Improved graph plots and code

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)