From 122acae34ec511fc41b3a3b5d16d4c9f5fd97a6a Mon Sep 17 00:00:00 2001
From: noah <noah@theschricks.com>
Date: Mon, 21 Mar 2022 19:12:24 -0500
Subject: [PATCH] Recursive Newman Modularity

---
 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 d1d5211..b7216a6 100644
--- a/Schrick-Noah_CS-7863_Homework-3.R
+++ b/Schrick-Noah_CS-7863_Homework-3.R
@@ -6,7 +6,7 @@
 # Imports
 library(igraph)
 library(igraphdata)
-install.packages("./WGCNA_1.67.tar.gz")
+library(WGCNA)
 
 data(karate)
 data(yeast)
@@ -23,6 +23,26 @@ g2.netname <- "Yeast"
 
 
 ##################### Part 3: Recursive Newman Modularity #####################
+# Using igraph
+karate.modularity <- fastgreedy.community(karate,merges=TRUE, modularity=TRUE, membership=TRUE)
+#memberships <-community.to.membership(karate, karate.modularity$merges, 
+  # steps=which.max(fgreedy$modularity)-1)
+karate.modularity$membership
+karate.modularity$merges
+membership.ids <- unique(karate.modularity$membership)
+membership.ids
+cat(paste('Number of detected communities =',length(membership.ids)))
+cat("community sizes: ")
+sapply(membership.ids,function(x) {sum(x==karate.modularity$membership)})
+cat("modularity: ")
+max(karate.modularity$modularity)
+#karate.modularity$modularity
+
+V(karate)$color[karate.modularity$membership==1] <- "green"
+V(karate)$color[karate.modularity$membership==2] <- "red"
+V(karate)$color[karate.modularity$membership==3] <- "blue"
+
+plot(karate,vertex.size=10,vertex.label=V(karate)$label,vertex.color=V(karate)$color)
 
 
 ###################### Part 4: TOM and Dynamic Tree Cut ######################