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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Issue Creating Metacells #168

Closed Sandman-1 closed 1 month ago

Sandman-1 commented 6 months ago

Hello! Thank you for creating such an awesome package! I am running into an issue that was reported as closed/resolved in an earlier thread from January-February of this year. I ran this same code with no issues for another subset of cells from the same Seurat object and provided a larger list of genes to be analyzed and grouped into modules. Any suggestions on how to resolve this would be greatly appreciated. I also tried adjusting the minimum module size to 25 from the default value of 50, but that didn't seem to help. The error is as follows when constructing a second cell type-specific network on my Seurat object: Error in apply(scoreAll[modGenes[candidates], ], 1, which.max) : dim(X) must have a positive length

Code to run hdWGCNA initialization: LF_int <- SetupForWGCNA( LF_int, wgcna_name = "stel_wgcna", features = stel_wgcna_genes) %>% MetacellsByGroups( group.by = c("Sample", "Cell_Type_Subclusters"), k = round(0.001*nrow(subset(LF_int@meta.data, Cell_Type == "Hepatic Stellate Cells"))), cells.use = rownames(subset(LF_int@meta.data, Cell_Type == "Hepatic Stellate Cells")), reduction = "spca", assay = "SCT", min_cells = round(0.003*nrow(subset(LF_int@meta.data, Cell_Type == "Hepatic Stellate Cells"))), max_shared = round(0.001*nrow(subset(LF_int@meta.data, Cell_Type == "Hepatic Stellate Cells"))), ident.group = 'Cell_Type_Subclusters') %>% NormalizeMetacells() %>% SetDatExpr( group.by = "Cell_Type_Subclusters", group_name = unique(subset(LF_int@meta.data, Cell_Type == "Hepatic Stellate Cells")$Cell_Type_Subclusters), assay = "SCT", slot = "data") %>% TestSoftPowers(networkType = 'signed') %>% ConstructNetwork( setDatExpr = FALSE, overwrite_tom = TRUE)

Session Info: `sessioninfo::session_info() ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.3.0 (2023-04-21 ucrt) os Windows 11 x64 (build 22621) system x86_64, mingw32 ui RStudio language (EN) collate English_United States.utf8 ctype English_United States.utf8 tz America/Chicago date 2023-10-28 rstudio 2023.06.0+421 Mountain Hydrangea (desktop) pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

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[1] C:/Users/hebbale/AppData/Local/R/win-library/4.3 [2] C:/Program Files/R/R-4.3.0/library`

smorabit commented 6 months ago

Hi, I am happy to try to help you resolve this error. First, could you please format your code so that it is more easily readable? It is difficult to understand when it is all on one line. Also could you let me know which function is causing the error?

Sandman-1 commented 6 months ago

Apologies for the formatting. I think I resolved the previous error mentioned by playing around with the k and max_shared parameters. However, I am now running into a new error regardless of which cells I subset or what parameters I supply when creating metacells. The error is as follows: Error in .subscript.2ary(x, i, j, drop = drop) : subscript out of bounds

My code for this is as follows: LF_int <- SetupForWGCNA(LF_int, wgcna_name = "wgcna", features = wgcna_genes) %>% MetacellsByGroups(group.by = c("Sample", "Cell_Type"), k = 25, cells.use = rownames(subset(LF_int@meta.data, Cell_Type_Subclusters != "Ignore")), reduction = "spca", assay = "SCT", min_cells = 50, max_shared = 12, ident.group = "Cell_Type")

Sandman-1 commented 6 months ago

Ah, I am sorry for the formatting again. How do I separate it by line?

smorabit commented 2 months ago

Please refer to the Markdown style guide.

smorabit commented 1 month ago

Closing due to inactivity.