Summarize and Print Features of a cna Network Graph

Usage

"print"(x, ...) "summary"(object, verbose=TRUE, ...)

Arguments

x
A cna network and community object as obtained from the function ‘cna’.
object
A cna network and community object as obtained from the function ‘cna’.
verbose
Logical, if TRUE a community summary table is prited to screen.
...
Extra arguments passed to the ‘write.table’ function.

Description

These functions attempt to summarize and print a cna network graph to the terminal in a human readable form.

Details

Simple summary and print methods for protein dynamic networks.

Value

The function summary.cna returns a list with the following components:
id
A community number/identifier vector with an element for each community.

size
A numeric community size vector, with elements giving the number of nodes within each community.

members
A lst detailing the nodes within each community.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples


## Load the correlation network
attach(hivp)

## Read the starting PDB file to determine atom correspondence
pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
pdb <- read.pdb(pdbfile)

## Examine network composition
print(net)




Call:
  cna.dccm(cij = cij)

Structure: 
 - NETWORK NODES#:   198 	EDGES#: 1756 
 - COMMUNITY NODES#: 18 	EDGES#: 13 

 + attr: network, communities, community.network,
        community.cij, cij, call



x<- summary(net)



 id size                      members
  1   24      c(1:4, 94:107, 193:198)
  2    4                          5:8
  3   22               c(9:23, 64:70)
  4    4                        24:27
  5    2                        28:29
  6   49              c(30:63, 71:85)
  7    1                           86
  8    1                           87
  9    2                        88:89
 10    4                        90:93
 11   20 c(108:113, 117:122, 163:170)
 12   50 c(114:116, 129:162, 171:183)
 13    4                      123:126
 14    2                      127:128
 15    1                          184
 16    2                      185:186
 17    2                      187:188
 18    4                      189:192



x$members[[2]]



5 6 7 8 
5 6 7 8 




detach(hivp)

See also

cna, print.igraph, str.igraph, igraph.plotting

Author

Guido Scarabelli and Barry Grant