fix squashing of plots

phipsonlab · Jan 24, 2024 · 29f8435 · 29f8435
1 parent fe2c5c9
commit 29f8435
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/vignettes/interoperability_with_sce.Rmd b/vignettes/interoperability_with_sce.Rmd
@@ -143,6 +143,9 @@ Any functions which operate on SCE object should work.
 For example, we can use `plotExpression` in `scater` package to create violin plots
 of the markers against clusters.
 
+Note, the y-axis says "logcounts", but the data is actually arcsinh transformed, not log
+transformed.
+
 ```{r}
 plotExpression(supercell_sce, c("CD4", "CD8", "CD19", "CD34", "CD11b"), 
                x = "label", colour_by = "sample")
@@ -194,6 +197,8 @@ plotReducedDim(sce, dimred="UMAP", colour_by="cluster")
 ```
 
 Or violin plot to see the distribution of their marker expressions.
+Note, the y-axis says "logcounts", but the data is actually arcsinh transformed, not log
+transformed.
 
 ```{r}
 plotExpression(sce, c("CD4", "CD8", "CD19", "CD34", "CD11b"), 

diff --git a/vignettes/interoperability_with_seurat.Rmd b/vignettes/interoperability_with_seurat.Rmd
@@ -146,8 +146,8 @@ supercell_seurat_obj <- RunUMAP(supercell_seurat_obj, dims = 1:10)
 DimPlot(supercell_seurat_obj, reduction = "umap")
 ```
 
-```{r}
-FeaturePlot(supercell_seurat_obj, features = c("CD4", "CD8", "CD19", "CD34", "CD11b"))
+```{r height=10, width=10}
+FeaturePlot(supercell_seurat_obj, features = c("CD4", "CD8", "CD19", "CD34", "CD11b"), ncol = 3)
 ```
 
 ## Transfer information from supercells Seurat object to single cell Seurat object
@@ -207,7 +207,7 @@ DimPlot(seurat_obj, reduction = "umap")
 ```
 
 ```{r}
-FeaturePlot(seurat_obj, features = c("CD4", "CD8", "CD19", "CD34", "CD11b"))
+FeaturePlot(seurat_obj, features = c("CD4", "CD8", "CD19", "CD34", "CD11b"), ncol = 3)
 ```