Skip to content

Commit

Permalink
add note about groups
Browse files Browse the repository at this point in the history
  • Loading branch information
nsohail19 committed Nov 18, 2024
1 parent 8a21a68 commit 7f793e1
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion lessons/08_differential_abundance.md
Original file line number Diff line number Diff line change
Expand Up @@ -249,7 +249,7 @@ plotNhoodSizeHist(traj_milo)
```

<p align="center">
<img src="../img/milo_nhood_hist.png" width="400">
<img src="../img/milo_nhood_hist.png" width="600">
</p>


Expand Down Expand Up @@ -374,6 +374,7 @@ da_results <- annotateNhoods(traj_milo, da_results, coldata_col = "vsm_clusters"

The final piece of information is added to this dataframe of differential abundance results with the `groupNhoods()` function. This will run the louvain clustering algorithm to identify neighborhoods that are overlapping and similar to one another. This `max.lfc.delta` specifies a cutoff of fold change difference where two neighborhoods would not be considered a part of the same group.

> Note that the exact number of groups may vary due to randomness in the model. Even if the results are not identical to what is displayed here, the general trends of the data should be similar.
```r
# Find group structure of neighborhoods
Expand Down

0 comments on commit 7f793e1

Please sign in to comment.