Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

writing + change to stage.mapped instead of celltype.mapped (too many… #63

Merged
merged 1 commit into from
Dec 10, 2024
Merged

writing + change to stage.mapped instead of celltype.mapped (too many… #63

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions episodes/intro-sce.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down