Hi,
The RunGLMPCA() wrapper for glmpca by @willtownes is not working with the latest versions of Seurat and SeuratWrappers. I'm aware thanks to willtownes/glmpca@0536890 that Will Townes hasn't had as much availability as he used to to maintain glmpca. However, hopefully this is something that the Seurat maintainers can help resolve.
There's also a minor typo in the example of RunGLMPCA(): redunction -> reduction.
library("Seurat")
#> Loading required package: SeuratObject
#> Loading required package: sp
#>
#> Attaching package: 'SeuratObject'
#> The following objects are masked from 'package:base':
#>
#> intersect, t
library("SeuratWrappers")
library("sessioninfo")
## Run example from
## https://github.com/satijalab/seurat-wrappers/blob/a1eb0d8b039ad6d5ef0ff1332fd8eb1c0c223553/R/glmpca.R#L24-L26
pbmc_small
#> An object of class Seurat
#> 230 features across 80 samples within 1 assay
#> Active assay: RNA (230 features, 20 variable features)
#> 3 layers present: counts, data, scale.data
#> 2 dimensional reductions calculated: pca, tsne
pbmc_small <- RunGLMPCA(pbmc_small)
#> Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
#> ℹ Please use the `layer` argument instead.
#> ℹ The deprecated feature was likely used in the SeuratWrappers package.
#> Please report the issue to the authors.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
#> Sparse matrices are not supported for minibatch='none'. Coercing to dense matrix. If this exhausts memory, consider setting minibatch to 'stochastic' or 'memoized'.
DimPlot(pbmc_small, redunction = 'glmpca')
#> Error in DimPlot(pbmc_small, redunction = "glmpca"): unused argument (redunction = "glmpca")
## Reproducibility information
print("Reproducibility information:")
#> [1] "Reproducibility information:"
Sys.time()
#> [1] "2025-07-03 13:54:43 EDT"
proc.time()
#> user system elapsed
#> 2.030 0.209 5.004
options(width = 120)
session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.5.0 (2025-04-11)
#> os macOS Sequoia 15.5
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2025-07-03
#> pandoc 3.2 @ /opt/homebrew/bin/ (via rmarkdown)
#> quarto 1.4.550 @ /usr/local/bin/quarto
#>
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#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────Created on 2025-07-03 with reprex v2.1.1
Note that in version 4.4.0 of Seurat my colleague Jisu Ha was getting the following error:
Invalid class "DimReduc" object: invalid object for slot "misc" in class "Dimeduc": got class "glmpca", should be or extend class "list"
I'll ask him to provide the reprex::reprex() output for the following R code:
library("Seurat")
library("SeuratWrappers")
library("sessioninfo")
## Run example from
## https://github.com/satijalab/seurat-wrappers/blob/a1eb0d8b039ad6d5ef0ff1332fd8eb1c0c223553/R/glmpca.R#L24-L26
pbmc_small
pbmc_small <- RunGLMPCA(pbmc_small)
DimPlot(pbmc_small, redunction = 'glmpca')
## Reproducibility information
print("Reproducibility information:")
Sys.time()
proc.time()
options(width = 120)
session_info()Best,
Leo
Hi,
The
RunGLMPCA()wrapper forglmpcaby @willtownes is not working with the latest versions ofSeuratandSeuratWrappers. I'm aware thanks to willtownes/glmpca@0536890 that Will Townes hasn't had as much availability as he used to to maintainglmpca. However, hopefully this is something that theSeuratmaintainers can help resolve.There's also a minor typo in the example of
RunGLMPCA(): redunction -> reduction.Created on 2025-07-03 with reprex v2.1.1
Note that in version 4.4.0 of
Seuratmy colleague Jisu Ha was getting the following error:I'll ask him to provide the
reprex::reprex()output for the following R code:Best,
Leo