mcxalter(1) USER COMMANDS mcxalter(1)
NAME
mcxalter - various network transformations
SYNOPSIS
mcxalter [-imx <fname> (specify matrix input)] [-abc <fname> (specify label input)] [-tab <fname> (use tab file)] [-o <fname> (output)] [-tf
spec (apply tf-spec to input matrix)]
DESCRIPTION
This utility supplies various transformations of networks.
OPTIONS
-abc <fname> (label input)
The file name for input that is in label format.
-imx <fname> (input matrix)
The file name for input that is in mcl native matrix format.
-tab <fname> (use tab file)
This option causes the output to be printed with the labels found in the tab file. With -abc this option will, additionally, construct a
graph only on the labels found in the tab file. If this option is used in conjunction with -imx the tab domain and the matrix domain are
required to be identical.
-tf <tf-spec> (transform input matrix values)
Transform the input matrix values according to the syntax described in mcxio(5).
-o fname (output file)
Output file.
AUTHOR
Stijn van Dongen.
SEE ALSO
mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
mcxalter 12-068 8 Mar 2012 mcxalter(1)
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mcxmap(1) USER COMMANDS mcxmap(1)
NAME
mcxmap - permute or remap the indices of graphs and matrices.
SYNOPSIS
mcxmap -imx fname (input) [-o fname (output)] [-make-map (output map file name)] [-make-mapc (output map file name)] [-make-mapr (output map
file name)] [-cmul a (coefficient)] [-cshift b (translate)] [-rmul c (coefficient)] [-rshift d (translate)] [-mul e (coefficient)] [-shift f
(translate)] [-map fname (row/col map file)] [-rmap fname (row map file)] [-cmap fname (column map file)] [-mapi fname (row/col map file
(use inverse))] [-rmapi fname (row map file (use inverse))] [-cmapi fname (column map file (use inverse))] [-tab fname (read (and map) tab
file)]
DESCRIPTION
This utility relabels graphs or matrices. Its main use is in applying a map file to a given matrix or graph. A map file contains a so called
map matrix in mcl format that has some special properties (given further below). The functionality of mcxmap can also be provided by mcx, as
a mapped matrix (i.e. the result of applying a map matrix to another matrix) is simply the usual matrix product of a matrix and a map
matrix. However, mcx will construct a new matrix and leave the original matrix to be mapped alone. When dealing with huge matrices, consid-
erable gains in efficiency memory-wise and time-wise can be achieved by doing the mapping in-place. This is what mcxmap does. In the
future, its functionality may be embedded in mcx with new mcx operators.
The special properties of a map matrix are
o The column domain and row domain are of the same cardinality.
o Each column has exactly one entry.
o Each row domain index occurs in exactly one column.
These properties imply that the matrix can be used as a map from the column domain onto the row domain. An example map matrix is found in
the EXAMPLES Section.
OPTIONS
-o fname (output file)
Output file.
-imx fname (input file)
Input file.
-map fname (row/col map file))
-rmap fname (row map file)
-cmap fname (column map file)
-mapi fname (row/col map file (use inverse))
-rmapi fname (row map fil (use inverse))
-cmapi fname (column map fil (use inverse))
Different ways to specify map files.
-make-map (output map file name)
-make-mapc (output map file name)
-make-mapr (output map file name)
Generate a map that maps the specified domain onto the appropriate canonical domain and write the map matrix to file.
-cmul a (coefficient)
-cshift b (translate)
These options have affect if neither a column map file nor column canonification is specified. If any of the first two options is used,
column indices i are mapped to a*i+b.
-rmul c (coefficient)
-rshift d (translate)
These options have affect if neither a row map file nor row canonification is specified. If any of the first two options is used,
indices i are mapped to c*i+d.
-mul e (coefficient)
-shift f (translate)
If a map file is specified for a given domain, neither a map file nor canonification is specified. If any of the first two options is
used, the indices i will be mapped to e*i+f.
-tab fname (read (and map) tab file)
This option requires the -map option. mcxmap will output the mapped tab definition.
EXAMPLES
The matrix below has two canonical domains which are identical. It denotes a map of the canonical domain onto itself, in which node 0 is
relabeled to 8, node 1 is relabeled to 5, et cetera.
(mclheader
mcltype matrix
dimensions 12x12
)
(mclmatrix
begin
0 8 $
1 5 $
2 3 $
3 2 $
4 4 $
5 6 $
6 7 $
7 9 $
8 1 $
9 10 $
10 11 $
11 0 $
)
AUTHOR
Stijn van Dongen.
SEE ALSO
mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
mcxmap 12-068 8 Mar 2012 mcxmap(1)