Help - Set distance values by node/branch data

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TreeGraph allows to display node/branch data distance values (e.g. line width or font height). You can choose any node/branch data column that contains numeric values as source. (The tutorial "Taxon counts as branch widths" also demonstrates this feature.)

ArticleOnLatestVersion.png This article describes this feature for the latest version of TreeGraph 2. For older versions the following articles are available:
Set line branch widths by node/branch data (until 2.0.22)


The dialog

The "Set distance values by node/branch data"-dialog

You can access the Set distance values by node/branch data-dialog by selecting "Set distance values by node/branch data" from the format menu.

Source

You can specify the type of node/branch data that contains the source values for the branch widths here. If the selected column contains numeric and textual values the textual values are treated like undefined (empty) lines.

Minimal / maximal value

These two values describe how distance values are calculated from the node/branch data values of the selected formats. All calculated values will be between the specified minimum (which displays a node/branch data value of 0) and the specified maximum (which displays the maximal value contained in the selected node/branch data column). This means that the format values are calculated in the following way:

DistanceValueFormati = Minimum + ((Maximum - Minimum) / MaxNodeBranchData) * NodeBranchDataValuei

Set undefined nodes to minimal width

Furthermore you can define what shall happen to elements which have no according node/branch data in the selected data column. If you check the "Set undefined nodes to minimal width"-option all elements which have no node/branch data assigned will get the specified minimal distance value. Otherwise their current value will remain unchanged.

Set parent value to terminals

If you check this option all terminal elements will adopt the value of their parent element. If a defined source value exists for a terminal element this value is used to calculate the distance value no matter if this option is checked or not.

This option can be useful if terminals do not have defined values in the selected source node/branch data column (e.g. if the source data are branch support values).

Target

In this list you can select which elements shall get a distance value format defined by the selected node/branch data column.

If you select the branch width to be set for some cases it may be useful to use a constant branch width instead of having the branch width taper to the parent node line width. (See example below for details.)

Example

The following example shows a tree that displays absolute substitution rates in SSB (substitutions per site per billion years) by its line colors, branch widths and text labels. Of course you could also use these three formatting options to display three different kinds of data associated with the branches or nodes in your tree. (You can download the TreeGraph 2 source file here.)

Ratogram.png

See also