197 lines
5.4 KiB
R
197 lines
5.4 KiB
R
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")
|
|
|
|
|