From fc5c1340250c542491a7d9bb7e5a0198c886cf56 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Tue, 17 Sep 2024 15:32:51 +0300
Subject: [PATCH] update vignettes and dependencies

---
 DESCRIPTION                                        | 1 +
 vignettes/pseudobulk_transcriptomics.Rmd           | 8 ++++----
 vignettes/solutions_transcriptomics.Rmd            | 4 ++--
 vignettes/spatial_bioconductor_transcriptomics.Rmd | 2 +-
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8ebff0e..b72c421 100644
--- 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
index 9173bc0..aa39f43 100644
--- 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
index 0dbcc2c..ed43297 100644
--- 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
index 002106b..3bbaa6a 100644
--- 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
 ```