User Guide - PathVisio/RegInt-Plugin GitHub Wiki
Here you will learn how you can use the RegInt Plugin for PathVisio to visualize regulatory interactions in the side panel of PathVisio.
1. Installing the RegInt plugin
- Start PathVisio
- Go to Plugins -> Plugin Manager -> Select the RegInt plugin in the list
- Click Install
2. Loading regulatory interaction files
Regulatory interaction files usually consist of four columns:
- source identifier
- source system code
- target identifier
- target system code
It is also possible to choose the system code in the import dialog if it is the same for all source / target nodes. Optionally, the user can add pubmed identifiers in an additional column that shows the evidence for the regulatory interaction.
- Go to Plugins -> RegInt -> Load interaction files
- You can select one or multiple files (only txt or csv format allowed)
- For each interaction file you need to select the source and target identifier columns and specify the system codes for each.
- After the interaction files are loaded, the dialog will state how many interactions were loaded. Now you can start investigating your pathway of interest.
3. Show regulatory interactions in side panel
- The plugin added a side panel called RegInt Plugin.
- Select a data node of interest in the pathway and check if there are known regulators or targets for the data node.
- If you load a dataset that contains data for the data nodes in the side panel, the data will also be visualized on the data nodes there.
- If you click on the info button next to a data node in the side panel, more information about the data node is loaded in the bottom half of the side panel.