5. Visualisation
Visualizing your taxonomic databases is an invaluable process for understanding the connections between different taxa and for reviewing any updates or modifications made to your FlexTaxD database. For visual representations, FlexTaxD offers a straightforward command that renders your specified taxonomy into a tree-like structure.
To visualize a part of your database, particularly focusing on a specific node such as "Francisellaceae" within a GTDB-database, use the following command:
flextaxd --db gtdb.fdb --vis_type tree --vis_node "Francisellaceae" --vis_depth 0This command will generate a visualization like the one displayed in the provided image, showing the taxonomic tree with "Francisellaceae" as the root node.
-
--vis_type tree: This specifies the type of visualization, which in this case is a tree structure. -
--vis_node "Francisellaceae": Indicates the taxonomic node from which the visualization will start. -
--vis_depth 0: Determines the depth of the tree to visualize. A value of 0 means that all descendant levels from the specified node will be included in the visualization.
For extensive databases, visualizing the entire structure may be impractical due to the vast number of nodes. To handle this, you can:
- Use
--vis_depthwith a specific depth to limit the complexity of the visualization. - Focus on specific sub-trees or nodes of interest to avoid overwhelming the visual output.
For further customization and additional parameters, the FlexTaxD tool provides help documentation:
flextaxd --helpThis command will display various options and flags that you can use to tailor the visualization to your needs, including different visualization types, formatting options, and more.
By using the visualization capabilities of FlexTaxD, you'll be able to gain a clearer picture of the taxonomic relationships within your database, aiding in analysis and communication of your data.