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    <p>Okay, so I figured it out myself and I'll leave the details here to help anyone with the same questions.</p> <p><strong>Single color graph with labels on the nodes:</strong></p> <p>This will generate a graph much like the one on the question, with lines connecting circles with labels inside.</p> <p><img src="https://i.stack.imgur.com/m1BYy.png" alt="Single color graph with labels on the nodes"></p> <pre><code>plot 'edges.dat' u 1:2 with lines lc rgb "black" lw 2 notitle,\ 'edges.dat' u 1:2:(0.6) with circles fill solid lc rgb "black" notitle,\ 'edges.dat' using 1:2:($0) with labels tc rgb "white" offset (0,0) font 'Arial Bold' notitle </code></pre> <p>With little changes it can exaclty match the one on the question picture.</p> <p><img src="https://i.stack.imgur.com/ra5lh.png" alt="enter image description here"></p> <pre><code>plot 'edges.dat' u 1:2 with lines lc rgb "black" lw 2 notitle,\ 'edges.dat' u 1:2:(0.8) with circles linecolor rgb "white" lw 2 fill solid border lc lt 0 notitle, \ 'edges.dat' using 1:2:($0) with labels offset (0,0) font 'Arial Bold' notitle </code></pre> <hr> <p><strong>Cluster-colored graph:</strong></p> <p><img src="https://i.stack.imgur.com/Vy4Iz.png" alt="Cluster-colored graph"></p> <pre><code>unset colorbox set palette model RGB defined ( 0 0 0 0 , 1 1 0 0 , 2 1 0.9 0, 3 0 1 0, 4 0 1 1 , 5 0 0 1 , 6 1 0 1 ) plot 'edges.dat' u 1:2:3 with lines lc palette notitle,\ 'edges.dat' u 1:2:(0.15):3 with circles fill solid palette notitle </code></pre> <hr> <p>The data used on all plots follow this structure:</p> <pre><code>21.53 9.55 0 24.26 7.92 0 5.63 3.23 1 2.65 1.77 1 5.63 3.23 0 4.27 7.04 0 (...) </code></pre>
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