plot

Draw phylogenetic tree

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    Syntax

    plot(Tree)
    plot(Tree,ActiveBranches)
    plot(___,Name=Value)
    H = plot(___)

    Description

    plot(Tree) draws a phylogenetic tree object into a figure as a phylogram. The significant distances between branches and nodes are in the horizontal direction. Vertical distances are arbitrary and have no significance.

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

    plot(___,Name=Value) specifies options using one or more name-value arguments in addition to the input arguments in previous syntaxes.

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

    example

    Examples

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    Open Live Script

    Create a phytree object from a file.

    tr = phytreeread("pf00002.tree")
        Phylogenetic tree object with 33 leaves (32 branches)

    Plot the tree and return a structure with handles to the graphic elements of the phytree object.

    h = plot(tr,Type="angular")

    Figure contains an axes object. The axes object contains 100 objects of type line, text. One or more of the lines displays its values using only markers

    h = struct with fields:
                  axes: [1×1 Axes]
           BranchLines: [65×1 Line]
            BranchDots: [1×1 Line]
              LeafDots: [1×1 Line]
      branchNodeLabels: [32×1 Text]
        leafNodeLabels: [33×1 Text]
    terminalNodeLabels: [33×1 Text]

    Modify the font size and color of the leaf node labels by using one of the handles in the return structure.

    set(h.terminalNodeLabels,FontSize=8,Color=[1 0 0])

    Figure contains an axes object. The axes object contains 100 objects of type line, text. One or more of the lines displays its values using only markers

    Input Arguments

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    Phylogenetic tree, specified as a phytree object.

    Active branches to plot, specified as a logical array of size numBranches-by-1. This array indicates the active branches, which are displayed in the Figure window.

    Data Types: logical

    Name-Value Arguments

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    Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

    Example: plot(tr,Type="square",LeafLabels="true")

    Method for drawing a phylogenetic tree, specified as one of these values.

    "square" (default)

    "angular"

    "radial"

    "equalangle"

    This method hides the significance of the root node and emphasizes clusters, thereby making it useful for visually assessing clusters and detecting outliers.

    "equaldaylight"

    This method hides the significance of the root node and emphasizes clusters, thereby making it useful for visually assessing clusters and detecting outliers.

    Data Types: char | string

    Orientation of a phylogram or cladogram tree, specified as

    Position of the root node, specified as "left", "right", "top", or "bottom". This position defines the orientation of a phylogram or cladogram phylogenetic tree in the Figure window when Type is "square" or "angular".

    Data Types: char | string

    Rotation angle of phylogenetic tree in the Figure window, specified as a number between 0 and 360. The angle is measured in degrees. Type must be "radial", "equalangle", or "equaldaylight".

    Data Types: double

    Control for displaying branch labels next to branch nodes, specified as true or false.

    Data Types: logical

    Control for displaying leaf labels next to leaf nodes, specified as true or false. The default is:

    • true — When Type is "radial", "equalangle", or "equaldaylight"

    • false — When Type is "square" or "angular"

    Data Types: logical

    Control for displaying terminal labels over the axis tick labels when Type is "square" or "angular", specified as true or false.

    Data Types: logical

    Control for rotation of leaf labels so that the text aligns to the root node when Type is "radial", "equalangle", or "equaldaylight", specified as true or false.

    Data Types: logical

    Output Arguments

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    Handles to seven graph elements, specified as a structure array with these fields:

    • axes

    • BranchLines

    • BranchDots

    • LeafDots

    • branchNodeLabels

    • leafNodeLabels

    • terminalNodeLabels

    Use the set function with the handles in this structure and their related properties to modify the plot. For more information on the properties you can modify using the axes handle, see Axes Properties. For more information on the properties you can modify using the BranchLines, BranchDots, or LeafDots handle, see Line Properties. For more information on the properties you can modify using the branchNodeLabels, leafNodeLabels, or terminalNodeLabels handle, see Text Properties.

    Version History

    Introduced in R2006a

    See Also

    Objects

    Functions