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Add uwot.approx_pow option to RunUMAP for better reproducibility #9449

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Add uwot.approx_pow option to RunUMAP for better reproducibility #9449

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6 changes: 6 additions & 0 deletions R/dimensional_reduction.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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
)
Expand All @@ -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
)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down