Practical_b.Rmd: add UMAP plot

Practical_b.Rmd

@@ -544,6 +544,22 @@ adjustedRandIndex(
 </details>
 
 
+## Graph-based dimension reduction
 
+Uniform Manifold Approximation and Projection (UMAP) is an algorithm for dimensional reduction. Its details are described by [McInnes, Healy, and Melville](https://arxiv.org/abs/1802.03426) and its official implementation is available through a python package [umap-learn](https://github.com/lmcinnes/umap).
+
+```{r}
+library(umap)
+data_umap <- umap(data_pca$x[, 1:10])
+data_umap$layout %>% 
+  as_tibble() %>% 
+  mutate(cell_type = cell_annotation) %>% 
+  ggplot() +
+  geom_point(aes(x = V1, y = V2, color = cell_type))
+```
+
+<div class="pencadre">
+What can you say about the axes of this plot ?
+</div>
 
 [The .Rmd file corresponding to this page is available here under the AGPL3 Licence](https://lbmc.gitbiopages.ens-lyon.fr/hub/formations/ens_m1_ml/Practical_b.Rmd)