Cannot pass "igraph" method to Seurat::FindClusters in addClusters

[tiffanyformosa]

I wanted to use the leidenalg option for Seurat::FindClusters in addClusters(), However, my dataset is 65,000 cells, which is too large to pass as a dense matrix. I would like to set the option for method = "igraph" in Seurat::FindClusters, which is a known workaround for large datasets. However since method is already a parameter of addClusters to select between Seurat and scran, this parameter is not accessible. Could a workaround be added?

My code is:

    input = wt_atlas,
    reducedDims = "IterativeLSI",
    dimsToUse = dims,
    method = "Seurat",
    name = "Clusters",
    maxClusters = NULL,
    force = TRUE,
    knn = k,
    algorithm = 4, #this sets Seurat::FindClusters to leidenalg
    method = "igraph" #cannot pass this to FindClusters, since method is already a parameter
)

And the error message I get is:
Error in addClusters(input = wt_atlas, reducedDims = "IterativeLSI", dimsToUse = dims, : formal argument "method" matched by multiple actual arguments

Session Info: addClusters_sessionInfo_2022-08-15.txt

[rcorces]

Hi @tiffanyformosa! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

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[rcorces]

I've added a new parameter to addClusters() called FCmethod. Whatever you pass to FCmethod will get passed as the method parameter for Seurat::FindClusters().

This has been implemented on the dev_leidenalg branch via 6ce3e0a. Please test and report back. To install:

devtools::install_github("GreenleafLab/ArchR", ref="dev_leidenalg", repos = BiocManager::repositories())
detach("package:ArchR", unload=TRUE)
library(ArchR)

[tiffanyformosa]

I tested this on the example Hematopoeisis dataset and my own dataset, and it worked perfectly! Thanks so much!

[rcorces]

Thanks for confirming. These changes have been merged into the dev branch and will become a part of release_1.0.3