Loading Network Data into Virtualitics Explore Desktop

There are multiple ways to observe your Network Data in Virtualitics Explore Desktop. You can quickly generate a Network Graph using Network Extractor or load and dive into your own Network Data.

In order to load data into Virtualitics Explore Desktop, it needs to be in a compatible Network Data Format.

Network Data Formats

Virtualitics supports the following formats for loading network data:

JSON

JSON (JavaScript Object Notation) is a human-readable data format to encode attribute-value pairs and array/list style data.

Note: This format is strongly recommended by Virtualitics.

A JSON file contains data stored as attributes – value pairs and arrays; importantly, JSON files enable analysis of node attributes. This data format will automatically be recognized by Explore when loaded, as long as the file is structured as illustrated in the image below.

While the JSON format is very flexible, Virtualitics Explore Desktop uses a specific ontology/format within JSON format to encode networks. First, we encode the node data under the Nodes key. The value will be an array of nested JSON data, where each element of the list describes all the data for one node. The name for the node should be stored in the Name key and the value must be a string. The remaining key-value pairs for the given node, must have strings for keys and one of int, float, double, Boolean, or string data type as their value.

The additional keys (other than Name) will be available as columns of data in Virtualitics Explore Desktop, which allow the user to bring in important metadata for each node and provide more context for the network. If there is no value for a given key, simply exclude that key from the nested JSON for the given node. Then, we encode the edge data under the Edges key. The value will be an array of nested JSON data, where each element of the list describes the information for one edge.

Edge List

Edge Lists are a common data format used for low-level networks without node attributes. These can be loaded in from a tabular format (such as a .csv) by specifying Edge List in the Data Format drop-down so long as the data contains only a source, target, and weight column (optional).

While networks are comprised of just nodes and edges, it is possible to encode the data for a network by just listing the edges. This is because the names of the nodes are used to define the edges. As a result, the nodes in the network are just the unique set of nodes referenced in the list of edges. We can also include a column of data to describe the edge weights. When loading in a dataset formatted as an edge list, order matters.

Note: Ensure the first two columns specify the nodes which have an edge between them. The third column can be used as the weight of the edge between the nodes; however, it is not necessary to provide an edge weight column.

Adjacency Matrix

Another way of encoding networks is to use a matrix (with node IDs as the first row, and an imaginary copy of the node IDs in the same order along the first column).

In this format, we have a square matrix where each column name represents the name of a node. There is also a hidden/invisible first column where the column names are repeated in the same order as the column names. The values in the matrix represent the strength of the edges between the nodes described by the column name and the hidden row name. A value of 0 implies that there is no edge between these nodes. Adjacency matrices can be weighted or unweighted.

Note: This format of encoding of network data is very memory inefficient and Virtualitics recommends using one of the other formats (edge list or JSON).

Edge List and Adjacency Matrix are more basic formats that can include edges and their respective weights, while the JSON format enables users to input metadata for each node in addition to the edges and weights.

Note: These formats must be specified in the Dataset Preview window when loading the dataset so that Virtualitics Explore Desktop will recognize them properly.

Below Files on the left-side bar, click Local. Alternatively, click File > Load Dataset.
Navigate to the file you would like to load.

After loading in the data, the Dataset Preview window will appear.

Note: Depending on the network data format, Dataset Preview may not be shown.

Depending on your filetype, ensure you've selected the correct options in Dataset Preview:

JSON File (.json)

This data format will automatically be recognized by Virtualitics Explore Desktop when loaded in as long as the file is structured correctly.

Edge List

These can be loaded in from a tabular format (such as a .csv) by specifying “Edge List” in the Data Format drop-down so long as the data contains only a source, target, and weight column (optional),

Adjacency Matrix

Can be loaded from any kind of tabular data file (such as .csv or excel). It must follow the format where columns represent the nodes and each row represents the nodes' interactions with other nodes in a network. Adjacency matrices can be weighted or un-weighted.

To load in this network data format properly, select Adjacency Matrix.

(Optional) Ensure to set the Edge Weight Format, if applicable.
- Similarity vs Distance: Similarity is the default when previewing a load of your dataset. However, if your edge weights are values that represent distance, you can specify them as such on the dropdown of Edge Weight Format before loading in the dataset.
- Besides an adjacency matrix where a zero represents no edge between the relevant nodes, weighted edge lists and .json files must specify edge weights that are greater than zero.
- Our network graphs currently only support undirected graphs. Support for directed graphs will be coming soon in a future release.
Click Load at the bottom of the Dataset Preview window.
Spreadsheet View will appear. Click Explore Data at the bottom of the screen.
Your network data will automatically be displayed in 3D. You will find a few key network features on the axes in the Mapping Panel:
- Spatial dimensions for the Network to be visualized in 3D
  - X - Network X
  - Y - Network Y
  - Z - Network Z
- Color - Segments
  - Segments represent groupings based on the density of edges between nodes.
- Size - Weighted Degree
  - Represents the number of edges connected to a node, factoring in any edge weights in the input data

Network Settings

Plot Settings

When interacting with a Network Graph in Virtualitics Explore Desktop, click the Menu icon ( ) on the top right of the Mapping Panel and navigate to the Plot Settings to customize your visualizations. You may toggle points, designate Edge Curvature, and choose to toggle edges or simply show a sample of them.

Note: In order to be able to adjust the Edge Curvature, Network Graph Edge Subdivisions must be increased above 1 in the global Plot settings in Settings > Plot > Default Plot Options.

Appearance Settings

There are several options available in the Appearance section of the Settings window to adjust the Default Edge Color, Default Maps Edge Color, Default Edge Insight Color and Edge Alpha. The Edge Alpha adjusts the opacity of the edges to make them bolder or fainter.

Analyzing Networks

Network Data Formats