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CoNet - Documentation - Tutorial (Chaffron data)

The goal of this tutorial is to infer relationships between the presence/absence data set assembled by Chaffron.

Tutorial files
Chaffron's presence/absence data spanning multiple environments
metadata accompanying Chaffron's data (to set node colors)
vizmap properties file
settings file

Short version (using the CoNet settings file)

1. Open the CoNet plugin in Cytoscape and click the "Settings loading/saving" button.
2. In the Settings menu, click "Select file" and browse the file tree to the settings file.
3. Click the "Apply settings in selected file" button and close the Settings menu.
4. In the Data menu, click on the top-most "Select file" and browse the file tree to select the Chaffron data file.
5. In the Data menu, click the "Metadata and features" button to open the metadata submenu.
6. In the Metadata submenu, click the left "Select file" button and select the metadata file.
7. In the main menu, click the GO button.

Long version (entering everything manually in the CoNet interface)

1. Open the CoNet plugin in Cytoscape and open the Data menu
2. In the Data menu, click on the top-most "Select file" and browse the file tree to select the Chaffron data file.
3. Set the matrix type to "incidence".
4. Click the "Metadata and features" button to open the metadata submenu.
5. In the Metadata submenu, click the left "Select file" button and select the metadata file.
6. In the text area below, enter the metadata columns contained in the metadata file: lineage/taxon/domain/phylum
7. Close the Metadata and Data menus and open the "Preprocessing and filtering" menu.
8. In "Output filtering", select "copresences only".
9. Close the "Preprocessing and filtering" menu and open the Methods menu, then click the "Incidence methods menu" button.
10. In the incidence methods menu, enable the "Hypergeometric distribution" checkbox and enter 1 in the text field.
11. In the main menu, click the GO button. The computation takes some time (2 minutes on a machine with 8GB RAM).

Result

The network returned by CoNet has no layout, as layout computation can be time-consuming, depending on the chosen algorithm. You can layout the network using one of Cytoscape's supported layouts, for instance the yFiles-layout Organic. You can then use the VizMapper^TM to set phylum-specific node colors or load this tutorial's vizmap property file to set pre-assigned phylum colors. After these processing steps, the network looks like this:

You can save the current CoNet setting by clicking on the "Settings loading/saving" button in the main menu and then selecting a folder and typing a file name to which to save the current settings.