Bioinformatics Toolbox

select (phytree)

Select tree branches and leaves in phytree object

Syntax

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

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

Arguments

`Tree`	Phylogenetic tree created with the function phytree (phytree).
`N`	Number of closest nodes to the root node.
`ReferenceValue`	Property to select a reference point for measuring distance.
`CriteriaValue`	Property to select a criteria for measuring distance.
`ThresholdValue`	Property to select a distance value. Nodes with distances below this value are selected.
`ExcludeValue`	Property to remove (exclude) branch or leaf nodes from the output. Enter `'none'`, `'branchs'`, or `'leaves'`. The default value is `'none'`.
`PropagateValue`	Property to select propagating nodes toward the leaves or the root.

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 = 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.

S = 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.

S = select(..., 'Threshold', ThresholdValue) selects all the nodes where closeness is less than or equal to the threshold value V. Notice that 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.

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

S = 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.

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

Examples

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

% To find close products for a given protein (e.g. vips_human):
ind = getbyname(tr,'vips_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)

select (phytree)

Syntax

Arguments

Description

Examples

See Also