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microbiome · Aug 30, 2023 · 241a823 · 241a823
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commit 241a823
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/R/plotAbundance.R b/R/plotAbundance.R
@@ -110,7 +110,7 @@
 #' ## Compositional barplot with top 5 taxa and samples sorted by "Bacteroidetes"
 #' 
 #' # Getting top taxa on a Phylum level
-#' se <- transformCounts(se, method="relabundance")
+#' se <- transformAssay(se, method="relabundance")
 #' se_phylum <- agglomerateByRank(se, rank ="Phylum", onRankOnly=TRUE)
 #' top_taxa <- getTopTaxa(se_phylum,top = 5, assay.type = "relabundance")
 #' 

diff --git a/R/plotAbundanceDensity.R b/R/plotAbundanceDensity.R
@@ -94,7 +94,7 @@
 #' plotAbundanceDensity(tse, assay.type = "counts")
 #' 
 #' # Counts relative abundances
-#' tse <- transformCounts(tse, method = "relabundance")
+#' tse <- transformAssay(tse, method = "relabundance")
 #' 
 #' # Plots the relative abundance of 10 most abundant taxa. 
 #' # "nationality" information is used to color the points. X-axis is log-scaled.

diff --git a/R/plotSeries.R b/R/plotSeries.R
@@ -67,7 +67,7 @@
 #'            colour_by = "Family")
 #' 
 #' # Counts relative abundances
-#' object <- transformCounts(object, method = "relabundance")
+#' object <- transformAssay(object, method = "relabundance")
 #' 
 #' # Selects taxa
 #' taxa <- c("seq_1", "seq_2", "seq_3", "seq_4", "seq_5")

diff --git a/man/plotAbundance.Rd b/man/plotAbundance.Rd
diff --git a/man/plotAbundanceDensity.Rd b/man/plotAbundanceDensity.Rd
diff --git a/man/plotSeries.Rd b/man/plotSeries.Rd