods for R-defined generics +#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # Internal #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/R/objects.R b/R/objects.R index 361626979..eb6310712 100644 --- a/R/objects.R +++ b/R/objects.R @@ -1235,6 +1235,11 @@ as.Graph.matrix <- function(x, ...) { #' @export #' @method as.loom Seurat #' +#' @examples +#' \dontrun{ +#' lfile <- as.loom(x = pbmc_small) +#' } +#' as.loom.Seurat <- function( x, assay = NULL, @@ -1406,6 +1411,12 @@ as.loom.Seurat <- function( #' @export #' @method as.Seurat loom #' +#' @examples +#' \dontrun{ +#' lfile <- as.loom(x = pbmc_small) +#' pbmc <- as.Seurat(x = lfile) +#' } +#' as.Seurat.loom <- function( x, cells = 'CellID', diff --git a/man/as.Seurat.Rd b/man/as.Seurat.Rd index 23b31e0b0..bdfdb9416 100644 --- a/man/as.Seurat.Rd +++ b/man/as.Seurat.Rd @@ -66,3 +66,10 @@ will not be pulled as these depend on normalized data. The following is a list o with the value of \code{assay} } } +\examples{ +\dontrun{ +lfile <- as.loom(x = pbmc_small) +pbmc <- as.Seurat(x = lfile) +} + +} diff --git a/man/as.loom.Rd b/man/as.loom.Rd index d21ae5c63..0b73c3479 100644 --- a/man/as.loom.Rd +++ b/man/as.loom.Rd @@ -58,6 +58,12 @@ will not be filled, since those depend on scaled data. The following is a list o \item Nearest-neighbor graphs that start with the name of the assay will be stored in \code{col_graphs} \item Assay information will be stored as an HDF5 attribute called \code{assay} at the root level } +} +\examples{ +\dontrun{ +lfile <- as.loom(x = pbmc_small) +} + } \seealso{ \code{\link[loomR]{create}}