Bioinformatics Toolbox

plot (phytree)

Draw a phylogenetic tree

Syntax

plot(Tree)
plot(Tree, ActiveBranches)

plot(..., 'Type', TypeValue)
plot(..., 'Orientation', OrientationValue)
plot(..., 'BranchLabels', BranchLabelsValue)
plot(..., 'LeafLabels', LeafLabelsValue)
plot(..., 'TerminalLabels', TerminalLabelsValue)

Arguments

`Tree`	`phytree` object created with the function phytree (phytree)
`ActiveBranches`	Branches veiwable in the figure window.
`TypeValue`	Property to select a method for drawing a phylogenetic tree. Enter `'square'` , `'angular'`, or `'radial'`. The default value is `'square'.`
`OrientationValue`	Property to orient a phylogram or cladogram tree. Enter `'top'`, `'bottom'`, `'left'`, or `'right'`. The default value is `'left'`.
`BranchLabelsValue`	Property to control displaying branch labels. Enter either `true` or `false`. The default value is `false`.
`LeafLabelsValue`	Property to control displaying leaf labels. Enter either `true` or `false`. The default value is `false`.
`TerminalLabels`	Property to control displaying terminal labels. Enter either `true` or `false`. The default value is `false`.

Description

plot(Tree) draws a phylogenetic tree object into a MATLAB figure as a phylogram. The significant distances between branches and nodes are in the horizontal direction. Vertical distances have no significance and are selected only for display purposes. Handles to graph elements are stored in the figure field UserData so that you can easily modify graphic properties.

plot(Tree, ActiveBranches) hides the nonactive branches and all of their descendants. ActiveBranches is a logical array of size numBranches x 1 indicating the active branches.

plot(..., 'Type', TypeValue) selects a method for drawing a phylogenetic tree.

plot(...,'Orientation', OrientationValue) orients a phylogenetic tree within a figure window. The Orientation property is valid only for phylogram and cladogram trees.

plot(...,'BranchLabels', BranchLabelsValue) hides or displays branch labels placed next to the branch node.

plot(...,'LeafLabels', LeafLabelsValue) hides or displays leaf labels placed next to the leaf nodes.

plot(...,'TerminalLabels', TerminalLabelsValue) hides or displays terminal labels. Terminal labels are placed over the axis tick labels and ignored when Type= 'radial'.

H = plot(...) returns a structure with handles to the graph elements.

Examples

tr = phytreeread('pf00002.tree')
plot(tr,'Type','radial')

Graph element properties can be modified as follows:

h=get(gcf,'UserData')
set(h.branchNodeLabels,'FontSize',6,'Color',[.5 .5 .5])

plot (phytree)

Syntax

Arguments

Description

Examples

See Also