Optional 2

.~lock.Schrick-Noah_CS-6643_Lab-4.docx#

@@ -1 +1 @@
-,noah,NovaArchSys,30.09.2022 12:52,file:///home/noah/.config/libreoffice/4;
+,noah,NovaArchSys,30.09.2022 13:06,file:///home/noah/.config/libreoffice/4;

Schrick-Noah_CS-6643_Lab-4.R

@@ -146,3 +146,28 @@ rownames(d)
 mddTree = hclust(as.dist(d))
 mddTree$labels <- phenos.df$X
 plot(mddTree)
+
+
+#### Optional 2: Compare MDS and UMAP clustering
+if (!require("umap")) install.packages("umap")
+library(umap)
+# change umap config parameters
+custom.config = umap.defaults
+custom.config$random_state = 123
+custom.config$n_epochs = 500
+
+SxG.df <- data.frame(t(GxS.covfilter))
+
+obs_mds = cmdscale(d, k=2)
+#add colors for MDD/HC
+colors = rep("black",nrow(SxG.df))
+colors[startsWith(rownames(SxG.df),"MDD")] <- "red"
+plot(obs_mds, col=colors, 
+     main="mds of observations", xlab="mds dim1", ylab="mds dim2")
+
+obs_umap = umap(SxG.df, config=custom.config)
+#add colors for MDD/HC
+colors = rep("black",nrow(SxG.df))
+colors[startsWith(rownames(SxG.df),"MDD")] <- "red"
+plot(obs_umap$layout, col=colors, 
+     main="umap of observations", xlab="umap dim1", ylab="umap dim2")