On Sep 1, 2012, at 10:20 PM, Sancar Adali <sadali@gmail.com> wrote:
worm includes two (weighted) graphs Achem , Agap  -- N=279 . The names of
the neurons are listed in "Neuron_ordered"  in the same ordering as the two
matrices. 
I can't remember if the last one is from Joshua or I imported it to MATLAB,
myself.

require(R.matlab)
dat <- readMat(url("http://www.cis.jhu.edu/~parky/SGM/graph_data/elegansGraph.mat"))
summary(dat)
               Length Class     Mode
Neuron.ordered   279  -none-    list
Achem          77841  dgCMatrix S4  
Agap           77841  dgCMatrix S4  

dim(dat$Achem)
[1] 279 279
dim(dat$Agap)
[1] 279 279

279^2
[1] 77841
sum( dat$Achem == t(dat$Achem) )
[1] 74035  # Achem is NOT symmetric
sum( dat$Agap == t(dat$Agap) )
[1] 77841  # Agap is symmetric

sum(apply( dat$Achem+t(dat$Achem) , 1 , sum ) == 0)
[1] 0      # Achem has  0 isolates
sum(apply( dat$Agap+t(dat$Agap) , 1 , sum ) == 0)
[1] 26     # Agap has 26 isolates

sum(diag(dat$Achem))
[1] 0      # Achem has no loops
sum(diag(dat$Agap))
[1] 3      # Agap has YES loops

=========================================================================

On Nov 27, 2012, at 2:16 AM, Sancar Adali <sadali@gmail.com> wrote:
here is the male version of worm (only 170 neurons for Achem and 167 for Agap)

datM <- readMat(url("http://www.cis.jhu.edu/~parky/SGM/graph_data/elegansGraph_male.mat"))
summary(datM)
           Length Class  Mode   
Achem       28900  -none- numeric
Agap        27889  -none- numeric
Agap.names    167  -none- list   
Achem.names   170  -none- list   

dim(datM$Agap) # 167x167
isSymmetric(datM$Agap) #[1] TRUE
sum(apply( datM$Agap+t(datM$Agap) , 1 , sum ) == 0) # 2 isolates
sum(diag(datM$Agap)) # 37 loops

dim(datM$Achem) # 170x170
isSymmetric(datM$Achem) #[1] FALSE
sum(apply(datM$Achem,1,sum)==0) # 2 isolates
sum(apply( datM$Achem+t(datM$Achem) , 1 , sum ) == 0) # 2 isolates
sum(diag(datM$Achem)) # 355 loops