Help - Hidden node/branch data

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TreeGraph 2 allows you to attach data to a node or a branch that is not directly displayed in the document (in contrast to e.g. text labels) and therefore is called hidden node data or hidden branch data.

To create hidden node or branch data columns you can use the Add support values- or Copy node/branch data-function. (The tutorial "Taxon counts as branch widths" also demonstrates the use of hidden node data.) Additionally hidden node/branch data columns are created when hot comments are imported from a Newick or Nexus document, during the import of phyloXML or when a table is imported.


Purpose

Hidden node or branch data columns were included in TreeGraph 2 for two major reasons. First you might want to store data that is only relevant during the development process of the tree but shall not be shown in the resulting tree. This could e.g. be lab codes which shall still be available for later editing of the tree (like adding new support values that are identified by lab codes) although the terminal node names already consist of real taxon names.

Second hidden branch or node data columns can be used to store source data for pie chart labels or data which is used with the Set distance values by node/branch data or Set colors by node/branch data functions.

Difference between hidden node and branch data

TreeGraph distingiushes between annotations that are attached to nodes or to branches. This difference is important if a tree is rerooted. In that case branches previously leading to a node from the parent side might now branch from that node to the child side. That means that data attached to the branch (hidden branch data or labels) change their position relative to the node whereas hidden node data will remain at the same position.

Example

The tree in this example contains the same annotations twice, once stored in a hidden node data column and once stored in a hidden branch data column. That tree is than rerooted at the red branch.

The example tree after the reroot operation where the values are illustrated as text labels (hidden node data in green and hidden node data in blue). [Download XTG]
The example tree before the reroot operation. [Download XTG]
The example tree after the reroot operation. [Download XTG]

You can see that the annotations "1" and "3" in the two columns have different positions after the reroot depending if they were stored as hidden node or hidden branch data. When you use hidden data elements you should always ask yourself if the annotations are branch related (e.g. bootstrap values that represent the support for a branch seperating the taxa of a tree in two groups) or node realed (e.g. alternative taxon names for your node) and use hidden branch data or hidden node data accordingly.

See also