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)
Check Out this Related Man Page
mcx clcf(1) USER COMMANDS mcx clcf(1)
NAME
mcx clcf - compute the clustering coefficient of a graph
SYNOPSIS
mcx clcf [options] [matrix-file]
mcxclcf is not in actual fact a program. This manual page documents the behaviour and options of the mcx program when invoked in mode clcf.
The options -h, --apropos, --version, -set, --nop, -progress <num> are accessible in all mcx modes. They are described in the mcx manual
page.
mcx clcf [-abc <fname> (specify label input)] [-imx <fname> (specify matrix input)] [-tab <fname> (use tab file)] [-o <fname> (write to this
file)] [-t <int> (use <int> threads)] [-J <intJ> (a total of <intJ> jobs are used)] [-j <intj> (this job has index <intj>)] [--summary
(return mean clustering coefficient)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]
DESCRIPTION
mcx clcf computes the clustering coefficient of a graph.
The input graph/matrix, if specified with the -imx option, has to be in mcl matrix/graph format. You can use label input instead by using
the -abc option. Refer to mcxio(5) for a description of these two input formats. By default mcx diameter reads from STDIN and expects
matrix format. To specify label input from STDIN use -abc -.
OPTIONS
-abc <fname> (label input)
The file name for input that is in label format.
-imx <fname> (input matrix)
The file name for input. STDIN is assumed if not specified.
-o <fname> (output file)
The file name for output. STDOUT is the default output stream.
-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.
--summary (return mean clustering coefficient)
By the default a 1-column table (with row names included) is output, one row for each node. This option causes the output of the average
clustering coefficient only.
-t <int> (use <int> threads)
-J <intJ> (a total of <intJ> jobs are used)
-j <intj> (this job has index <intj>)
Computing clustering coefficients is time-intensive for large graphs. If you have multiple CPUs available consider using as many threads.
Additionally it is possible to spread the computation over multiple jobs/machines. Conceptually, each job takes a number of threads from
the total thread pool. If job control is used (the -J option is used) then the number of jobs should not exceed the number of threads.
The total number of threads divided by the total number of jobs defines the number of threads that will be used by the current job. Addi-
tionally, the number of threads specified signifies the total added amount of all threads across all machines and must be the same for all
jobs. This number is used by each job to infer its own set of tasks. The following set of options, if given to as many commands, defines
three jobs, each running four threads.
-t 12 -G 3 -g 0
-t 12 -G 3 -g 1
-t 12 -G 3 -g 2
SEE ALSO
mcxio(5), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
mcx clcf 12-068 8 Mar 2012 mcx clcf(1)