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graph analysis

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* community detection at P3, P8
* edge weights
* fig 4 update
This commit is contained in:
ackman678
2014-02-12 11:53:57 -05:00
parent 6827cf4d77
commit 0284b324c6
31 changed files with 5763 additions and 11 deletions
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32
analysis/quantif_20131105/2013-11-05_wholeBrain_graphTest.R
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@@ -140,9 +140,13 @@ quartz.save(file=paste(dateStr, "-", fnm, ".pdf",sep=""), type = "pdf")
edgelist<-read.delim('/Users/ackman/Data/2photon/131208/2014-01-07-003602/dCorr.txt')
edgelist<-read.delim('/Users/ackman/Data/2photon/120518i/2014-01-03-231550/dCorr.txt')
rthresh <- 0.2
fnm <- '131208_09'
for(j in c(0.1,0.15,0.2)) {
for(i in c('131208_01','131208_03','131208_04','131208_05')) {
# for(i in c('120518_06','120518_07','120518_08','120518_09')) {
rthresh <- j
fnm <- i
fnm2 <- paste(fnm,".tif",sep="")
lo <- 'layout.fruchterman.reingold'
# lo <- 'layout.kamada.kawai'
@@ -161,14 +165,14 @@ V(g)$color <- fastgreedyCom$membership
# 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)$width, edge.color="black", vertex.label.color="black")
# palette("default")
title(paste(fnm,', fastgreedy default, ', lo, 'r>', rthresh))
dateStr=format(Sys.time(),"%y%m%d-%H%M%S")
quartz.save(file=paste(dateStr, "-", fnm, ".png",sep=""), type = "png", dpi=150)
quartz.save(file=paste(dateStr, "-", fnm, ".pdf",sep=""), type = "pdf")
# plot(g, layout=eval(parse(text=lo)), edge.width=E(g)$width, edge.color="black", vertex.label.color="black")
# 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")
print(transitivity(g))
}
}
# 2014-01-14 14:59:18 Make mean summary graphs for P3 and P8
@@ -188,7 +192,7 @@ rvalue.sem = rvalue.sd/sqrt(N))
colnames(d2)[colnames(d2) == 'rvalue.mean'] <- 'rvalue'
rthresh <- 0.15
fnm <- 'P8'
fnm <- '131208'
# fnm2 <- paste(fnm,".tif",sep="")
lo <- 'layout.fruchterman.reingold'
# lo <- 'layout.kamada.kawai'
@@ -223,6 +227,12 @@ average.path.length(g)
diameter(g)
hub.score(g)$vector
mean(degree(g))
transitivity(g)
centralization.degree(g)
is.connected(g)
no.clusters(g)
clusters(g)
#------Histogram of degree distribution-------------------------------------------------------------
df <- data.frame(degree(g))