From f56bedbfbacc185cc080b154d05a8b709f29a11a Mon Sep 17 00:00:00 2001 From: Dan Skelly Date: Mon, 28 Oct 2024 14:56:48 -0400 Subject: [PATCH] Add uwot.approx_pow option to RunUMAP --- R/dimensional_reduction.R | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 4450054fe..b0955d30d 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -1303,6 +1303,7 @@ RunUMAP.default <- function( a = NULL, b = NULL, uwot.sgd = FALSE, + uwot.approx_pow = TRUE, seed.use = 42, metric.kwds = NULL, angular.rp.forest = FALSE, @@ -1426,6 +1427,7 @@ RunUMAP.default <- function( a = a, b = b, fast_sgd = uwot.sgd, + approx_pow = uwot.approx_pow, verbose = verbose, ret_model = return.model ) @@ -1447,6 +1449,7 @@ RunUMAP.default <- function( a = a, b = b, fast_sgd = uwot.sgd, + approx_pow = uwot.approx_pow, verbose = verbose, ret_model = return.model ) @@ -1716,6 +1719,7 @@ RunUMAP.Neighbor <- function( #' automatically as determined by min. dist and spread. Parameter of differentiable approximation of #' right adjoint functor. #' @param uwot.sgd Set \code{uwot::umap(fast_sgd = TRUE)}; see \code{\link[uwot]{umap}} for more details +#' @param uwot.approx_pow Set \code{uwot::umap(approx_pow = TRUE)}; see \code{\link[uwot]{umap}} for more details #' @param metric.kwds A dictionary of arguments to pass on to the metric, such as the p value for #' Minkowski distance. If NULL then no arguments are passed on. #' @param angular.rp.forest Whether to use an angular random projection forest to initialise the @@ -1781,6 +1785,7 @@ RunUMAP.Seurat <- function( a = NULL, b = NULL, uwot.sgd = FALSE, + uwot.approx_pow = TRUE, seed.use = 42L, metric.kwds = NULL, angular.rp.forest = FALSE, @@ -1873,6 +1878,7 @@ RunUMAP.Seurat <- function( a = a, b = b, uwot.sgd = uwot.sgd, + uwot.approx_pow = uwot.approx_pow, seed.use = seed.use, metric.kwds = metric.kwds, angular.rp.forest = angular.rp.forest,