From f41067646962790d64fdfbe490879a07b3c4a70d Mon Sep 17 00:00:00 2001 From: ackman678 Date: Mon, 13 Jan 2014 10:44:22 -0500 Subject: [PATCH] Merged autosaved graph test code --- ...3-11-05_wholeBrain_graphTest (Autosaved).R | 196 ------------------ .../2013-11-05_wholeBrain_graphTest.R | 99 +++++++++ 2 files changed, 99 insertions(+), 196 deletions(-) delete mode 100644 analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest (Autosaved).R diff --git a/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest (Autosaved).R b/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest (Autosaved).R deleted file mode 100644 index 58ecff9..0000000 --- a/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest (Autosaved).R +++ /dev/null @@ -1,196 +0,0 @@ -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)$width, edge.color="black") - - diff --git a/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R b/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R index 2f48100..58ecff9 100644 --- a/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R +++ b/analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R @@ -95,3 +95,102 @@ colnames(df) <- c("degree") p <- ggplot(df, aes(x=degree)) + xlab("degree") + theme_bw() p + geom_histogram(binwidth = 2) + scale_colour_brewer(palette="Set1") + opts(aspect.ratio=1) #raw counts ggsave(file=paste("120518_07-degreeDist", format(Sys.time(),"%y%m%d-%H%M%S"), ".pdf",sep="")) + + + + + + +# 2014-01-07 09:07:59 + + +edgelist<-read.delim('/Users/ackman/Data/2photon/120518i/2014-01-03-231550/dCorr.txt') + +d2 <- subset(edgelist,filename!='120518_09.tif') + +d3 <- subset(d2,filename=='120518_06.tif') +d4 <- with(d3,data.frame(node1,node2,rvalue)) +edgelist2<-subset(d4,rvalue > 0.1) +g <- graph.data.frame(edgelist2, directed=FALSE) +E(g)$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") + +