Bioinformatics Toolbox™

select (phytree) - Select tree branches and leaves in phytree object

Syntax

S = select(Tree, N)
[S, Selleaves, Selbranches] = select(...)

select(..., 'Reference', ReferenceValue, ...)
select(..., 'Criteria', CriteriaValue, ...)
select(..., 'Threshold', ThresholdValue, ...)
select(..., 'Exclude', ExcludeValue, ...)
select(..., 'Propagate', PropagateValue, ...)

Arguments

Description

S = select(Tree, N) returns a logical vector (S) of size [NumNodes x 1] indicating the N closest nodes to the root node of a phytree object (Tree) where NumNodes = NumLeaves + NumBranches. The first criterion select uses is branch levels, then patristic distance (also known as tree distance). By default, select uses inf as the value of N, and select(Tree) returns a vector with values of true.

[S, Selleaves, Selbranches] = select(...) returns two additional logical vectors, one for the selected leaves and one for the selected branches.

select(..., 'PropertyName', PropertyValue, ...) calls select with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

select(..., 'Reference', ReferenceValue, ...) changes the reference point(s) to measure the closeness. Reference can be the root (default) or leaves. When using leaves, a node can have multiple distances to its descendant leaves (nonultrametric tree). If this the case, select considers the minimum distance to any descendant leaf.

select(..., 'Criteria', CriteriaValue, ...) changes the criteria select uses to measure closeness. If C = 'levels' (default), the first criterion is branch levels and then patristic distance. If C = 'distance', the first criterion is patristic distance and then branch levels.

select(..., 'Threshold', ThresholdValue, ...) selects all the nodes where closeness is less than or equal to the threshold value (ThresholdValue). Notice, you can also use either of the properties 'criteria' or 'reference', if N is not specified, then N = infF; otherwise you can limit the number of selected nodes by N.

select(..., 'Exclude', ExcludeValue, ...) when ExcludeValue = 'branches', sets a postfilter that excludes all the branch nodes from S, or when ExcludeValue = 'leaves', all the leaf nodes. The default is 'none'.

select(..., 'Propagate', PropagateValue, ...) activates a postfunctionality that propagates the selected nodes to the leaves when P=='toleaves' or toward the root finding a common ancestor when P == 'toroot'. The default value is 'none'. P may also be 'both'. The 'Propagate' property acts after the 'Exclude' property.

Examples

% Load a phylogenetic tree created from a protein family:
tr = phytreeread('pf00002.tree');

% To find close products for a given protein (e.g. vipr2_human):
ind = getbyname(tr,'vipr2_human');
[sel,sel_leaves] = select(tr,'criteria','distance',...
                          'threshold',0.6,'reference',ind);
view(tr,sel_leaves)
 
% To find potential outliers in the tree, use
[sel,sel_leaves] = select(tr,'criteria','distance',...
                             'threshold',.3,...
                             'reference','leaves',...
                             'exclude','leaves',...
                             'propagate','toleaves');
view(tr,~sel_leaves)

See Also

Bioinformatics Toolbox functions: phytree (object constructor), phytreetool

Bioinformatics Toolbox methods of phytree object: get, pdist, prune

rownames (DataMatrix)

set (biograph)