Dear Seurat Team,

The issue of UMAP reproducibility using the uwot method has been raised before #6722, and as noted in that PR this was discussed in a uwot issue jlmelville/uwot#46. Specifically the observation is that OS differences in the underlying implementation of some C/C++ libraries causes very small numerical differences OSs that produce different UMAP results. An option that corrects this was added to uwot version 0.1.8 as discussed in jlmelville/uwot#46. Given that Seurat requires uwot >0.1.10, I thought it would be useful to include this option in Seurat's RunUMAP functions.

I tested this option on two systems (Mac and CentOS). Without the new uwot.approx_pow option (setting it to FALSE) the UMAPs are different, but when setting uwot.approx_pow = TRUE the results are identical. I am not sure why #6722 noted that approx_pow did not solve the issue -- it does solve the problem for my example. See details below for how I tested this using a simple UMAP on pbmc_small:

Running on Mac laptop

install_github('daskelly/seurat@umap-approx-pow')
suppressPackageStartupMessages(library(Seurat))
Sys.info()['sysname']

##  sysname 
## "Darwin"

RunUMAP(pbmc_small, verbose = FALSE, dims = 1:5, uwot.approx_pow = FALSE) |>
  Embeddings(object = _, 'umap') |> head(3)

##                  umap_1    umap_2
## ATGCCAGAACGACT 4.692863  1.759652
## CATGGCCTGTGCAT 5.494108  1.453728
## GAACCTGATGAACC 2.188469 -5.069190

RunUMAP(pbmc_small, verbose = FALSE, dims = 1:5, uwot.approx_pow = TRUE) |>
  Embeddings(object = _, 'umap') |> head(3)

##                   umap_1    umap_2
## ATGCCAGAACGACT 0.1691852 0.2062277
## CATGGCCTGTGCAT 1.4661827 0.7792036
## GAACCTGATGAACC 4.8212224 0.0872156

Running on CentOS

install_github('daskelly/seurat@umap-approx-pow')
suppressPackageStartupMessages(library(Seurat))
Sys.info()['sysname']

## sysname 
## "Linux"

RunUMAP(pbmc_small, verbose = FALSE, dims = 1:5, uwot.approx_pow = FALSE) |>
  Embeddings(object = _, 'umap') |> head(3)

##                  umap_1    umap_2
## ATGCCAGAACGACT 2.765658  3.131156
## CATGGCCTGTGCAT 2.465478  2.309039
## GAACCTGATGAACC 2.971336 -2.502957

RunUMAP(pbmc_small, verbose = FALSE, dims = 1:5, uwot.approx_pow = TRUE) |>
  Embeddings(object = _, 'umap') |> head(3)

##                   umap_1    umap_2
## ATGCCAGAACGACT 0.1691852 0.2062277
## CATGGCCTGTGCAT 1.4661827 0.7792036
## GAACCTGATGAACC 4.8212224 0.0872156

The results above show that the UMAP results are identical across OSs when uwot.approx_pow = TRUE only.