From f763bbc36f301aede8d481ecd488f1eaf2725d64 Mon Sep 17 00:00:00 2001
From: Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com>
Date: Tue, 10 Dec 2024 13:25:23 -0500
Subject: [PATCH] writing + change to stage.mapped instead of celltype.mapped
 (too many cell types)

---
 episodes/intro-sce.Rmd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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")
 ```
 
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