update vignettes and dependencies

tidyomics · Sep 17, 2024 · fc5c134 · fc5c134
1 parent 47c792f
commit fc5c134
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Showing 4 changed files with 8 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -58,6 +58,7 @@ Imports:
     tidybulk,
     glue,
     scater,
+    scran,
     batchelor
 Suggests:
     knitr,

diff --git a/vignettes/pseudobulk_transcriptomics.Rmd b/vignettes/pseudobulk_transcriptomics.Rmd
@@ -184,19 +184,19 @@ pseudo_bulk_nested =
 	pseudo_bulk_nested |>
 	
 	# Identify top significant genes
-	mutate(top_genes = map_chr(
+	mutate(top_genes = map(
 		grouped_summarized_experiment, 
 		~ .x |> 
 			pivot_transcript() |> 
 			arrange(pvalue) |> 
-			head(1) |> 
-			pull(.feature)
+			dplyr::slice(1:10) |> 
+			pull(.feature) 
 	)) |> 
 	
 	# Filter top gene
 	mutate(grouped_summarized_experiment = map2(
 		grouped_summarized_experiment, top_genes,
-		~ filter(.x, .feature == .y)
+		~ .x |> filter(.feature %in% .y)
 	)) 
 
 pseudo_bulk_nested

diff --git a/vignettes/solutions_transcriptomics.Rmd b/vignettes/solutions_transcriptomics.Rmd
@@ -38,8 +38,8 @@ seurat_obj |>
 
   mutate(gamma_delta = signature_score > 0.7) |>
   
-  dplyr::count(gamma_delta) |> 
-  summarise(proportion = n/sum(n))
+  count(gamma_delta) |> 
+  metate(proportion = n/sum(n))
 ```
 
 ## Question 2

diff --git a/vignettes/spatial_bioconductor_transcriptomics.Rmd b/vignettes/spatial_bioconductor_transcriptomics.Rmd
@@ -341,7 +341,7 @@ The gated cells can then be divided into pseudobulks within a SummarizedExperime
 ```{r , eval=FALSE}
 spe_regions_aggregated <-
   spatial_data |>
-  aggregate_cells(c(.gated))
+  aggregate_cells(.gated)
 
 spe_regions_aggregated
 ```