diff --git a/R/plotAbundance.R b/R/plotAbundance.R index afc1cf1a..78df4715 100644 --- a/R/plotAbundance.R +++ b/R/plotAbundance.R @@ -276,8 +276,9 @@ setMethod("plotAbundance", signature = c("SummarizedExperiment"), # If user wants to calculate relative abundances, apply relative transform # and use relative assay instead of the original assay in plotting. if( use_relative ){ - x <- transformAssay(x, assay.type = assay.type, method = "relabundance") - assay.type <- "relabundance" + temp_name <- "temporary_relative_abundance" + x <- transformAssay(x, assay.type = assay.type, method = "relabundance", name = temp_name) + assay.type <- temp_name } # Samples must have names. In theory, TreeSE can include columns without # names. If that is the case, add names. diff --git a/vignettes/miaViz.Rmd b/vignettes/miaViz.Rmd index 26caea71..fa254614 100644 --- a/vignettes/miaViz.Rmd +++ b/vignettes/miaViz.Rmd @@ -32,7 +32,7 @@ several options, such as `plotColData`, `plotExpression` and `plotRowData`. To install `miaViz`, install `BiocManager` first, if it is not installed. Afterwards use the `install` function from `BiocManager` and load `miaViz`. -```{r} +```{r install, eval=FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("miaViz")