Fix build

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")
 #' 

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.

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")

vignettes/miaViz.Rmd

@@ -63,7 +63,7 @@ However, if the `rank` is set not `NULL` a bar plot is returned. At the same
 time the `features` argument can be set to `NULL` (default).
 
 ```{r}
-GlobalPatterns <- transformCounts(GlobalPatterns, method = "relabundance")
+GlobalPatterns <- transformAssay(GlobalPatterns, method = "relabundance")
 ```
 
 ```{r}
@@ -261,7 +261,7 @@ plotColGraph(altExp(GlobalPatterns,"Genus"),
 library("miaTime")
 data(SilvermanAGutData, package="miaTime")
 tse <- SilvermanAGutData
-tse <- transformCounts(tse, method = "relabundance")
+tse <- transformAssay(tse, method = "relabundance")
 taxa <- getTopTaxa(tse, 2)
 ```
 
@@ -334,7 +334,7 @@ if(!requireNamespace("devtools", quietly = TRUE)){
     BiocManager::install("devtools")
 }
 if(!requireNamespace("miaTime", quietly = TRUE)){
-    devtools::install_github("microbiome/miaTime")
+    devtools::install_github("microbiome/miaTime", upgrade = "never")
 }
 ```
 
@@ -345,7 +345,7 @@ Principal Coordinates Analysis using Bray-Curtis dissimilarity on the
 library(miaTime)
 data(hitchip1006, package = "miaTime")
 tse <- hitchip1006
-tse <- transformCounts(tse, method = "relabundance")
+tse <- transformAssay(tse, method = "relabundance")
 ## Ordination with PCoA with Bray-Curtis dissimilarity
 tse <- runMDS(tse, FUN = vegan::vegdist, method = "bray", name = "PCoA_BC",
               assay.type = "relabundance", na.rm = TRUE)