From 42ce871e52237cd1f5b9f52c5b434f0c3f8650f5 Mon Sep 17 00:00:00 2001 From: noah Date: Tue, 22 Mar 2022 16:35:56 -0500 Subject: [PATCH] UMAP --- Schrick-Noah_CS-7863_Homework-3.R | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/Schrick-Noah_CS-7863_Homework-3.R b/Schrick-Noah_CS-7863_Homework-3.R index f2370f7..fd9638c 100644 --- a/Schrick-Noah_CS-7863_Homework-3.R +++ b/Schrick-Noah_CS-7863_Homework-3.R @@ -105,4 +105,24 @@ g2.TOM TOMplot(g1.TOM, lap_tree1, main=paste(g1.netname, " Heatmap Plot")) TOMplot(g2.TOM, lap_tree2, main=paste(g2.netname, " Heatmap Plot")) -################################ Part 5: UMAP ################################ \ No newline at end of file +################################ Part 5: UMAP ################################ +g1.dist2 <- 1- as.matrix(g1.adj) +g2.dist2 <- 1- as.matrix(g2.adj) + +# first cluster with hierarchical clustering + +g1.tree2 <- hclust(as.dist(g1.dist2), method = "average") +g2.tree2 <- hclust(as.dist(g2.dist2), method = "average") + +g1.tree2.2clust <- cutree(g1.tree2,k=2) # predicted 2-clusters +g2.tree2.2clust <- cutree(g2.tree2,k=2) # predicted 2-clusters + +#g1.tree2$labels <- V(g1)[Faction] # true clusters +#g2.tree2$labels <- V(g2)[Faction] # true clusters +g1.tree2$labels <- g1.tree2.2clust +g2.tree2$labels <- g2.tree2.2clust + +# if you want to label tree with predicted clusters +plot(g1.tree2, main = paste(g1.netname, " HClust")) +plot(g2.tree2, main = paste(g2.netname, " HClust")) +