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UMAP

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This commit is contained in:
Noah L. Schrick 2022-03-22 16:35:56 -05:00
parent fb9b7b8e5e
commit 42ce871e52
1 changed files with 21 additions and 1 deletions
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Schrick-Noah_CS-7863_Homework-3.R
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@ -106,3 +106,23 @@ TOMplot(g1.TOM, lap_tree1, main=paste(g1.netname, " Heatmap Plot"))
TOMplot(g2.TOM, lap_tree2, main=paste(g2.netname, " Heatmap Plot")) TOMplot(g2.TOM, lap_tree2, main=paste(g2.netname, " Heatmap Plot"))
################################ Part 5: UMAP ################################ ################################ 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"))