diff --git a/episodes/intro-sce.Rmd b/episodes/intro-sce.Rmd index cf73da0..1baef65 100644 --- a/episodes/intro-sce.Rmd +++ b/episodes/intro-sce.Rmd @@ -233,12 +233,12 @@ As for the other slots, we have the usual setter/getter, but it is somewhat rare It is more common for other functions to _store_ this information in the object, e.g., the `runPCA` function from the `scater` package. -Here, we use `scater`'s `plotReducedDim` function as an example of how to extract this information _indirectly_ from the objects. Note that one could obtain the same results (somewhat less efficiently) by extracting the corresponding `reducedDim` matrix and `ggplot`. +Here, we use `scater`'s `plotReducedDim` function as an example of how to extract this information _indirectly_ from the objects. Note that one could obtain the same results by manually extracting the corresponding `reducedDim` matrix and cell type labels then passing them to `ggplot` in a data frame. ```{r, message = FALSE, warning = FALSE} library(scater) -plotReducedDim(sce, "pca.corrected.E8.5", colour_by = "celltype.mapped") +plotReducedDim(sce, "pca.corrected.E8.5", colour_by = "stage.mapped") ``` :::::::::::::::::::::::::::::::::: challenge