182 lines
5.2 KiB
R
182 lines
5.2 KiB
R
require(igraph)
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edgelist<-read.delim('/Users/ackman/Documents/MATLAB/dCorrpairs-20131105-125023.txt')
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edgelist2<-subset(edgelist,rvalue > 0.1)
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g <- graph.data.frame(edgelist2, directed=FALSE)
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#V(g)$label <- V(g)$name #gets the actual vertice labels
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plot(g,layout=layout.lgl,vertex.size=5)
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title('layoutLgl, vertex size5')
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quartz();
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plot(g, layout=layout.fruchterman.reingold, vertex.size=3)
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title('layoutFR, vertex size3')
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quartz();
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com <- spinglass.community(g, spins=5) #finds communities
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V(g)$color <- com$membership+1
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plot(g, layout=layout.fruchterman.reingold)
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title('spinglass, layoutFR, default vertex size')
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walktrapCom<-walktrap.community(g)
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V(g)$color <- walktrapCom$membership+1
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quartz();
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palette(rainbow(max(V(g)$color),alpha=0.5))
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plot(g, layout=layout.fruchterman.reingold)
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palette("default")
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title('walktrap, layoutFR, default vertex size,alpha0.5')
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quartz();
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palette(rainbow(max(V(g)$color),alpha=0.5))
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plot(g, layout=layout.lgl)
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palette("default")
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title('walktrap, layoutLgl, default vertex size,alpha0.5')
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quartz();
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palette(rainbow(max(V(g)$color),alpha=0.5))
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plot(g, layout=layout.kamada.kawai)
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palette("default")
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title('walktrap, layout.kamada.kawai, default vertex size,alpha0.5')
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g <- graph.data.frame(edgelist2, directed=FALSE)
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fastgreedyCom<-fastgreedy.community(g)
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V(g)$color <- fastgreedyCom$membership+1
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quartz();
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palette(rainbow(max(V(g)$color),alpha=0.5))
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plot(g, layout=layout.kamada.kawai)
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palette("default")
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title('fastgreedy, layout.kamada.kawai, default vertex size,alpha0.5')
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edgelist2<-subset(edgelist,rvalue > 0.1)
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g <- graph.data.frame(edgelist2, directed=FALSE)
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fastgreedyCom<-fastgreedy.community(g)
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V(g)$color <- fastgreedyCom$membership+1
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quartz();
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palette(rainbow(max(V(g)$color),alpha=0.5))
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plot(g, layout=layout.fruchterman.reingold)
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palette("default")
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title('fastgreedy, layout.fruchterman.reingold, default vertex size,alpha0.5')
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# Edgelist > 0.2
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edgelist2<-subset(edgelist,rvalue > 0.2)
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g <- graph.data.frame(edgelist2, directed=FALSE)
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fastgreedyCom<-fastgreedy.community(g)
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V(g)$color <- fastgreedyCom$membership+1
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quartz();
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palette(rainbow(max(V(g)$color),alpha=0.5))
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plot(g, layout=layout.fruchterman.reingold)
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palette("default")
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title('fastgreedy, layout.fruchterman.reingold, rvalue >0.2')
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degree(g)
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degree.distribution(g)
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degree.distribution(g,cumulative = TRUE)
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#------Histogram of degree distribution-------------------------------------------------------------
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df <- data.frame(degree(g))
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colnames(df) <- c("degree")
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p <- ggplot(df, aes(x=degree)) + xlab("degree") + theme_bw()
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p + geom_histogram(binwidth = 2) + scale_colour_brewer(palette="Set1") + opts(aspect.ratio=1) #raw counts
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ggsave(file=paste("120518_07-degreeDist", format(Sys.time(),"%y%m%d-%H%M%S"), ".pdf",sep=""))
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# 2014-01-07 09:07:59
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edgelist<-read.delim('/Users/ackman/Data/2photon/120518i/2014-01-03-231550/dCorr.txt')
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# d2 <- subset(edgelist,filename!='120518_09.tif')
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rthresh <- 0.2
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fnm <- '120518_07'
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fnm2 <- paste(fnm,".tif",sep="")
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lo <- 'layout.fruchterman.reingold'
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# lo <- 'layout.kamada.kawai'
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# lo <- 'layout.lgl'
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d3 <- subset(edgelist,filename==fnm2)
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d4 <- with(d3,data.frame(node1,node2,rvalue))
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edgelist2<-subset(d4,rvalue > rthresh)
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g <- graph.data.frame(edgelist2, directed=FALSE)
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E(g)$weight <- E(g)$rvalue
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E(g)$width <- 1
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E(g)[ weight >= 0.3 ]$width <- 3
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E(g)[ weight >= 0.5 ]$width <- 5
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fastgreedyCom<-fastgreedy.community(g,weights=E(g)$weight)
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V(g)$color <- fastgreedyCom$membership
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# quartz();
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# palette(rainbow(max(V(g)$color),alpha=0.5))
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mypalette <- adjustcolor(brewer.pal(max(V(g)$color),"Set1"),0.6)
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palette(mypalette)
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plot(g, layout=eval(parse(text=lo)), edge.width=E(g)$width, edge.color="black", vertex.label.color="black")
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# palette("default")
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title(paste(fnm,', fastgreedy default, ', lo, 'r>', rthresh))
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dateStr=format(Sys.time(),"%y%m%d-%H%M%S")
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quartz.save(file=paste(dateStr, fnm, ".png",sep=""), type = "png", dpi=150)
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quartz.save(file=paste(dateStr, fnm, ".pdf",sep=""), type = "pdf")
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# 131208
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edgelist<-read.delim('/Users/ackman/Data/2photon/131208/2014-01-07-003602/dCorr.txt')
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rthresh <- 0.2
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fnm <- '131208_09'
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fnm2 <- paste(fnm,".tif",sep="")
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lo <- 'layout.fruchterman.reingold'
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# lo <- 'layout.kamada.kawai'
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# lo <- 'layout.lgl'
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d3 <- subset(edgelist,filename==fnm2)
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d4 <- with(d3,data.frame(node1,node2,rvalue))
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edgelist2<-subset(d4,rvalue > rthresh)
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g <- graph.data.frame(edgelist2, directed=FALSE)
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E(g)$weight <- E(g)$rvalue
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E(g)$width <- 1
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E(g)[ weight >= 0.3 ]$width <- 3
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E(g)[ weight >= 0.5 ]$width <- 5
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fastgreedyCom<-fastgreedy.community(g,weights=E(g)$weight)
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V(g)$color <- fastgreedyCom$membership
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# quartz();
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# palette(rainbow(max(V(g)$color),alpha=0.5))
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mypalette <- adjustcolor(brewer.pal(max(V(g)$color),"Set1"),0.6)
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palette(mypalette)
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plot(g, layout=eval(parse(text=lo)), edge.width=E(g)$width, edge.color="black", vertex.label.color="black")
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# palette("default")
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title(paste(fnm,', fastgreedy default, ', lo, 'r>', rthresh))
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dateStr=format(Sys.time(),"%y%m%d-%H%M%S")
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quartz.save(file=paste(dateStr, fnm, ".png",sep=""), type = "png", dpi=150)
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quartz.save(file=paste(dateStr, fnm, ".pdf",sep=""), type = "pdf")
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g <- graph.ring(10)
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E(g)$weight <- runif(ecount(g))
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E(g)$width <- 1
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E(g)[ weight >= 0.5 ]$width <- 3
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plot(g, layout=layout.circle, edge.width=E(g)$width, edge.color="black")
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