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diff --git a/doc/f3m.1.html b/doc/f3m.1.html new file mode 100644 index 0000000..3890394 --- /dev/null +++ b/doc/f3m.1.html @@ -0,0 +1,235 @@ +<!DOCTYPE html> +<html> +<head> + <meta http-equiv='content-type' value='text/html;charset=utf8'> + <meta name='generator' value='Ronn/v0.7.3 (http://github.com/rtomayko/ronn/tree/0.7.3)'> + <title>f3m(1) - Count all the 3-node subgraphs of a directed graph</title> + <style type='text/css' media='all'> + /* style: man */ + body#manpage {margin:0} + .mp {max-width:100ex;padding:0 9ex 1ex 4ex} + .mp p,.mp pre,.mp ul,.mp ol,.mp dl {margin:0 0 20px 0} + .mp h2 {margin:10px 0 0 0} + .mp > p,.mp > pre,.mp > ul,.mp > ol,.mp > dl {margin-left:8ex} + .mp h3 {margin:0 0 0 4ex} + .mp dt {margin:0;clear:left} + .mp dt.flush {float:left;width:8ex} + .mp dd {margin:0 0 0 9ex} + .mp h1,.mp h2,.mp h3,.mp h4 {clear:left} + .mp pre {margin-bottom:20px} + .mp pre+h2,.mp pre+h3 {margin-top:22px} + .mp h2+pre,.mp h3+pre {margin-top:5px} + .mp img {display:block;margin:auto} + .mp h1.man-title {display:none} + .mp,.mp code,.mp pre,.mp tt,.mp kbd,.mp samp,.mp h3,.mp h4 {font-family:monospace;font-size:14px;line-height:1.42857142857143} + .mp h2 {font-size:16px;line-height:1.25} + .mp h1 {font-size:20px;line-height:2} + .mp {text-align:justify;background:#fff} + .mp,.mp code,.mp pre,.mp pre code,.mp tt,.mp kbd,.mp samp {color:#131211} + .mp h1,.mp h2,.mp h3,.mp h4 {color:#030201} + .mp u {text-decoration:underline} + .mp code,.mp strong,.mp b {font-weight:bold;color:#131211} + .mp em,.mp var {font-style:italic;color:#232221;text-decoration:none} + .mp a,.mp a:link,.mp a:hover,.mp a code,.mp a pre,.mp a tt,.mp a kbd,.mp a samp {color:#0000ff} + .mp b.man-ref {font-weight:normal;color:#434241} + .mp pre {padding:0 4ex} + .mp pre code {font-weight:normal;color:#434241} + .mp h2+pre,h3+pre {padding-left:0} + ol.man-decor,ol.man-decor li {margin:3px 0 10px 0;padding:0;float:left;width:33%;list-style-type:none;text-transform:uppercase;color:#999;letter-spacing:1px} + ol.man-decor {width:100%} + ol.man-decor li.tl {text-align:left} + ol.man-decor li.tc {text-align:center;letter-spacing:4px} + ol.man-decor li.tr {text-align:right;float:right} + </style> + <style type='text/css' media='all'> + /* style: toc */ + .man-navigation {display:block !important;position:fixed;top:0;left:113ex;height:100%;width:100%;padding:48px 0 0 0;border-left:1px solid #dbdbdb;background:#eee} + .man-navigation a,.man-navigation a:hover,.man-navigation a:link,.man-navigation a:visited {display:block;margin:0;padding:5px 2px 5px 30px;color:#999;text-decoration:none} + .man-navigation a:hover {color:#111;text-decoration:underline} + </style> +</head> +<!-- + The following styles are deprecated and will be removed at some point: + div#man, div#man ol.man, div#man ol.head, div#man ol.man. + + The .man-page, .man-decor, .man-head, .man-foot, .man-title, and + .man-navigation should be used instead. +--> +<body id='manpage'> + <div class='mp' id='man'> + + <div class='man-navigation' style='display:none'> + <a href="#NAME">NAME</a> + <a href="#SYNOPSIS">SYNOPSIS</a> + <a href="#DESCRIPTION">DESCRIPTION</a> + <a href="#PARAMETERS">PARAMETERS</a> + <a href="#OUTPUT">OUTPUT</a> + <a href="#MOTIF-NUMBERS">MOTIF NUMBERS</a> + <a href="#EXAMPLES">EXAMPLES</a> + <a href="#SEE-ALSO">SEE ALSO</a> + <a href="#REFERENCES">REFERENCES</a> + <a href="#AUTHORS">AUTHORS</a> + </div> + + <ol class='man-decor man-head man head'> + <li class='tl'>f3m(1)</li> + <li class='tc'>www.complex-networks.net</li> + <li class='tr'>f3m(1)</li> + </ol> + + <h2 id="NAME">NAME</h2> +<p class="man-name"> + <code>f3m</code> - <span class="man-whatis">Count all the 3-node subgraphs of a directed graph</span> +</p> + +<h2 id="SYNOPSIS">SYNOPSIS</h2> + +<p><code>f3m</code> <var>graph_in</var> [<var>num_random</var>]</p> + +<h2 id="DESCRIPTION">DESCRIPTION</h2> + +<p><code>f3m</code> performs a motif analysis on <var>graph_in</var>, i.e., it counts all the +3-node subgraphs and computes the z-score of that count with respect +to the corresponding configuration model ensemble.</p> + +<h2 id="PARAMETERS">PARAMETERS</h2> + +<dl> +<dt><var>graph_in</var></dt><dd><p> input graph (edge list). It must be an existing file.</p></dd> +<dt><var>num_random</var></dt><dd><p> The number of random graphs to sample from the configuration model + for the computation of the z-score of the motifs.</p></dd> +</dl> + + +<h2 id="OUTPUT">OUTPUT</h2> + +<p><code>f3m</code> prints on the standard output a table with 13 rows, one for each +of the 13 possible 3-node motifs. Each line is in the format:</p> + +<pre><code> motif_number count mean_rnd std_rnd z-score +</code></pre> + +<p>where <code>motif_number</code> is a number between 1 and 13 that identifies the +motif (see <a href="#MOTIF-NUMBERS" title="MOTIF NUMBERS" data-bare-link="true">MOTIF NUMBERS</a> below), <code>count</code> is the number of +subgraphs ot type <code>motif_number</code> found in <var>graph_in</var>, <code>mean_rnd</code> is +the average number of subgraphs of type <code>motif_number</code> in the +corresponding configuration model ensemble, and <code>std_rnd</code> is the +associated standard deviation. Finally, <code>z-score</code> is the quantity:</p> + +<pre><code> (count - mean_rnd) / std_rnd +</code></pre> + +<p>The program also prints a progress bar on STDERR.</p> + +<h2 id="MOTIF-NUMBERS">MOTIF NUMBERS</h2> + +<p>We report below the correspondence between the 13 possible 3-node +subgraphs and the corresponding <code>motif_number</code>. In the diagrams, +'O--->O' indicates a single edge form the left node to the right node, +while 'O<var>==</var>O' indicates a double (bi-directional) edge between the +two nodes:</p> + +<pre><code> (1) O<---O--->O + + (2) O--->O--->O + + (3) O<==>O--->O + + (4) O--->O<---O + + (5) O--->O--->O + \ ^ + \_______| + + (6) O<==>O--->O + \ ^ + \_______| + + (7) O<==>O<---O + + (8) O<==>O<==>O + + (9) O<---O<---O + \ ^ + \_______| + + (10) O<==>O<---O + \ ^ + \_______| + + (11) O--->O<==>O + \ ^ + \_______| + + (12) O<==>O<==>O + \ ^ + \_______| + + (13) O<==>O<==>O + ^\ ^/ + \\_____// + \_____/ +</code></pre> + +<h2 id="EXAMPLES">EXAMPLES</h2> + +<p>To perform a motif analysis on the E.coli transcription regulation +graph, using 1000 randomised networks, we run the command:</p> + +<pre><code> $ f3m e_coli.net 1000 + 1 4760 4400.11 137.679 +2.614 + 2 162 188.78 8.022 -3.338 + 3 0 0.89 3.903 -0.228 + 4 226 238.32 7.657 -1.609 + 5 40 6.54 2.836 +11.800 + 6 0 0.01 0.077 -0.078 + 7 0 0.12 0.642 -0.192 + 8 0 0.00 0.032 -0.032 + 9 0 0.01 0.109 -0.110 + 10 0 0.00 0.000 +0.000 + 11 0 0.00 0.032 -0.032 + 12 0 0.00 0.000 +0.000 + 13 0 0.00 0.000 +0.000 + $ +</code></pre> + +<p>Notice that the motif <code>5</code> (the so-called "feed-forward loop") has a +z-score equal to 11.8, meaning that it is highly overrepresented in +the E.coli graph with respect to the corresponding configuration model +ensemble. Conversely, the motif <code>2</code> (three-node chain) is +underrepresented, as made evident by value of the z-score (-3.338).</p> + +<h2 id="SEE-ALSO">SEE ALSO</h2> + +<p><a class="man-ref" href="johnson_cycles.1.html">johnson_cycles<span class="s">(1)</span></a></p> + +<h2 id="REFERENCES">REFERENCES</h2> + +<ul> +<li><p>R. Milo et al. "Network Motifs: Simple Building Blocks of Complex +Networks". Science 298 (2002), 824-827.</p></li> +<li><p>R. Milo et al. "Superfamilies of evolved and designed networks." +Science 303 (2004), 1538-1542</p></li> +<li><p>V. Latora, V. Nicosia, G. Russo, "Complex Networks: Principles, +Methods and Applications", Chapter 8, Cambridge University Press +(2017)</p></li> +<li><p>V. Latora, V. Nicosia, G. Russo, "Complex Networks: Principles, +Methods and Applications", Appendix 16, Cambridge University Press +(2017)</p></li> +</ul> + + +<h2 id="AUTHORS">AUTHORS</h2> + +<p>(c) Vincenzo 'KatolaZ' Nicosia 2009-2017 <code><v.nicosia@qmul.ac.uk></code>.</p> + + + <ol class='man-decor man-foot man foot'> + <li class='tl'>www.complex-networks.net</li> + <li class='tc'>September 2017</li> + <li class='tr'>f3m(1)</li> + </ol> + + </div> +</body> +</html> |