Hello,
I'm trying to take the correlation of two distance matrices and get 
the r2 value
ex)


         Ndisc     PS1    Ntet   Nsito     NcB     NcA     PS3     NcC 
NiB     NiA
PS1 
0.08945                                                                       
Ntet  0.08601 
0.02020                                                               
Nsito 0.09361 0.02780 
0.02260                                                       
NcB   0.09479 0.03258 0.02914 
0.03674                                               
NcA   0.09363 0.03142 0.02798 0.03558 
0.02190                                       
PS3   0.09145 0.02924 0.02580 0.03340 0.02446 
0.02330                               
NcC   0.08919 0.02698 0.02354 0.03114 0.02220 0.02104 
0.01670                       
NiB   0.09749 0.03802 0.03458 0.04218 0.04336 0.04220 0.04002 
0.03776               
NiA   0.09571 0.03624 0.03280 0.04040 0.04158 0.04042 0.03824 0.03598 
0.02170       
PS2   0.09234 0.03287 0.02943 0.03703 0.03821 0.03705 0.03487 0.03261 
0.03289 0.03111


and
          Ndisc      PS1     Ntet      NcB      NcA      NcC      PS3 
Nsito      PS2      NiB
PS1 
2.981494                                                                                
Ntet  2.949046 
1.003718                                                                       
NcB   3.212256 1.266928 
1.178326                                                              
NcA   3.531725 1.586397 1.497795 
1.217055                                                     
NcC   3.111421 1.166093 1.077491 0.944637 
1.264106                                            
PS3   3.115273 1.169945 1.081343 1.000991 1.320460 
0.900156                                   
Nsito 2.994152 1.131330 1.098882 1.362092 1.681561 1.261257 
1.265109                          
PS2   2.843805 1.228361 1.195913 1.459123 1.778592 1.358288 1.362140 
1.241019                 
NiB   2.805537 1.375615 1.343167 1.606377 1.925846 1.505542 1.509394 
1.388273 1.237926        
NiA   2.752269 1.322347 1.289899 1.553109 1.872578 1.452274 1.456126 
1.335005 1.184658 1.018210


The problem is that these matrices are the endpoint of an extensive 
simulation involving phylogenetic trees and the order of the columns 
and rows shifts around according to how they were ordered in the 
tree. I used cophenetic.phylo to get the distance matrix and now I 
need to find a way to reorder or sort the columns and rows such that 
the two matrices match and cor is taking the correlation of the 
corresponding column and row and not just the  one in the same 
position. I don't want to sort the values in the columns and rows but 
the entire column and their associated rows. I've looked at order , 
sort, and match and can't figure out a way to do it based on the 
alphanumeric name of the columns.  Does anyone have any suggestions?
Sincerely,
Betty




-- 
Betty Gilbert
lgilbert@berkeley.edu
Taylor Lab
Plant and Microbial Biology
321 Koshland Hall
U.C. Berkeley
Berkeley, Ca 94720
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