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b/analysis/quantif_20131105/140113-170350131208_09.pdf differ diff --git a/analysis/quantif_20131105/140113-170350131208_09.png b/analysis/quantif_20131105/140113-170350131208_09.png new file mode 100644 index 0000000..5874149 Binary files /dev/null and b/analysis/quantif_20131105/140113-170350131208_09.png differ diff --git a/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R b/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R index 58ecff9..c616a40 100644 --- a/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R +++ b/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R @@ -105,62 +105,34 @@ ggsave(file=paste("120518_07-degreeDist", format(Sys.time(),"%y%m%d-%H%M%S"), ". edgelist<-read.delim('/Users/ackman/Data/2photon/120518i/2014-01-03-231550/dCorr.txt') +# d2 <- subset(edgelist,filename!='120518_09.tif') -d2 <- subset(edgelist,filename!='120518_09.tif') - -d3 <- subset(d2,filename=='120518_06.tif') +rthresh <- 0.2 +fnm <- '120518_07' +fnm2 <- paste(fnm,".tif",sep="") +lo <- 'layout.fruchterman.reingold' +# lo <- 'layout.kamada.kawai' +# lo <- 'layout.lgl' +d3 <- subset(edgelist,filename==fnm2) d4 <- with(d3,data.frame(node1,node2,rvalue)) -edgelist2<-subset(d4,rvalue > 0.1) +edgelist2<-subset(d4,rvalue > rthresh) 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)$color),alpha=0.5)) -plot(g, layout=layout.fruchterman.reingold) -palette("default") -title('120518_08, fastgreedy, layout.fruchterman.reingold, default vertex size,alpha0.5') - - +V(g)$color <- fastgreedyCom$membership +# quartz(); +# palette(rainbow(max(V(g)$color),alpha=0.5)) +mypalette <- adjustcolor(brewer.pal(max(V(g)$color),"Set1"),0.6) +palette(mypalette) +plot(g, layout=eval(parse(text=lo)), edge.width=E(g)$width, edge.color="black", vertex.label.color="black") +# palette("default") +title(paste(fnm,', fastgreedy default, ', lo, 'r>', rthresh)) +dateStr=format(Sys.time(),"%y%m%d-%H%M%S") +quartz.save(file=paste(dateStr, fnm, ".png",sep=""), type = "png", dpi=150) +quartz.save(file=paste(dateStr, fnm, ".pdf",sep=""), type = "pdf") @@ -169,22 +141,35 @@ title('120518_08, fastgreedy, layout.fruchterman.reingold, default vertex size,a edgelist<-read.delim('/Users/ackman/Data/2photon/131208/2014-01-07-003602/dCorr.txt') -d3 <- subset(edgelist,filename=='131208_08.tif') +rthresh <- 0.2 +fnm <- '131208_09' +fnm2 <- paste(fnm,".tif",sep="") +lo <- 'layout.fruchterman.reingold' +# lo <- 'layout.kamada.kawai' +# lo <- 'layout.lgl' +d3 <- subset(edgelist,filename==fnm2) d4 <- with(d3,data.frame(node1,node2,rvalue)) - -edgelist2<-subset(d4,rvalue > 0.1) +edgelist2<-subset(d4,rvalue > rthresh) g <- graph.data.frame(edgelist2, directed=FALSE) -fastgreedyCom<-fastgreedy.community(g) -V(g)$color <- fastgreedyCom$membership+1 -E(g)$weight <- runif(ecount(g)) +E(g)$weight <- E(g)$rvalue E(g)$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') +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$membership +# quartz(); +# palette(rainbow(max(V(g)$color),alpha=0.5)) +mypalette <- adjustcolor(brewer.pal(max(V(g)$color),"Set1"),0.6) +palette(mypalette) +plot(g, layout=eval(parse(text=lo)), edge.width=E(g)$width, edge.color="black", vertex.label.color="black") +# palette("default") +title(paste(fnm,', fastgreedy default, ', lo, 'r>', rthresh)) +dateStr=format(Sys.time(),"%y%m%d-%H%M%S") +quartz.save(file=paste(dateStr, fnm, ".png",sep=""), type = "png", dpi=150) +quartz.save(file=paste(dateStr, fnm, ".pdf",sep=""), type = "pdf") + + + g <- graph.ring(10)