Chapter 2. Basic Graph Manipulations

In this chapter, we will cover the following recipes:

Generating a random graph
Selecting and highlighting nodes in the graph
Coloring and sizing nodes in the graph
Adding nodes and edges to the graph
Editing node attributes in the graph
Finding out the shortest path in the graph
Setting the edge and label properties
Setting basic properties for graphs, nodes, edges, and labels
Changing the background color of the graph
Generating a heat map for the graph
Showing convex hulls for a graph where a hierarchy exists
Showing/hiding various parts of the graph
Reverting changes in the graph to the original presets
Creating a PNG file directly from the graph window in user-specified sizes

Introduction

This chapter teaches you how to perform basic graph manipulations in Gephi. Manipulations such as modifying network structure by adding or deleting nodes and edges, editing node attributes, and applying filters on the network can be very easily done in Gephi, owing to its user-friendly interface.

Generating a random graph

A random graph with n nodes is a graph generated by starting with n nodes with no edges existing between any pair of nodes, and then randomly adding edges between nodes in a probabilistic fashion. This recipe describes the process of generating one such random graph in Gephi.

How to do it…

The steps to generate a random graph with n nodes are as follows:

Click on File in the menu bar.
Choose Generate in the drop-down menu.
Choose Random Graph in the extended menu. You'll see the following pop-up window on the screen:
In the Number of nodes textbox, enter the number of nodes (n) that you want the random graph to have.
In the Wiring probability textbox, enter the probability (p), according to where you would like the edges to be added between different pairs of nodes in the random graph. A low wiring probability will result in a regular lattice. On the other hand, the higher the wiring probability is, the more random the resulting graph will be.
Click on OK....

Selecting and highlighting nodes in the graph

In this recipe, you will learn how to selectively pick up specific nodes in the graph and how to highlight them for closer study.

How to do it…

There are two different ways in which nodes can be selected in Gephi: direct selection and rectangle selection. Here's how we go about selecting the nodes in Gephi:

To directly select a node and view its neighbors/adjacent nodes, click on the little arrow button towards the upper-left corner of the Graph panel, as shown in the following screenshot:
Navigate to the node that you want to highlight and place the arrow on the node. You will notice that the node on which you have placed the arrow, along with the neighboring nodes and the edges connecting them, has become highlighted while the other nodes are dimmed. This is shown in the following screenshot:
To select a node using rectangle selection, click on the button with the little rectangle depicted on it towards the upper-left corner of the...

Coloring and sizing nodes in the graph

Sometimes, while studying the properties of a network, we need to manually alter some of the attributes of the nodes, such as their color and size. This section explains how to achieve this.

How to do it…

The following steps illustrate how to resize individual nodes in the graph:

Click on the diamond-shaped button in the toolbar placed on the left-hand side of the Graph panel. The mouse pointer, when placed over it, should show a descriptor textbox that reads Sizer.
Click on the node that you want to resize and while holding the mouse button, drag the mouse vertically upwards or downwards. Dragging the mouse upwards will increase the size of the node and dragging it downwards will decrease the size.
If the resized node now hides a part of the graph that you otherwise want to continue looking at, click on the button in the same toolbar with a hand symbol on it. Placing the mouse pointer on this button should show up a descriptor textbox that reads...

Adding nodes and edges to the graph

Gephi allows its users to alter graphs on-the-fly by offering capabilities such as adding node(s) or edge(s) to the graph in just one click. This recipe discusses how to carry out these actions.

How to do it…

The following steps illustrate the procedure to add a new node to the graph:

Click on the pencil-shaped button in the toolbar, placed vertically on the upper-left side of the edge of the Graph panel. When a mouse pointer is placed on the icon, it should show a descriptor textbox that reads Node Pencil.
In the upper-right corner of the Graph panel, choose the color that you would like to assign to the node and set the desired size for it.
Now, click on the area of the Graph panel where you want to place the new node. This will create a new node with the selected color and size, as shown in the following screenshot:

Follow these steps to add a new edge to the graph:

Click on the pencil-shaped button in the toolbar that is placed vertically on the upper...

Editing node attributes in the graph

There might be cases where one would like to change some attributes for specific nodes manually. Gephi offers a very easy way to do so. In this recipe, we will discuss how, with just a single click, you can alter node attributes such as size, position, color, label, and so on.

How to do it…

The following steps illustrate the way to change node attributes such as size, position, color, label, and so on.

Click on the button with an arrow and a question mark on it that is placed last on the toolbar located vertically on the upper-left edge of the Graph panel. When a mouse pointer is placed over this button, it should read Edit-Edit node attributes.
Now click on the node whose attributes you want to alter.
This opens a new panel titled Edit on the upper-left corner of the screen.
Click on the attribute(s) that you want to modify and assign new value(s).

There's more…

You cannot modify attributes such as ID, since those are unique values.

Introduction

This chapter teaches you how to perform basic graph manipulations in Gephi. Manipulations such as modifying network structure by adding or deleting nodes and edges, editing node attributes, and applying filters on the network can be very easily done in Gephi, owing to its user-friendly interface.

Generating a random graph

A random graph with n nodes is a graph generated by starting with n nodes with no edges existing between any pair of nodes, and then randomly adding edges between nodes in a probabilistic fashion. This recipe describes the process of generating one such random graph in Gephi.

How to do it…

The steps to generate a random graph with n nodes are as follows:

Click on File in the menu bar.
Choose Generate in the drop-down menu.
Choose Random Graph in the extended menu. You'll see the following pop-up window on the screen:
In the Number of nodes textbox, enter the number of nodes (n) that you want the random graph to have.
In the Wiring probability textbox, enter the probability (p), according to where you would like the edges to be added between different pairs of nodes in the random graph. A low wiring probability will result in a regular lattice. On the other hand, the higher the wiring probability is, the more random the resulting graph will be.
Click on OK. This generates...

Selecting and highlighting nodes in the graph

In this recipe, you will learn how to selectively pick up specific nodes in the graph and how to highlight them for closer study.

How to do it…

There are two different ways in which nodes can be selected in Gephi: direct selection and rectangle selection. Here's how we go about selecting the nodes in Gephi:

To directly select a node and view its neighbors/adjacent nodes, click on the little arrow button towards the upper-left corner of the Graph panel, as shown in the following screenshot:
Navigate to the node that you want to highlight and place the arrow on the node. You will notice that the node on which you have placed the arrow, along with the neighboring nodes and the edges connecting them, has become highlighted while the other nodes are dimmed. This is shown in the following screenshot:
To select a node using rectangle selection, click on the button with the little rectangle depicted on it towards the upper-left corner of the Graph panel:
Place...

Coloring and sizing nodes in the graph

Sometimes, while studying the properties of a network, we need to manually alter some of the attributes of the nodes, such as their color and size. This section explains how to achieve this.

How to do it…

The following steps illustrate how to resize individual nodes in the graph:

Click on the diamond-shaped button in the toolbar placed on the left-hand side of the Graph panel. The mouse pointer, when placed over it, should show a descriptor textbox that reads Sizer.
Click on the node that you want to resize and while holding the mouse button, drag the mouse vertically upwards or downwards. Dragging the mouse upwards will increase the size of the node and dragging it downwards will decrease the size.
If the resized node now hides a part of the graph that you otherwise want to continue looking at, click on the button in the same toolbar with a hand symbol on it. Placing the mouse pointer on this button should show up a descriptor textbox that reads Drag.
Now...

Adding nodes and edges to the graph

Gephi allows its users to alter graphs on-the-fly by offering capabilities such as adding node(s) or edge(s) to the graph in just one click. This recipe discusses how to carry out these actions.

How to do it…

The following steps illustrate the procedure to add a new node to the graph:

Click on the pencil-shaped button in the toolbar, placed vertically on the upper-left side of the edge of the Graph panel. When a mouse pointer is placed on the icon, it should show a descriptor textbox that reads Node Pencil.
In the upper-right corner of the Graph panel, choose the color that you would like to assign to the node and set the desired size for it.
Now, click on the area of the Graph panel where you want to place the new node. This will create a new node with the selected color and size, as shown in the following screenshot:

Follow these steps to add a new edge to the graph:

Click on the pencil-shaped button in the toolbar that is placed vertically on the upper-left...

Editing node attributes in the graph

There might be cases where one would like to change some attributes for specific nodes manually. Gephi offers a very easy way to do so. In this recipe, we will discuss how, with just a single click, you can alter node attributes such as size, position, color, label, and so on.

How to do it…

The following steps illustrate the way to change node attributes such as size, position, color, label, and so on.

Click on the button with an arrow and a question mark on it that is placed last on the toolbar located vertically on the upper-left edge of the Graph panel. When a mouse pointer is placed over this button, it should read Edit-Edit node attributes.
Now click on the node whose attributes you want to alter.
This opens a new panel titled Edit on the upper-left corner of the screen.
Click on the attribute(s) that you want to modify and assign new value(s).

There's more…

You cannot modify attributes such as ID, since those are unique values.

Finding out the shortest path in the graph

Finding the shortest path in a graph is one of the problems that is widely encountered in many different situations across many different domains. This is one of the fundamental problems in graph theory. It has applications in domains such as computer networks, inventory optimization, flow networks, and so on. In this recipe, we will learn how to compute and visualize the shortest path in a graph in Gephi.

Getting ready

Load a pre-existing network in which you would like to find the shortest path, such as Les Misérables, or create one.

How to do it…

To compute and visualize the shortest path for a pair of nodes in a network, follow these steps:

Click on the button with an airplane symbol on it in the vertically placed left-hand side toolbar in the Graph panel. When placed over this button, the mouse pointer displays a descriptor textbox that reads Shortest Path.
Now click on the source node in the graph from where the path should start.
Select the target...

Setting the edge and label properties

Gephi offers functionality to set up edge and label properties such as edge weight, edge color, label weight, label color, and so on. These functionalities will be discussed in this recipe.

How to do it…

To set edge and label properties explicitly, follow these steps:

Load the Les Misérables graph in Gephi.
Click on the upward-pointing arrow located at the bottom-right corner of the Graph panel to expand a new panel.
In that panel, click on the Labels tab.
Check the checkbox located next to Nodes. This will display all the node labels.
The first button we will discuss defines how the edges will be colored. This is the button with a line segment and a mini-rainbow-like structure as its icon placed at the fourth position in the horizontal toolbar located towards the bottom of the Graph panel. Hovering the mouse pointer on top of it should show a descriptor textbox that reads Edges have source node color.
When toggled on, this will result in the edges taking the...

Setting basic properties for graphs, nodes, edges, and labels

Apart from what has been discussed so far in this chapter, Gephi also offers some additional options for configuring the basic properties of the graphs, nodes, edges, and labels. This section discusses these functionalities.

Getting ready

Load the Les Misérables graph in Gephi.

How to do it…

In the following steps, we will discuss various functionalities offered by Gephi to set the basic properties of graphs, nodes, edges, and labels.

Click on the upward-pointing arrow located in the bottom-right corner of the Graph panel to expand a new toolbar with four tabs: Global, Nodes, Edges, and Labels.
Click on the Global tab.
Click on the button next to Background Color to open a color palette window where you can select the background for the graph.
The Autoselect neighbor checkbox is used to turn the toggle on and off for selecting the neighbors when a node is selected.
Move the Zoom slider back and forth to zoom-in and zoom-out of the graph...