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plger / scDblFinder

Methods for detecting doublets in single-cell sequencing data
https://plger.github.io/scDblFinder/
GNU General Public License v3.0
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Running into Grid Error when Running scDblFinder #81

Closed Sandman-1 closed 9 months ago

Sandman-1 commented 1 year ago

Hello! I seem to be running into the following error when running scDblFinder on a single cell experiment atac object derived from a Seurat/Signac object. I have tried eliminating the dims, npcs, and k arguments, setting the processing mode to normFeatures as shown in the vignette, and reducing the number of maximum artificial doublets. They all give me the same error, though. Here is the code I used, followed by the error.

Code: TCF7L2_filt <- readRDS("Seurat Objects/TCF7L2 with Called Peaks.rds") TCF7L2_filt_sce_ATAC <- as.SingleCellExperiment(TCF7L2_filt, assay = "Peaks") TCF7L2_filt_sce_ATAC@int_colData@listData[["reducedDims"]]@listData[["PCA"]] <- TCF7L2_filt_sce_ATAC@int_colData@listData[["reducedDims"]]@listData[["LSI"]] TCF7L2_filt_sce_ATAC@int_colData@listData[["reducedDims"]]@listData[["LSI"]] <- NULL TCF7L2_filt_sce_ATAC <- scDblFinder(TCF7L2_filt_sce_ATAC, clusters = TCF7L2_filt_sce_ATAC$seurat_clusters, Samples = TCF7L2_filt_sce_ATAC$Sample, aggregateFeatures = TRUE, dims = 50, includePCs = 2:40, k = 20, artificialDoublets = ncol(TCF7L2_filt))

Output: Aggregating features... Error in set_grid_context(X[[1]], X[[2]]) : argument "current_viewport" is missing, with no default

PeteHaitch commented 1 year ago

I think you need to upgrade your Bioconductor installation to the latest version of DelayedArray (context: https://github.com/Bioconductor/DelayedArray/issues/104). You can do this with BiocManager::install().

After upgrading, restart R and try the code again. If that doesn't help, please provide the output of BiocManager::valid().

plger commented 1 year ago

(Thanks Peter) @Sandman-1 can you confirm that this solved your problem?