Network Visualization in R

# Network Visualization in R
## using ggraph and graphlayouts
### David Schoch
### University of Manchester

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# about me

<br>

- Research on social media and social networks

- R developer since 2012

- Self taught in data/network visualization

- I blog about R dev (blog.schochastics.net)

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# about today

- No introduction to R 😞

- No introduction to network analysis 😞

- Just drawing pretty pictures 😀

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---
# ordinary data 
.left-code[
<table>
 <thead>
  <tr>
   <th style="text-align:left;">   </th>
   <th style="text-align:right;"> mpg </th>
   <th style="text-align:right;"> cyl </th>
   <th style="text-align:right;"> disp </th>
   <th style="text-align:right;"> hp </th>
   <th style="text-align:right;"> drat </th>
   <th style="text-align:right;"> wt </th>
   <th style="text-align:right;"> qsec </th>
   <th style="text-align:right;"> vs </th>
   <th style="text-align:right;"> am </th>
   <th style="text-align:right;"> gear </th>
   <th style="text-align:right;"> carb </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Mazda RX4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.0 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.620 </td>
   <td style="text-align:right;"> 16.46 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Mazda RX4 Wag </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.0 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.875 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Datsun 710 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 22.8 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 108 </td>
   <td style="text-align:right;"> 93 </td>
   <td style="text-align:right;"> 3.85 </td>
   <td style="text-align:right;"> 2.320 </td>
   <td style="text-align:right;"> 18.61 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet 4 Drive </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.4 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 258 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.08 </td>
   <td style="text-align:right;"> 3.215 </td>
   <td style="text-align:right;"> 19.44 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet Sportabout </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 18.7 </td>
   <td style="text-align:right;"> 8 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 360 </td>
   <td style="text-align:right;"> 175 </td>
   <td style="text-align:right;"> 3.15 </td>
   <td style="text-align:right;"> 3.440 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 2 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Valiant </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 18.1 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 225 </td>
   <td style="text-align:right;"> 105 </td>
   <td style="text-align:right;"> 2.76 </td>
   <td style="text-align:right;"> 3.460 </td>
   <td style="text-align:right;"> 20.22 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
</tbody>
</table>
]

# ordinary data 
.left-code[
<table>
 <thead>
  <tr>
   <th style="text-align:left;">   </th>
   <th style="text-align:right;"> mpg </th>
   <th style="text-align:right;"> cyl </th>
   <th style="text-align:right;"> disp </th>
   <th style="text-align:right;"> hp </th>
   <th style="text-align:right;"> drat </th>
   <th style="text-align:right;"> wt </th>
   <th style="text-align:right;"> qsec </th>
   <th style="text-align:right;"> vs </th>
   <th style="text-align:right;"> am </th>
   <th style="text-align:right;"> gear </th>
   <th style="text-align:right;"> carb </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Mazda RX4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.0 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.620 </td>
   <td style="text-align:right;"> 16.46 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Mazda RX4 Wag </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.0 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.875 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Datsun 710 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 22.8 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 108 </td>
   <td style="text-align:right;"> 93 </td>
   <td style="text-align:right;"> 3.85 </td>
   <td style="text-align:right;"> 2.320 </td>
   <td style="text-align:right;"> 18.61 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet 4 Drive </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 258 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.08 </td>
   <td style="text-align:right;"> 3.215 </td>
   <td style="text-align:right;"> 19.44 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet Sportabout </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 18.7 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 8 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 360 </td>
   <td style="text-align:right;"> 175 </td>
   <td style="text-align:right;"> 3.15 </td>
   <td style="text-align:right;"> 3.440 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 2 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Valiant </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 18.1 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 225 </td>
   <td style="text-align:right;"> 105 </td>
   <td style="text-align:right;"> 2.76 </td>
   <td style="text-align:right;"> 3.460 </td>
   <td style="text-align:right;"> 20.22 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
</tbody>
</table>
]

---

# ordinary data 
.left-code[
<table>
 <thead>
  <tr>
   <th style="text-align:left;">   </th>
   <th style="text-align:right;"> mpg </th>
   <th style="text-align:right;"> cyl </th>
   <th style="text-align:right;"> disp </th>
   <th style="text-align:right;"> hp </th>
   <th style="text-align:right;"> drat </th>
   <th style="text-align:right;"> wt </th>
   <th style="text-align:right;"> qsec </th>
   <th style="text-align:right;"> vs </th>
   <th style="text-align:right;"> am </th>
   <th style="text-align:right;"> gear </th>
   <th style="text-align:right;"> carb </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Mazda RX4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.0 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 160 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.620 </td>
   <td style="text-align:right;"> 16.46 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Mazda RX4 Wag </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.0 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 160 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.875 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Datsun 710 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 22.8 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 108 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 93 </td>
   <td style="text-align:right;"> 3.85 </td>
   <td style="text-align:right;"> 2.320 </td>
   <td style="text-align:right;"> 18.61 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet 4 Drive </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 21.4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 258 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 110 </td>
   <td style="text-align:right;"> 3.08 </td>
   <td style="text-align:right;"> 3.215 </td>
   <td style="text-align:right;"> 19.44 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet Sportabout </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 18.7 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 8 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 360 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 175 </td>
   <td style="text-align:right;"> 3.15 </td>
   <td style="text-align:right;"> 3.440 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 2 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Valiant </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 18.1 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 225 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 105 </td>
   <td style="text-align:right;"> 2.76 </td>
   <td style="text-align:right;"> 3.460 </td>
   <td style="text-align:right;"> 20.22 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
</tbody>
</table>
]

---

# ordinary data 
.left-code[
<table>
 <thead>
  <tr>
   <th style="text-align:left;">   </th>
   <th style="text-align:right;"> mpg </th>
   <th style="text-align:right;"> cyl </th>
   <th style="text-align:right;"> disp </th>
   <th style="text-align:right;"> hp </th>
   <th style="text-align:right;"> drat </th>
   <th style="text-align:right;"> wt </th>
   <th style="text-align:right;"> qsec </th>
   <th style="text-align:right;"> vs </th>
   <th style="text-align:right;"> am </th>
   <th style="text-align:right;"> gear </th>
   <th style="text-align:right;"> carb </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Mazda RX4 </td>
   <td style="text-align:right;"> 21.0 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 3.90 </td>
   <td style="text-align:right;"> 2.620 </td>
   <td style="text-align:right;"> 16.46 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Mazda RX4 Wag </td>
   <td style="text-align:right;"> 21.0 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 3.90 </td>
   <td style="text-align:right;"> 2.875 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Datsun 710 </td>
   <td style="text-align:right;"> 22.8 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 4 </td>
   <td style="text-align:right;"> 108 </td>
   <td style="text-align:right;"> 93 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 3.85 </td>
   <td style="text-align:right;"> 2.320 </td>
   <td style="text-align:right;"> 18.61 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet 4 Drive </td>
   <td style="text-align:right;"> 21.4 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;"> 258 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 3.08 </td>
   <td style="text-align:right;"> 3.215 </td>
   <td style="text-align:right;"> 19.44 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet Sportabout </td>
   <td style="text-align:right;"> 18.7 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 8 </td>
   <td style="text-align:right;"> 360 </td>
   <td style="text-align:right;"> 175 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 3.15 </td>
   <td style="text-align:right;"> 3.440 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 2 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Valiant </td>
   <td style="text-align:right;"> 18.1 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6 </td>
   <td style="text-align:right;"> 225 </td>
   <td style="text-align:right;"> 105 </td>
   <td style="text-align:right;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 2.76 </td>
   <td style="text-align:right;"> 3.460 </td>
   <td style="text-align:right;"> 20.22 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
</tbody>
</table>
]

---

# why visualizing networks is hard(er)

**ordinary data**

- clear file format (spreadsheet, csv)
- clear data format (rows: observations, columns: variables)
- plot style dependent on variable scale (barchart, scatterplot,boxplot,...) 
- illustrate relations between variables
- given relative positions

**network data**

- many different file formats (csv,graphml,dot,dl,gexf,net,gdf,gml,nnf,sif,xgmml)
- different data formats (adjacency matrix,edgelist,adjaceny list,incidence matrix)
- how to choose a proper layout algorithm?
- more degrees of freedom
- can we draw any conclusions from a network plot?

---

# network visualization software

## gephi
works quite well for visualizing large networks

## visone
well designed GUI and algorithms (`graphlayouts` implements most algorithms from it)

## and many more

cytoscape, NodeXL, Graphviz, python, ...

---
layout: false
class: normal-bg

.center[
<img src="http://social-dynamics.org/wp-content/uploads/2011/11/gephi.png" height="700px">
]

---

.center[
<img src="https://visone.ethz.ch/wiki/images/thumb/5/55/Caltech36-Quadrilateral-Backbone.png/770px-Caltech36-Quadrilateral-Backbone.png" height="600px">
]

---

---

# network visualization in R

**why R?**  
open source, cross-platform, CRAN, more than SNA, community (#rstats/RLadies)

**different file/data formats**  
R can handle many file formats, RStudio addin `Netreader`

**how to choose a proper layout algorithm?**  
`graphlayouts` &rArr; layout_with_stress(), layout_as_backbone(), ...

**more degrees of freedom**  
manage degrees of freedom via grammar of graphics (see `ggplot2`)

**more complex?**  
RStudio addin `SNAhelper` (no coding needed!)

---

# which packages to choose?

<br>

- `igraph`: great for analyses, but plotting can be tricky  
  (check out https://kateto.net/network-visualization)
  
- `visNetwork`: interactive network visualizations using the vis.js

- `threejs`: interactive (3D) network visualizations using three.js

- `ggnet2`: plot network objects as `ggplot2` objects

- .highlight[`ggraph`:  an implementation of grammar of graphics for networks]

---

# grammar of graphics

---

# network data: the graph?

# network data: data frames!
<div style="position:absolute;left:10%;top:25%">
<table class="table" style="width: auto !important; margin-left: auto; margin-right: auto;">
<caption>Nodes</caption>
 <thead>
  <tr>
   <th style="text-align:left;"> name </th>
   <th style="text-align:left;"> sex </th>
   <th style="text-align:left;"> homeworld </th>
   <th style="text-align:left;"> species </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> R2-D2 </td>
   <td style="text-align:left;"> none </td>
   <td style="text-align:left;"> Naboo </td>
   <td style="text-align:left;"> Droid </td>
  </tr>
  <tr>
   <td style="text-align:left;"> NUTE GUNRAY </td>
   <td style="text-align:left;"> male </td>
   <td style="text-align:left;"> Cato Neimoidia </td>
   <td style="text-align:left;"> Neimodian </td>
  </tr>
  <tr>
   <td style="text-align:left;"> OBI-WAN </td>
   <td style="text-align:left;"> male </td>
   <td style="text-align:left;"> Stewjon </td>
   <td style="text-align:left;"> Human </td>
  </tr>
  <tr>
   <td style="text-align:left;"> EMPEROR </td>
   <td style="text-align:left;"> male </td>
   <td style="text-align:left;"> Naboo </td>
   <td style="text-align:left;"> Human </td>
  </tr>
  <tr>
   <td style="text-align:left;"> JAR JAR </td>
   <td style="text-align:left;"> male </td>
   <td style="text-align:left;"> Naboo </td>
   <td style="text-align:left;"> Gungan </td>
  </tr>
  <tr>
   <td style="text-align:left;"> TARPALS </td>
   <td style="text-align:left;"> male </td>
   <td style="text-align:left;"> Naboo </td>
   <td style="text-align:left;"> Gungan </td>
  </tr>
</tbody>
</table>
</div>

<div style="position:absolute;right:10%;top:25%">
<table class="table" style="width: auto !important; margin-left: auto; margin-right: auto;">
<caption>Edges</caption>
 <thead>
  <tr>
   <th style="text-align:left;"> from </th>
   <th style="text-align:left;"> to </th>
   <th style="text-align:right;"> weight </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> KI-ADI-MUNDI </td>
   <td style="text-align:left;"> YODA </td>
   <td style="text-align:right;"> 3 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> QUI-GON </td>
   <td style="text-align:left;"> JAR JAR </td>
   <td style="text-align:right;"> 22 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> TC-14 </td>
   <td style="text-align:left;"> OBI-WAN </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> ANAKIN </td>
   <td style="text-align:left;"> BRAVO TWO </td>
   <td style="text-align:right;"> 2 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> SIO BIBBLE </td>
   <td style="text-align:left;"> JAR JAR </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> ANAKIN </td>
   <td style="text-align:left;"> C-3PO </td>
   <td style="text-align:right;"> 3 </td>
  </tr>
</tbody>
</table>
</div>

<span style="position:absolute;bottom:10%;left:5%;font-size:40px;font-weight:700">+layout </span>
<span style="position:absolute;bottom:5%;right:5%;">see `tidygraph` </span>

---

# first full example (don't panic!)

```r
ggraph(graph = g,layout = "stress") + 
  geom_edge_link0(edge_colour = "grey25",
                  aes(edge_width = weight)) +
  geom_node_point(shape = 21, color = "black",stroke = 1,
                  aes(fill = sex,size = interactions)) +
  geom_node_text(color = "grey25", fontface = "bold", size = 6, repel = TRUE, 
                 aes(filter = (interactions>=65),label = name))+
  scale_edge_width(range = c(0.1,1.5),guide = "none")+
  scale_size(range = c(3,10),guide = "none")+
  scale_fill_manual(values = sw_palette, na.value = "grey",name = "")+
  theme_graph() +
  theme(legend.position = "bottom") +
  guides(fill = guide_legend(override.aes = list(size=6)))
```

---

---

---

# 1) layout

<span class="alert">`ggraph(graph = g,layout = "stress")`</span>

- graph: `igraph` object g (can also be a `tidygraph` object)

- layout: used algorithm (from `igraph` or .highlight[`graphlayouts`])

![](slides_files/figure-html/lay_algos-1.png)

see also https://www.data-imaginist.com/2017/ggraph-introduction-layouts/
---

# 2) edges

**edge geoms**  
there are many (see `geom_edge_*`) but  
`geom_edge_link0()` and `geom_edge_parallel0()` suffice

**mapping .underline[aes]thetics**  
.alert[global]: all edges have the same appearance (e.g. `edge_colour="grey25"`)  
.alert[via attributes]: appearance depends on attribute (e.g. `aes(edge_width = weight)`)

**available aesthetics**  
edge_colour, edge_width, edge_linetype, edge_alpha

---

# 3) nodes

.alert[`geom_node_point(shape = 21, color = "black",stroke = 1,`]  
<span style="margin-left: 7.5em;">.alert[`aes(fill = sex,size = interactions))`]</span>

**node geoms**  
there are some (see `geom_node_*`) but `geom_node_point()` suffices

**mapping .underline[aes]thetics**  
.alert[global]: all nodes have the same appearance (e.g. `shape = 21`)  
.alert[via attributes]: appearance depends on attribute (e.g. `aes(fill = sex)`)

**available aesthetics**  
alpha, colour, fill, shape, size, stroke  
(usage of colour and fill depend on shape)

---

# 4) labels

.alert[`geom_node_text(color = "grey25", fontface = "bold", size = 6, repel = TRUE, `]
<span style="margin-left: 7em;">.alert[`aes(filter = (interactions>=65),label = name))`]</span>

**mapping .underline[aes]thetics**  
.alert[global]: specify font properties  
.alert[via attributes]: set label to name attribute of node  
.alert[filter]: only display for nodes (or edges!) that fulfil a given criterion

**available aesthetics**  
many! but most important: label, colour, family, size, and repel

---

# 5) scales

.alert[`scale_edge_width(range = c(0.1,1.5),guide = "none")`]  
.alert[`scale_size(range = c(3,10),guide = "none")`]  
.alert[`scale_fill_manual(values = sw_palette, na.value = "grey",name = "")`]

control aesthetics that are mapped within `aes()`

**rule of thumb**  
although optional, set one `scale_*` per parameter in any `aes()`

**form of scale functions**  
`scale_<aes>_<variable type>()`

**additional options**  
`guide` (show in legend or not), `name` (label in legend), `na.value` (value for NA values)

---

# 5) scales

**node size and edge width (and node/edge alpha)**  
`scale_size()` and `scale_edge_width()` (`*_continuous` not needed)  
many parameters, but the most relevant is `range=c(min,max)`

**continuous variable to colour**  
e.g. `scale_(edge_)colour_gradient(low = ...,high = ...)`

**categorical variable to colour**  
e.g. `scale_colour_brewer()`, `scale_colour_manual(values = ...)`

**colour or fill?**  
node shapes 21-25 have both colour (border) and fill  
all others only have colour

<img src="http://www.sthda.com/sthda/RDoc/images/points-symbols.png" 
    style="position:absolute;bottom:5%;right:2%;background:white" height="330">
    
**misc**: `scale_shape()` and `scale_edge_linetype()`
---

# 6) themes

control the overall look of the plot  
`theme()` has a lot of options but we really don't need them  
`theme_graph()` erases all defaults (e.g. axis, grids, etc.)  
only worthwile option is `legend.position`

<br>

change appearance of geoms in legend (highly optional!)
---

# summary

**layout**  
`ggraph(graph,layout = "stress") + `

**edges**  
`geom_edge_link0(<<global>>,aes(<<via variables>>)) + `

**nodes**  
`geom_node_point(<global>,aes(<via variables>)) + `  
`geom_node_text(<global>,aes(<via variables>)) + `

**scales**  
`scale_<aes>_<variable type>() + ` (one per variable in `aes()`)

**themes**  
`theme_graph() + theme(legend.position = <position>)`

---

# first full example (revisited)

```r
ggraph(graph = g,layout = "stress") + 
  geom_edge_link0(edge_colour = "grey25", 
                  aes(edge_width = weight)) + 
  geom_node_point(shape = 21, color = "black",stroke = 1,
                  aes(fill = sex,size = interactions)) +
  geom_node_text(color = "grey25", fontface = "bold", size = 6, repel = TRUE, 
                 aes(filter = (interactions>=65),label = name))+
  scale_edge_width(range = c(0.1,1.5),guide = "none")+
  scale_size(range = c(3,10),guide = "none")+
  scale_fill_manual(values = sw_palette, na.value = "grey",name = "")+
  theme_graph() +
  theme(legend.position = "bottom") +
  guides(fill = guide_legend(override.aes = list(size=6)))
```

---
# beyond standard plots: layout = "focus"

Concentric circles help to emphasize the position of certain nodes in the network.

```r
ggraph(g,layout = "focus",focus = 19)+
  draw_circle(col = "#00BFFF", use = "focus",max.circle = 3)+
  geom_edge_link0(edge_colour = "grey25",edge_alpha = 0.5)+
  geom_node_point(shape = 21,size = 5,fill = "grey66")+
  geom_node_text(aes(filter = (name=="ANAKIN"),label = name))+
  theme_graph()+
  coord_fixed()
```

`focus=...` : id to be put in the center (other nodes are on concentric circles around it)  
`draw_circle`: draw the concentric circles  
`coord_fxed()`: make sure that circles are plot as circles and not ellipses

---
layout: false
class: normal-bg

---
layout: true
class: paint-bg

---

# beyond standard plots: layout = "centrality"

```r
ggraph(g,layout = "centrality",cent = graph.strength(g))+
  draw_circle(col = "#00BFFF", use = "cent")+
  geom_edge_link0(edge_colour = "grey25",edge_alpha = 0.5)+
  geom_node_point(shape = 21,size = 5,fill = "grey66")+
  geom_node_text(aes(filter = (name=="QUI-GON"),label = name))+
  theme_graph()+
  coord_fixed()
```

`cent = graph.strength(g)`: concentric layout according to weighted degree

---

---

# beyond standard plots: the backbone layout

`layout_as_backbone()` is an algorithm that can help emphasize hidden group structures.

```r
g <- sample_islands(9,40,0.4,15)
g <- simplify(g)
V(g)$grp <- as.character(rep(1:9,each = 40))
```

try the standard first

```r
ggraph(g,layout = "stress")+
  geom_edge_link0(edge_colour = "black",edge_width = 0.1, edge_alpha = 0.5)+
  geom_node_point(shape = 21, size = 3, aes(fill = grp))+
  scale_fill_brewer(palette = "Set1")+
  theme_graph()+
  theme(legend.position = "none")
```
---

---

---

# beyond standard plots: backbone

try to reveal the hidden group structure with `layout="backbone"`

```r
ggraph(g,"backbone")+
  geom_edge_link0(aes(edge_color=backbone),edge_width = 0.3)+
  geom_node_point(shape = 21,size = 3, aes(fill = grp))+
  scale_fill_brewer(palette = "Set1")+
  scale_edge_color_manual(values=c(rgb(0,0,0,0.3),rgb(0,0,0,1)))+
  theme_graph()+
  theme(legend.position = "none")
```

---

---

---

---

# beyond standard plots: large networks

`layout = "sparse_stress"` and `layout = "pmds"` work well for up to 50k nodes

<table>
 <thead>
  <tr>
   <th style="text-align:left;"> graph </th>
   <th style="text-align:left;"> stress </th>
   <th style="text-align:left;"> sparsestress(50) </th>
   <th style="text-align:left;"> sparsestress(100) </th>
   <th style="text-align:left;"> drl(igraph) </th>
   <th style="text-align:left;"> mds(igraph) </th>
   <th style="text-align:left;"> pivotmds(50) </th>
   <th style="text-align:left;"> pivotmds(100) </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> 1138bus (n=1138, m=1458) </td>
   <td style="text-align:left;"> 2.6s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 0.4s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 0.7s </td>
   <td style="text-align:left;"> 1.7s </td>
   <td style="text-align:left;"> 1.4s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 0.05s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 0.08s </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 3elt (n=4720, m=13722) </td>
   <td style="text-align:left;"> 113s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 3.4s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 5.2s </td>
   <td style="text-align:left;"> 8.4s </td>
   <td style="text-align:left;"> 95s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 1s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 1.1s </td>
  </tr>
  <tr>
   <td style="text-align:left;"> power grid (n=4941, m=6594) </td>
   <td style="text-align:left;"> 134s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 3.4s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 5.6s </td>
   <td style="text-align:left;"> 6.9s </td>
   <td style="text-align:left;"> 114s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 1s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 1.1s </td>
  </tr>
  <tr>
   <td style="text-align:left;"> pesa (n=11738 m=67828) </td>
   <td style="text-align:left;"> - </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 18.3s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 26.5s </td>
   <td style="text-align:left;"> 21s </td>
   <td style="text-align:left;"> - </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6.3s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 6.8s </td>
  </tr>
  <tr>
   <td style="text-align:left;"> cond-mat(n=13861 m=44619) </td>
   <td style="text-align:left;"> - </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 22.9s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 33.5s </td>
   <td style="text-align:left;"> 24.8s </td>
   <td style="text-align:left;"> - </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 8.0s </td>
   <td style="text-align:left;font-weight: bold;color: black !important;background-color: #ffc93c !important;"> 8.7s </td>
  </tr>
</tbody>
</table>

---

# layout summary

<br>

**most useful layouts**  
`layout = "stress"`: all purpose layout algorithm  
`layout = "focus"`: ego-centric type layouts  
`layout = "centrality"`: concentric centrality layout  
`layout = "backbone"`: emphasize a hidden group structure (**if it exists!!!**)  
`layout = "sparse_stress"`: large networks

<br>

**not covered here**  
multilevel layout algorithm (see [my blog](http://blog.schochastics.net/post/visualizing-multilevel-networks-with-graphlayouts/))  
dynamic layout algorithm (see [github](https://github.com/schochastics/graphlayouts#dynamic-layouts))  
constrained stress layout algorithm

---

# beyond standard plots: flow maps & edgebundling

R package `edgebundle` (github.com/schochastics/edgebundle)

<img src="slides_files/figure-html/edgebundle-1.png" style="display: block; margin: auto;" />
---

.center[
<img src = "https://github.com/schochastics/edgebundle/raw/main/man/figures/flights_fdeb.png" height="700px">
]

---

.center[
<img src = "https://github.com/schochastics/edgebundle/raw/main/man/figures/flights_heb.png" height="700px">
]

---

.center[
<img src = "https://github.com/schochastics/edgebundle/raw/main/man/figures/flights_seb.png" height="700px">
]

---

.center[
  <img src = "https://github.com/schochastics/edgebundle/raw/main/man/figures/cali2010_flow.png"  height="700px">
]
---

.center[
 <img src="http://minard.schochastics.net/img/038/viz.png" width="1200px" style="position:absolute;left:0%;top:10%">
]

---

---

---

# additional material

**slides**  
http://talks.schochastics.net/netVizR/slides.html

**tutorial**  
http://mr.schochastics.net/netVizR.html http://graphlayouts.schochastics.net/

**tips and tricks**  
http://blog.schochastics.net/post/ggraph-tricks-for-common-problems/

**multilayer layouts**  
http://blog.schochastics.net/post/visualizing-multilevel-networks-with-graphlayouts/

**edgebundling**  
http://blog.schochastics.net/post/non-hierarchical-edge-bundling-in-r/