fixed link

_site/index.html

@@ -199,7 +199,7 @@ <h2 class="anchored" data-anchor-id="material-and-video-recodings">Material and
 <li>Lecture of 2024-06-17
 <ul>
 <li>Video (not yet uploaded)</li>
-<li><a href="missing.html">Comparison of t-SNE and UMAP for our example data</a></li>
+<li><a href="umap_vs_tsne.html">Comparison of t-SNE and UMAP for our example data</a></li>
 <li><a href="tsne_umap_math.html">Mathematics of t-SNE and UMAP</a></li>
 <li><a href="UMAP_pedestrian.html">Reimplementing UMAP in Python</a></li>
 </ul></li>

index.qmd

@@ -85,7 +85,7 @@ Place:
   - [Laplacian eigenmaps](laplacian_eigenmap.html)
 - Lecture of 2024-06-17
   - Video (not yet uploaded)
-  - [Comparison of t-SNE and UMAP for our example data](missing.html)
+  - [Comparison of t-SNE and UMAP for our example data](umap_vs_tsne.html)
   - [Mathematics of t-SNE and UMAP](tsne_umap_math.html)
   - [Reimplementing UMAP in Python](UMAP_pedestrian.html)
 - prepared for following lectures 

umap_vs_tsne.qmd

@@ -1,5 +1,5 @@
 ---
-Comparing UMAP and t-SNE
+title: Comparing UMAP and t-SNE
 ---
 
 Here, we compare the two dimension reduction methods, t-SNE and UMAP, applied
@@ -59,30 +59,3 @@ sleepwalk::sleepwalk(
   list( Embeddings(seu,"pca"), Embeddings(seu,"pca") ),
   maxdists = c( 30, 30 ) )
 ```
-
-plot( NULL, xlim=c(1,1000), ylim=c(1,30000), log="xy", xlab="distance", ylab="#")
-for(j in 1:100 ) {
-  i <- sample.int(nrow(x),1)
-  lines( sort( sqrt(colSums( ( t(x) - x[i,] )^2 )) ), 1:nrow(x), col="#00000030" ) }
-
-plot( NULL, xlim=c(1,100), ylim=c(1,300), log="xy", xlab="distance", ylab="#")
-for(j in 1:100 ) {
-  i <- sample.int(nrow(x),1)
-  js <- sample.int(nrow(x), 300, replace=TRUE)
-  d <- sqrt(colSums( ( t(x[js,]) - x[i,] )^2 ))
-  lines( sort(d), 1:length(js), col="#00000030" ) }
-
-segments(20,1,200,1*10^c(1,2,3,5,10))
-
-
-nn <- FNN::get.knn(x,300)
-
-Embeddings(seu,"umap") %>%
-as_tibble() %>%
-add_column( dim = log(30)/log(nn$nn.dist[,300]/nn$nn.dist[,10]) ) %>%
-add_column( dens = log(1/nn$nn.dist[,300]) ) %>%  
-ggplot() +
-  geom_point( aes( x=dens, y=dim ), size=.1 ) 
-  geom_point( aes( x=umap_1, y=umap_2, col=dens ), size=.1 ) +
-  scale_color_viridis_c() #limits=c(1,10), oob=scales::oob_squish)
-