Some new graph testing

analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest (Autosaved).R

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+require(igraph) 
+
+edgelist<-read.delim('/Users/ackman/Documents/MATLAB/dCorrpairs-20131105-125023.txt')
+
+edgelist2<-subset(edgelist,rvalue > 0.1)
+
+
+g <- graph.data.frame(edgelist2, directed=FALSE)
+#V(g)$label <- V(g)$name  #gets the actual vertice labels
+plot(g,layout=layout.lgl,vertex.size=5)
+title('layoutLgl, vertex size5')
+
+quartz();
+plot(g, layout=layout.fruchterman.reingold, vertex.size=3)
+title('layoutFR, vertex size3')
+
+quartz();
+com <- spinglass.community(g, spins=5)   #finds communities
+V(g)$color <- com$membership+1
+plot(g, layout=layout.fruchterman.reingold)
+title('spinglass, layoutFR, default vertex size')
+
+
+walktrapCom<-walktrap.community(g)
+V(g)$color <- walktrapCom$membership+1
+
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.fruchterman.reingold)
+palette("default")
+title('walktrap, layoutFR, default vertex size,alpha0.5')
+
+
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.lgl)
+palette("default")
+title('walktrap, layoutLgl, default vertex size,alpha0.5')
+
+
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.kamada.kawai)
+palette("default")
+title('walktrap, layout.kamada.kawai, default vertex size,alpha0.5')
+
+g <- graph.data.frame(edgelist2, directed=FALSE)
+fastgreedyCom<-fastgreedy.community(g)
+V(g)$color <- fastgreedyCom$membership+1
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.kamada.kawai)
+palette("default")
+title('fastgreedy, layout.kamada.kawai, default vertex size,alpha0.5')
+
+
+
+
+edgelist2<-subset(edgelist,rvalue > 0.1)
+g <- graph.data.frame(edgelist2, directed=FALSE)
+fastgreedyCom<-fastgreedy.community(g)
+V(g)$color <- fastgreedyCom$membership+1
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.fruchterman.reingold)
+palette("default")
+title('fastgreedy, layout.fruchterman.reingold, default vertex size,alpha0.5')
+
+
+
+
+# Edgelist > 0.2
+
+edgelist2<-subset(edgelist,rvalue > 0.2)
+g <- graph.data.frame(edgelist2, directed=FALSE)
+fastgreedyCom<-fastgreedy.community(g)
+V(g)$color <- fastgreedyCom$membership+1
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.fruchterman.reingold)
+palette("default")
+title('fastgreedy, layout.fruchterman.reingold, rvalue >0.2')
+
+
+degree(g)
+degree.distribution(g)
+degree.distribution(g,cumulative = TRUE)
+
+
+
+
+#------Histogram of degree distribution-------------------------------------------------------------
+df <- data.frame(degree(g))
+colnames(df) <- c("degree")
+p <- ggplot(df, aes(x=degree)) + xlab("degree") + theme_bw()
+p + geom_histogram(binwidth = 2) + scale_colour_brewer(palette="Set1") + opts(aspect.ratio=1)  #raw counts
+ggsave(file=paste("120518_07-degreeDist", format(Sys.time(),"%y%m%d-%H%M%S"), ".pdf",sep=""))
+
+
+
+
+
+
+# 2014-01-07 09:07:59
+
+
+edgelist<-read.delim('/Users/ackman/Data/2photon/120518i/2014-01-03-231550/dCorr.txt')
+
+d2 <- subset(edgelist,filename!='120518_09.tif')
+
+d3 <- subset(d2,filename=='120518_06.tif')
+d4 <- with(d3,data.frame(node1,node2,rvalue))
+edgelist2<-subset(d4,rvalue > 0.1)
+g <- graph.data.frame(edgelist2, directed=FALSE)
+E(g)$weight <- E(g)$rvalue
+E(g)$width <- 1
+E(g)[ weight >= 0.3 ]$width <- 3
+E(g)[ weight >= 0.5 ]$width <- 5
+fastgreedyCom<-fastgreedy.community(g,weights=E(g)$weight)
+V(g)$color <- fastgreedyCom$membership+1
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.fruchterman.reingold, edge.width=E(g)$width, edge.color="black")
+palette("default")
+title('120518_06, fastgreedy, layout.fruchterman.reingold, default vertex size,alpha0.5')
+
+
+
+
+
+d3 <- subset(d2,filename=='120518_07.tif')
+d4 <- with(d3,data.frame(node1,node2,rvalue))
+edgelist2<-subset(d4,rvalue > 0.1)
+g <- graph.data.frame(edgelist2, directed=FALSE)
+E(g)$weight <- E(g)$rvalue
+E(g)$width <- 1
+E(g)[ weight >= 0.3 ]$width <- 3
+E(g)[ weight >= 0.5 ]$width <- 5
+fastgreedyCom<-fastgreedy.community(g,weights=E(g)$weight)
+V(g)$color <- fastgreedyCom$membership+1
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.fruchterman.reingold, edge.width=E(g)$width, edge.color="black")
+palette("default")
+title('120518_07, fastgreedy, layout.fruchterman.reingold, default vertex size,alpha0.5')
+
+
+
+
+d3 <- subset(d2,filename=='120518_08.tif')
+d4 <- with(d3,data.frame(node1,node2,rvalue))
+
+edgelist2<-subset(d4,rvalue > 0.1)
+g <- graph.data.frame(edgelist2, directed=FALSE)
+fastgreedyCom<-fastgreedy.community(g)
+V(g)$color <- fastgreedyCom$membership+1
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.fruchterman.reingold)
+palette("default")
+title('120518_08, fastgreedy, layout.fruchterman.reingold, default vertex size,alpha0.5')
+
+
+
+
+
+# 131208
+
+
+edgelist<-read.delim('/Users/ackman/Data/2photon/131208/2014-01-07-003602/dCorr.txt')
+
+d3 <- subset(edgelist,filename=='131208_08.tif')
+d4 <- with(d3,data.frame(node1,node2,rvalue))
+
+edgelist2<-subset(d4,rvalue > 0.1)
+g <- graph.data.frame(edgelist2, directed=FALSE)
+fastgreedyCom<-fastgreedy.community(g)
+V(g)$color <- fastgreedyCom$membership+1
+E(g)$weight <- runif(ecount(g))
+E(g)$width <- 1
+# E(g)[ weight >= 0.3 ]$width <- 2
+E(g)[ weight >= 0.5 ]$width <- 3
+quartz();
+palette(rainbow(max(V(g)$color),alpha=0.5))
+plot(g, layout=layout.fruchterman.reingold, edge.width=E(g)$width, edge.color="black")
+palette("default")
+title('131208_08, fastgreedy, layout.fruchterman.reingold, default vertex size,alpha0.5')
+
+
+g <- graph.ring(10)
+E(g)$weight <- runif(ecount(g))
+E(g)$width <- 1
+E(g)[ weight >= 0.5 ]$width <- 3
+plot(g, layout=layout.circle, edge.width=E(g)$width, edge.color="black")
+  
+