Bio::Tree
Statistics
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Summary
Bio::Tree::Statistics - Calculate certain statistics for a Tree
Package variables
No package variables defined.
Inherit
Synopsis
use Bio::Tree::Statistics;
Description
This should be where Tree statistics are calculated. It was
previously where statistics from a Coalescent simulation.
It now contains several methods for calculating
Tree-Trait
statistics.
Methods
Methods description
Title : assess_bootstrap
Usage : my $tree_with_bs = $stats->assess_bootstrap(\@bs_trees);
Function: Calculates the bootstrap for internal nodes based on
Returns : Bio::Tree::TreeI
Args : Arrayref of Bio::Tree::TreeIs |
Example : cherries($tree, $node);
Description: Count number of paired leaf nodes
in a binary tree
Returns : integer
Exceptions :
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Commonly used statistics assume a binary tree, but this methods
returns a value even for trees with polytomies. |
Example : fitch($tree, $key, $node);
Description: Calculates Parsimony Score (PS) and internal trait
values using the Fitch 1971 parsimony algorithm for
the subtree a defined by the (internal) node.
Node defaults to the root.
Returns : true on success
Exceptions : leaf nodes have to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. trait name string
3. Bio::Tree::NodeI object within the tree, optional
Runs first fitch_up that calculates parsimony scores and then
fitch_down that should resolve most of the trait/character state
ambiguities.
Fitch, W.M., 1971. Toward defining the course of evolution: minimal
change for a specific tree topology. Syst. Zool. 20, 406-416.
You can access calculated parsimony values using:
$score = $node->->get_tag_values('ps_score');
and the trait value with:
$traitvalue = $node->->get_tag_values('ps_trait'); # only the first
@traitvalues = $node->->get_tag_values('ps_trait');
Note that there can be more that one trait value, especially for the
root node. |
Example : ps($tree, $key, $node);
Description: Calculates Parsimony Score (PS) from Fitch 1971
parsimony algorithm for the subtree as defined
by the (internal) node.
Node defaults to the root.
Returns : integer, 1 < PS < n, where n is number of branches
Exceptions : leaf nodes have to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. trait name string
3. Bio::Tree::NodeI object within the tree, optional
This is the first half of the Fitch algorithm that is enough for
calculating the resolved parsimony values. The trait/chararacter
states are commonly left in ambiguous state. To resolve them, run
fitch_down. |
Example : fitch_up($tree, $key, $node);
Description: Calculates Parsimony Score (PS) from the Fitch 1971
parsimony algorithm for the subtree as defined
by the (internal) node.
Node defaults to the root.
Returns : integer, 1< PS < n, where n is number of branches
Exceptions : leaf nodes have to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. trait name string
3. Bio::Tree::NodeI object within the tree, optional
This is a more generic name for ps and indicates that it performs
the first bottom-up tree traversal that calculates the parsimony score
but usually leaves trait/character states ambiguous. If you are
interested in internal trait states, running fitch_down should
resolve most of the ambiguities. |
Example : fitch_down($tree, $node);
Description: Runs the second pass from Fitch 1971
parsimony algorithm to resolve ambiguous
trait states left by first pass.
by the (internal) node.
Node defaults to the root.
Returns : true
Exceptions : dies unless the trait is defined in all nodes
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Before running this method you should have ran fitch_up (alias to
ps ). Note that it is not guaranteed that all states are completely
resolved. |
Example : persistence($tree, $node);
Description: Calculates the persistence
for node in the subtree defined by the (internal)
node. Node defaults to the root.
Returns : int, number of generations trait value has to remain same
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Persistence measures the stability that the trait value has in a
tree. It expresses the number of generations the trait value remains
the same. All the decendants of the root in the same generation have
to share the same value.
Depends on Fitch's parsimony score (PS). |
Example : count_clusters($tree, $node);
Description: Calculates the number of sub-clusters
in the subtree defined by the (internal)
node. Node defaults to the root.
Returns : int, count
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Depends on Fitch's parsimony score (PS). |
Example : count_leaves($tree, $node);
Description: Calculates the number of leaves with same trait
value as root in the subtree defined by the (internal)
node. Requires an unbroken line of identical trait values.
Node defaults to the root.
Returns : int, number of leaves with this trait value
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Depends on Fitch's parsimony score (PS). |
Example : phylotype_length($tree, $node);
Description: Sums up the branch lengths within phylotype
exluding the subclusters where the trait values
are different
Returns : float, length
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Depends on Fitch's parsimony score (PS). |
Example : sum_of_leaf_distances($tree, $node);
Description: Sums up the branch lengths from root to leaf
exluding the subclusters where the trait values
are different
Returns : float, length
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Depends on Fitch's parsimony score (PS). |
Example : genetic_diversity($tree, $node);
Description: Diversity is the sum of root to leaf distances
within the phylotype normalised by number of leaf
nodes
Returns : float, value of genetic diversity
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Depends on Fitch's parsimony score (PS). |
Example : statratio($tree, $node);
Description: Ratio of the stem length and the genetic diversity of the
phylotype genetic_diversity
Returns : float, separation score
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional
Statratio gives a measure of separation and variability within the phylotype.
Larger values identify more rapidly evolving and recent phylotypes.
Depends on Fitch's parsimony score (PS). |
Example : ai($tree, $key, $node);
Description: Calculates the Association Index (AI) of Whang et
al. 2001 for the subtree defined by the (internal)
node. Node defaults to the root.
Returns : real
Exceptions : leaf nodes have to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. trait name string
3. Bio::Tree::NodeI object within the tree, optional
Association index (AI) gives a more fine grained results than PS since
the result is a real number. ~0 <= AI.
Wang, T.H., Donaldson, Y.K., Brettle, R.P., Bell, J.E., Simmonds, P.,
2001. Identification of shared populations of human immunodeficiency
Virus Type 1 infecting microglia and tissue macrophages outside the
central nervous system. J. Virol. 75 (23), 11686-11699. |
Example : mc($tree, $key, $node);
Description: Calculates the Monophyletic Clade (MC) size statistics
for the subtree a defined by the (internal) node.
Node defaults to the root;
Returns : hashref with trait values as keys
Exceptions : leaf nodes have to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. trait name string
3. Bio::Tree::NodeI object within the tree, optional
Monophyletic Clade (MC) size statistics by Salemi at al 2005. It is
calculated for each trait value. 1 <= MC <= nx, where nx is the
number of tips with value x:
pick the internal node with maximim value for
number of of tips with only trait x
MC was defined by Parker et al 2008.
Salemi, M., Lamers, S.L., Yu, S., de Oliveira, T., Fitch, W.M., McGrath, M.S.,
2005. Phylodynamic analysis of Human Immunodeficiency Virus Type 1 in
distinct brain compartments provides a model for the neuropathogenesis of
AIDS. J. Virol. 79 (17), 11343-11352.
Parker, J., Rambaut A., Pybus O., 2008. Correlating viral phenotypes
with phylogeny: Accounting for phylogenetic uncertainty Infection,
Genetics and Evolution 8 (2008), 239-246. |
Methods code
sub assess_bootstrap
{ my ($self,$bs_trees,$guide_tree) = @_;
my @consensus;
my (%lookup,%internal);
my $i = 0;
for my $tree ( $guide_tree, @$bs_trees ) {
my @allnodes = $tree->get_nodes;
my @internalnodes = grep { ! $_->is_Leaf } @allnodes;
for my $node ( @internalnodes ) {
my @tips = sort map { $_->id }
grep { $_->is_Leaf() } $node->get_all_Descendents;
my $id = "(".join(",", @tips).")";
if( $i == 0 ) {
$internal{$id} = $node->internal_id;
} else {
$lookup{$id}++;
}
}
$i++;
}
my @save;
for my $l ( keys %lookup ) {
if( defined $internal{$l} ) {
my $intnode = $guide_tree->find_node(-internal_id => $internal{$l});
$intnode->bootstrap(sprintf("%d",100 * $lookup{$l} / $i));
}
}
return $guide_tree; } | sub cherries
{($;$) { my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
my $cherries = 0;
my @descs = $node->each_Descendent;
if ($descs[0]->is_Leaf and $descs[1]->is_Leaf) {
if ($descs[3]) {
$cherries = 0;
} else {
$cherries = 1;
}
} else {
foreach my $desc (@descs) {
$cherries += $self->cherries($tree, $desc);
}
}
return $cherries;} | sub fitch
{ my $self = shift;
my $tree = shift;
my $key = shift || $self->throw("Trait name is needed");
my $node = shift || $tree->get_root_node;
$self->fitch_up($tree, $key, $node);
$self->fitch_down($tree, $node);} | sub ps
{ shift->fitch_up(@_) } | sub fitch_up
{ my $self = shift;
my $tree = shift;
my $key = shift || $self->throw("Trait name is needed");
my $node = shift || $tree->get_root_node;
if ($node->is_Leaf) {
$self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key")
unless $node->has_tag($key);
$node->set_tag_value('ps_trait', $node->get_tag_values($key) );
$node->set_tag_value('ps_score', 0 );
return;
}
foreach my $child ($node->each_Descendent) {
$self->fitch_up($tree, $key, $child);
}
my %intersection;
my %union;
my $score;
foreach my $child ($node->each_Descendent) {
foreach my $trait ($child->get_tag_values('ps_trait') ) {
$intersection{$trait}++ if $union{$trait};
$union{$trait}++;
}
$score += $child->get_tag_values('ps_score');
}
if (keys %intersection) {
$node->set_tag_value('ps_trait', keys %intersection);
$node->set_tag_value('ps_score', $score);
} else {
$node->set_tag_value('ps_trait', keys %union);
$node->set_tag_value('ps_score', $score+1);
}
if ($self->verbose) {
print "-- node --------------------------\n";
print "iID: ", $node->internal_id, " (", $node->id, ")\n";
print "Trait: ", join (', ', $node->get_tag_values('ps_trait') ), "\n";
print "length :", scalar($node->get_tag_values('ps_score')) , "\n";
}
return scalar $node->get_tag_values('ps_score');} | sub fitch_down
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
my $key = 'ps_trait';
$self->throw ("ERROR: ". $node->internal_id. " needs a value for $key")
unless $node->has_tag($key);
my $nodev;
foreach my $trait ($node->get_tag_values($key) ) {
$nodev->{$trait}++;
}
foreach my $child ($node->each_Descendent) {
next if $child->is_Leaf;
my $intersection;
foreach my $trait ($child->get_tag_values($key) ) {
$intersection->{$trait}++ if $nodev->{$trait};
}
$self->fitch_down($tree, $child);
$child->set_tag_value($key, keys %$intersection);
}
return 1;
} | sub _persistence
{ my $self = shift;
my $tree = shift;
my $node = shift;
my $value = shift || $self->throw("Value is needed");
my $key = 'ps_trait';
$self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI');
return 0 unless $node->get_tag_values($key) eq $value;
return 1 if $node->is_Leaf;
my $persistence = 10000000;
foreach my $child ($node->each_Descendent) {
my $pers = $self->_persistence($tree, $child, $value);
$persistence = $pers if $pers < $persistence;
}
return $persistence + 1;} | sub persistence
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
$self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI');
my $key = 'ps_trait';
my $value = $node->get_tag_values($key);
my $persistence = $self->_persistence($tree, $node, $value);
$node->set_tag_value('persistance', $persistence);
return $persistence;} | sub _count_subclusters
{ my $self = shift;
my $tree = shift;
my $node = shift;
my $value = shift || $self->throw("Value is needed");
my $key = 'ps_trait';
$self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key")
unless $node->has_tag($key);
if ($node->get_tag_values($key) eq $value) {
if ($node->get_tag_values('ps_score') == 0) {
return 0;
} else {
my $count = 0;
foreach my $child ($node->each_Descendent) {
$count += $self->_count_subclusters($tree, $child, $value);
}
return $count;
}
}
return 1;} | sub count_subclusters
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
$self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI');
my $key = 'ps_trait';
my $value = $node->get_tag_values($key);
return $self->_count_subclusters($tree, $node, $value);} | sub _count_leaves
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
my $value = shift;
my $key = 'ps_trait';
$self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key")
unless $node->has_tag($key);
if ($node->get_tag_values($key) eq $value) {
return 1 if $node->is_Leaf;
my $count = 0;
foreach my $child ($node->each_Descendent) {
$count += $self->_count_leaves($tree, $child, $value);
}
return $count;
}
return 0;} | sub count_leaves
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
$self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI');
my $key = 'ps_trait';
my $value = $node->get_tag_values($key);
return $self->_count_leaves($tree, $node, $value);} | sub _phylotype_length
{ my $self = shift;
my $tree = shift;
my $node = shift;
my $value = shift;
my $key = 'ps_trait';
$self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key")
unless $node->has_tag($key);
return 0 if $node->get_tag_values($key) ne $value;
return $node->branch_length if $node->is_Leaf;
my $length = 0;
foreach my $child ($node->each_Descendent) {
my $sub_len = $self->_phylotype_length($tree, $child, $value);
$length += $sub_len;
$length += $child->branch_length if not $child->is_Leaf and $sub_len;
}
return $length;} | sub phylotype_length
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
my $key = 'ps_trait';
my $value = $node->get_tag_values($key);
return $self->_phylotype_length($tree, $node, $value);} | sub _sum_of_leaf_distances
{ my $self = shift;
my $tree = shift;
my $node = shift;
my $value = shift;
my $key = 'ps_trait';
$self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key")
unless $node->has_tag($key);
return 0 if $node->get_tag_values($key) ne $value;
return 0 if $node->is_Leaf;
my $length = 0;
foreach my $child ($node->each_Descendent) {
$length += $self->_count_leaves($tree, $child, $value) * $child->branch_length +
$self->_sum_of_leaf_distances($tree, $child, $value);
}
return $length;} | sub sum_of_leaf_distances
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
my $key = 'ps_trait';
my $value = $node->get_tag_values($key);
return $self->_sum_of_leaf_distances($tree, $node, $value);} | sub genetic_diversity
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
return $self->sum_of_leaf_distances($tree, $node) /
$self->count_leaves($tree, $node);
} | sub statratio
{ my $self = shift;
my $tree = shift;
my $node = shift || $tree->get_root_node;
my $div = $self->genetic_diversity($tree, $node);
return 0 if $div == 0;
return $node->branch_length / $div;
} | sub _node_ai
{ my $self = shift;
my $node = shift;
my $key = shift;
my $traits;
my $leaf_count = 0;
for my $desc ( $node->get_all_Descendents ) {
next unless $desc->is_Leaf;
$leaf_count++;
$self->throw ("Node ". $desc->id. " needs a value for trait [$key]")
unless $desc->has_tag($key);
my $trait = $desc->get_tag_values($key);
$traits->{$trait}++;
}
my $most_common = 0;
foreach ( keys %$traits) {
$most_common = $traits->{$_} if $traits->{$_} > $most_common;
}
return sprintf "%1.6f", (1 - ($most_common/$leaf_count) ) / (2**($leaf_count-1) );} | sub ai
{ my $self = shift;
my $tree = shift;
my $key = shift || $self->throw("Trait name is needed");
my $start_node = shift || $tree->get_root_node;
return unless $start_node;
my $sum = 0;
for my $node ( $start_node->get_all_Descendents ) {
next if $node->is_Leaf;
$sum += $self->_node_ai($node, $key);
}
return $sum;} | sub _node_mc
{ my $self = shift;
my $node = shift;
my $key = shift;
my $traits;
my $leaf_count = 0;
for my $node2 ( $node->get_all_Descendents ) {
next unless $node2->is_Leaf;
$leaf_count++;
my $trait = $node2->get_tag_values($key);
$traits->{$trait}++;
}
return $traits;} | sub mc
{ my $self = shift;
my $tree = shift;
my $key = shift || die "Trait name is needed";
my $start_node = shift || $tree->get_root_node;
return unless $start_node;
my $sum;
my $keys;
foreach my $node ( $start_node->get_all_Descendents ) {
next if $node->is_Leaf;
my $traits = $self->_node_mc($node, $key);
if (scalar keys %$traits == 1) {
my ($value) = keys %$traits;
no warnings;
$sum->{$value} = $traits->{$value}
if $sum->{$value} < $traits->{$value};
} else {
map { $keys->{$_} = 1 } keys %$traits;
}
}
foreach my $value (keys %$keys) {
$sum->{$value} = 1 unless defined $sum->{$value};
}
return $sum;
}
1;} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
| AUTHOR - Jason Stajich | Top |
Email jason AT bioperl.org
Heikki Lehvaslaiho, heikki at bioperl dot org
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::Tree::Statistics->new();
Function: Builds a new Bio::Tree::Statistics object
Returns : Bio::Tree::Statistics
Args :
The following methods produce descriptors of trait distribution among
leaf nodes within the trees. They require that a trait has been set
for each leaf node. The tag methods of Bio::Tree::Node are used to
store them as key/value pairs. In this way, one tree can store more
than one trait.
Trees have method add_traits() to set trait values from a file. See the
add_trait() method in
Bio::Tree::TreeFunctionsI.