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EBI-Metagenomics · Sep 23, 2024 · 6e8a7e5 · 6e8a7e5
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diff --git a/vignettes/MGnifyR.Rmd b/vignettes/MGnifyR.Rmd
@@ -194,7 +194,11 @@ library(miaViz)
 
 # Plot top taxa
 top_taxa <- getTopFeatures(altExp(mae[[1]], "Phylum"), 10)
-plotAbundance(altExp(mae[[1]], "Phylum")[top_taxa, ], rank = "Phylum")
+plotAbundance(
+    altExp(mae[[1]], "Phylum")[top_taxa, ],
+    rank = "Phylum",
+    as.relative = TRUE
+    )
 ```
 
 We can also perform other analyses such as principal component analysis to

diff --git a/vignettes/MGnifyR_long.Rmd b/vignettes/MGnifyR_long.Rmd
@@ -268,7 +268,11 @@ plotColData(tse, "shannon", x = "sample_geo.loc.name")
 ```{r plot_abundance}
 library(miaViz)
 
-plotAbundance(tse[!is.na( rowData(tse)[["Kingdom"]] ), ], rank = "Kingdom")
+plotAbundance(
+    tse[!is.na( rowData(tse)[["Kingdom"]] ), ],
+    rank = "Kingdom",
+    as.relative = TRUE
+    )
 ```
 
 If needed, `TreeSE` can be converted to `phyloseq`.