hdWGCNA
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`ConstructMetaspots`: `seurat_obj` not found
Hey Sam, big fan of hdWGCNA. Thanks for continously maintaining it!
In the latest dev version (0.4.00, @9b2e71a), calling MetaspotsByGroups
fails due to an error in ConstructMetaspots
. The function argument representing the Seurat object is called cur_seurat
, but the check for the image class is done on seurat_obj
, which does not exist in the given scope.
https://github.com/smorabit/hdWGCNA/blob/9b2e71abd0eb5ffd89ca16e8898b915928502f8a/R/Metaspots.R#L32
This results in the error
Error in (function (cur_seurat, mode = "sum", assay = "Spatial", slot = "counts", : object 'seurat_obj' not found
Sorry to not provide a MRE, but the issue should be clear at first sight.
Relevant sessionInfo()
:
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
[...]
other attached packages:
[1] purrr_1.0.2 patchwork_1.2.0 hdWGCNA_0.4.00 GenomicRanges_1.54.1
[5] GenomeInfoDb_1.38.1 IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
[9] UCell_2.6.2 tidygraph_1.3.1 ggraph_2.2.1 igraph_2.0.3
[13] WGCNA_1.73 fastcluster_1.2.6 dynamicTreeCut_1.63-1 ggrepel_0.9.6
[17] Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-4 harmony_1.2.0
[21] Rcpp_1.0.12 ggplot2_3.5.1 GeneOverlap_1.38.0 furrr_0.3.1
[25] future_1.33.2 enrichR_3.2 dplyr_1.1.4 cowplot_1.1.3