.\" Copyright (c) 2022 Stijn van Dongen
.TH "mcxalter" 1 "9 Oct 2022" "mcxalter 22-282" "USER COMMANDS "
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.SH NAME
mcxalter \- various network transformations
.SH SYNOPSIS

\fBmcxalter\fP
\fB[-imx\fP <fname> (\fIspecify matrix/graph input\fP)\fB]\fP
\fB[-abc\fP <fname> (\fIspecify label input\fP)\fB]\fP
\fB[-tab\fP <fname> (\fIuse tab file\fP)\fB]\fP
\fB[-icl\fP <fname> (\fIspecify cluster input\fP)\fB]\fP
\fB[--block\fP (\fIuse within-cluster edges\fP)\fB]\fP
\fB[--blockc\fP (\fIuse between-cluster edges\fP)\fB]\fP
\fB[-o\fP <fname> (\fIoutput\fP)\fB]\fP
\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
.SH DESCRIPTION

This utility supplies various transformations of networks\&.
.SH OPTIONS

.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
\&
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The file name for input that is in label format\&.
.in -2m

.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
\&
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The file name for input that is in mcl native matrix format\&.
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.ZI 2m "\fB-tab\fP <fname> (\fIuse tab file\fP)"
\&
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This option causes the output to be printed with the labels
found in the tab file\&.
With \fB-abc\fP this option will, additionally, construct
a graph only on the labels found in the tab file\&.
If this option is used in conjunction with \fB-imx\fP the
tab domain and the matrix domain are required to be identical\&.
.in -2m

.ZI 2m "\fB-icl\fP <fname> (\fIspecify cluster input\fP)"
\&
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Read in a cluster file for use with either \fB--block\fP or \fB--blockc\fP\&.
.in -2m

.ZI 2m "\fB--block\fP (\fIuse within-cluster edges\fP)"
\&
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Remove between-cluster edges from the network\&. This is done first, before
other transformations take effect\&.
.in -2m

.ZI 2m "\fB--blockc\fP (\fIuse between-cluster edges\fP)"
\&
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Remove within-cluster edges from the network\&. This is done first, before
other transformations take effect\&.
.in -2m

.ZI 2m "\fB-tf\fP <tf-spec> (\fItransform input matrix values\fP)"
\&
.br
Transform the input matrix values according
to the syntax described in \fBmcxio(5)\fP\&.
.in -2m

.ZI 2m "\fB-o\fP fname (\fIoutput file\fP)"
\&
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Output file\&.
.in -2m
.SH AUTHOR

Stijn van Dongen\&.
.SH SEE ALSO

\fBmcxio(5)\fP,
\fBmcx(1)\fP,
\fBmcxsubs(1)\fP,
and \fBmclfamily(7)\fP for an overview of all the documentation
and the utilities in the mcl family\&.