Merge pull request #63 from carpentries-incubator/intro_upd

writing + change to stage.mapped instead of celltype.mapped (too many…

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")
 ```
 
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