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`ConstructMetaspots`: `seurat_obj` not found

Open ppm1337 opened this issue 4 months ago • 1 comments

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        

ppm1337 avatar Oct 18 '24 16:10 ppm1337