NAME
Bio::Phylo::Matrices::Matrix - Character state matrix
SYNOPSIS
use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;
# instantiate taxa object
my $taxa = $fac->create_taxa;
for ( 'Homo sapiens', 'Pan paniscus', 'Pan troglodytes' ) {
$taxa->insert( $fac->create_taxon( '-name' => $_ ) );
}
# instantiate matrix object, 'standard' data type. All categorical
# data types follow semantics like this, though with different
# symbols in lookup table and matrix
my $standard_matrix = $fac->create_matrix(
'-type' => 'STANDARD',
'-taxa' => $taxa,
'-lookup' => {
'-' => [],
'0' => [ '0' ],
'1' => [ '1' ],
'?' => [ '0', '1' ],
},
'-labels' => [ 'Opposable big toes', 'Opposable thumbs', 'Not a pygmy' ],
'-matrix' => [
[ 'Homo sapiens' => '0', '1', '1' ],
[ 'Pan paniscus' => '1', '1', '0' ],
[ 'Pan troglodytes' => '1', '1', '1' ],
],
);
# note: complicated constructor for mixed data!
my $mixed_matrix = Bio::Phylo::Matrices::Matrix->new(
# if you want to create 'mixed', value for '-type' is array ref...
'-type' => [
# ...with first field 'mixed'...
'mixed',
# ...second field is an array ref...
[
# ...with _ordered_ key/value pairs...
'dna' => 10, # value is length of type range
'standard' => 10, # value is length of type range
# ... or, more complicated, value is a hash ref...
'rna' => {
'-length' => 10, # value is length of type range
# ...value for '-args' is an array ref with args
# as can be passed to 'unmixed' datatype constructors,
# for example, here we modify the lookup table for
# rna to allow both 'U' (default) and 'T'
'-args' => [
'-lookup' => {
'A' => [ 'A' ],
'C' => [ 'C' ],
'G' => [ 'G' ],
'U' => [ 'U' ],
'T' => [ 'T' ],
'M' => [ 'A', 'C' ],
'R' => [ 'A', 'G' ],
'S' => [ 'C', 'G' ],
'W' => [ 'A', 'U', 'T' ],
'Y' => [ 'C', 'U', 'T' ],
'K' => [ 'G', 'U', 'T' ],
'V' => [ 'A', 'C', 'G' ],
'H' => [ 'A', 'C', 'U', 'T' ],
'D' => [ 'A', 'G', 'U', 'T' ],
'B' => [ 'C', 'G', 'U', 'T' ],
'X' => [ 'G', 'A', 'U', 'T', 'C' ],
'N' => [ 'G', 'A', 'U', 'T', 'C' ],
},
],
},
],
],
);
# prints 'mixed(Dna:1-10, Standard:11-20, Rna:21-30)'
print $mixed_matrix->get_type;DESCRIPTION
This module defines a container object that holds Bio::Phylo::Matrices::Datum objects. The matrix object inherits from Bio::Phylo::Listable, so the methods defined there apply here.
METHODS
CONSTRUCTOR
- new()
-
Matrix constructor.
Type : Constructor Title : new Usage : my $matrix = Bio::Phylo::Matrices::Matrix->new; Function: Instantiates a Bio::Phylo::Matrices::Matrix object. Returns : A Bio::Phylo::Matrices::Matrix object. Args : -type => optional, but if used must be FIRST argument, defines datatype, one of dna|rna|protein| continuous|standard|restriction|[ mixed => [] ] -taxa => optional, link to taxa object -lookup => character state lookup hash ref -labels => array ref of character labels -matrix => two-dimensional array, first element of every row is label, subsequent are characters - new_from_bioperl()
-
Matrix constructor from Bio::Align::AlignI argument.
Type : Constructor Title : new_from_bioperl Usage : my $matrix = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $aln ); Function: Instantiates a Bio::Phylo::Matrices::Matrix object. Returns : A Bio::Phylo::Matrices::Matrix object. Args : An alignment that implements Bio::Align::AlignI
MUTATORS
- set_special_symbols
-
Sets three special symbols in one call
Type : Mutator Title : set_special_symbols Usage : $matrix->set_special_symbols( -missing => '?', -gap => '-', -matchchar => '.' ); Function: Assigns state labels. Returns : $self Args : Three args (with distinct $x, $y and $z): -missing => $x, -gap => $y, -matchchar => $z Notes : This method is here to ensure you don't accidentally use the same symbol for missing AND gap - set_statelabels()
-
Sets argument state labels.
Type : Mutator Title : set_statelabels Usage : $matrix->set_statelabels( [ [ 'state1', 'state2' ] ] ); Function: Assigns state labels. Returns : $self Args : ARRAY, or nothing (to reset); The array is two-dimensional, the first index is to indicate the column the labels apply to, the second dimension the states (sorted numerically or alphabetically, depending on what's appropriate) - set_characters()
-
Sets the character set manager object Bio::Phylo::Matrices::Characters. Normally you never have to use this.
Type : Mutator Title : set_characters Usage : $matrix->set_characters( $characters ); Function: Assigns Bio::Phylo::Matrices::Characters object Returns : $self Args : Bio::Phylo::Matrices::Characters - set_charlabels()
-
Sets argument character labels.
Type : Mutator Title : set_charlabels Usage : $matrix->set_charlabels( [ 'char1', 'char2', 'char3' ] ); Function: Assigns character labels. Returns : $self Args : ARRAY, or nothing (to reset); - set_gapmode()
-
Defines matrix gapmode.
Type : Mutator Title : set_gapmode Usage : $matrix->set_gapmode( 1 ); Function: Defines matrix gapmode ( false = missing, true = fifth state ) Returns : $self Args : boolean - set_matchchar()
-
Assigns match symbol.
Type : Mutator Title : set_matchchar Usage : $matrix->set_matchchar( $match ); Function: Assigns match symbol (default is '.'). Returns : $self Args : ARRAY - set_polymorphism()
-
Defines matrix 'polymorphism' interpretation.
Type : Mutator Title : set_polymorphism Usage : $matrix->set_polymorphism( 1 ); Function: Defines matrix 'polymorphism' interpretation ( false = uncertainty, true = polymorphism ) Returns : $self Args : boolean - set_raw()
-
Set contents using two-dimensional array argument.
Type : Mutator Title : set_raw Usage : $matrix->set_raw( [ [ 'taxon1' => 'acgt' ], [ 'taxon2' => 'acgt' ] ] ); Function: Syntax sugar to define $matrix data contents. Returns : $self Args : A two-dimensional array; first dimension contains matrix rows, second dimension contains taxon name / character string pair. - set_respectcase()
-
Defines matrix case sensitivity interpretation.
Type : Mutator Title : set_respectcase Usage : $matrix->set_respectcase( 1 ); Function: Defines matrix case sensitivity interpretation ( false = disregarded, true = "respectcase" ) Returns : $self Args : boolean
ACCESSORS
- get_special_symbols()
-
Retrieves hash ref for missing, gap and matchchar symbols
Type : Accessor Title : get_special_symbols Usage : my %syms = %{ $matrix->get_special_symbols }; Function: Retrieves special symbols Returns : HASH ref, e.g. { -missing => '?', -gap => '-', -matchchar => '.' } Args : None. - get_characters()
-
Retrieves characters object.
Type : Accessor Title : get_characters Usage : my $characters = $matrix->get_characters Function: Retrieves characters object. Returns : Bio::Phylo::Matrices::Characters Args : None. - get_statelabels()
-
Retrieves state labels.
Type : Accessor Title : get_statelabels Usage : my @statelabels = @{ $matrix->get_statelabels }; Function: Retrieves state labels. Returns : ARRAY Args : None. - get_charlabels()
-
Retrieves character labels.
Type : Accessor Title : get_charlabels Usage : my @charlabels = @{ $matrix->get_charlabels }; Function: Retrieves character labels. Returns : ARRAY Args : None. - get_gapmode()
-
Returns matrix gapmode.
Type : Accessor Title : get_gapmode Usage : do_something() if $matrix->get_gapmode; Function: Returns matrix gapmode ( false = missing, true = fifth state ) Returns : boolean Args : none - get_matchchar()
-
Returns matrix match character.
Type : Accessor Title : get_matchchar Usage : my $char = $matrix->get_matchchar; Function: Returns matrix match character (default is '.') Returns : SCALAR Args : none - get_nchar()
-
Calculates number of characters.
Type : Accessor Title : get_nchar Usage : my $nchar = $matrix->get_nchar; Function: Calculates number of characters (columns) in matrix (if the matrix is non-rectangular, returns the length of the longest row). Returns : INT Args : none - get_ntax()
-
Calculates number of taxa (rows) in matrix.
Type : Accessor Title : get_ntax Usage : my $ntax = $matrix->get_ntax; Function: Calculates number of taxa (rows) in matrix Returns : INT Args : none - get_polymorphism()
-
Returns matrix 'polymorphism' interpretation.
Type : Accessor Title : get_polymorphism Usage : do_something() if $matrix->get_polymorphism; Function: Returns matrix 'polymorphism' interpretation ( false = uncertainty, true = polymorphism ) Returns : boolean Args : none - get_raw()
-
Retrieves a 'raw' (two-dimensional array) representation of the matrix's contents.
Type : Accessor Title : get_raw Usage : my $rawmatrix = $matrix->get_raw; Function: Retrieves a 'raw' (two-dimensional array) representation of the matrix's contents. Returns : A two-dimensional array; first dimension contains matrix rows, second dimension contains taxon name and characters. Args : NONE - get_respectcase()
-
Returns matrix case sensitivity interpretation.
Type : Accessor Title : get_respectcase Usage : do_something() if $matrix->get_respectcase; Function: Returns matrix case sensitivity interpretation ( false = disregarded, true = "respectcase" ) Returns : boolean Args : none
CALCULATIONS
- calc_prop_invar()
-
Calculates proportion of invariant sites.
Type : Calculation Title : calc_prop_invar Usage : my $pinvar = $matrix->calc_prop_invar; Function: Calculates proportion of invariant sites. Returns : Scalar: a number Args : Optional: # if true, counts missing (usually the '?' symbol) as a state # in the final tallies. Otherwise, missing states are ignored -missing => 1 # if true, counts gaps (usually the '-' symbol) as a state # in the final tallies. Otherwise, gap states are ignored -gap => 1 - calc_state_counts()
-
Calculates occurrences of states.
Type : Calculation Title : calc_state_counts Usage : my %counts = %{ $matrix->calc_state_counts }; Function: Calculates occurrences of states. Returns : Hashref: keys are states, values are counts Args : Optional - one or more states to focus on - calc_state_frequencies()
-
Calculates the frequencies of the states observed in the matrix.
Type : Calculation Title : calc_state_frequencies Usage : my %freq = %{ $object->calc_state_frequencies() }; Function: Calculates state frequencies Returns : A hash, keys are state symbols, values are frequencies Args : Optional: # if true, counts missing (usually the '?' symbol) as a state # in the final tallies. Otherwise, missing states are ignored -missing => 1 # if true, counts gaps (usually the '-' symbol) as a state # in the final tallies. Otherwise, gap states are ignored -gap => 1 Comments: Throws exception if matrix holds continuous values - calc_distinct_site_patterns()
-
Identifies the distinct distributions of states for all characters and counts their occurrences. Returns an array-of-arrays, where the first cell of each inner array holds the occurrence count, the second cell holds the pattern, i.e. an array of states. For example, for a matrix like this:
taxon1 GTGTGTGTGTGTGTGTGTGTGTG taxon2 AGAGAGAGAGAGAGAGAGAGAGA taxon3 TCTCTCTCTCTCTCTCTCTCTCT taxon4 TCTCTCTCTCTCTCTCTCTCTCT taxon5 AAAAAAAAAAAAAAAAAAAAAAA taxon6 CGCGCGCGCGCGCGCGCGCGCGC taxon7 AAAAAAAAAAAAAAAAAAAAAAAThe following data structure will be returned:
[ [ 12, [ 'G', 'A', 'T', 'T', 'A', 'C', 'A' ] ], [ 11, [ 'T', 'G', 'C', 'C', 'A', 'G', 'A' ] ] ]The patterns are sorted from most to least frequently occurring, the states for each pattern are in the order of the rows in the matrix. (In other words, the original matrix can more or less be reconstructed by inverting the patterns, and multiplying them by their occurrence, although the order of the columns will be lost.)
Type : Calculation Title : calc_distinct_site_patterns Usage : my $patterns = $object->calc_distinct_site_patterns; Function: Calculates distinct site patterns. Returns : A multidimensional array, see above. Args : NONE Comments: - calc_gc_content()
-
Calculates the G+C content as a fraction on the total
Type : Calculation Title : calc_gc_content Usage : my $fraction = $obj->calc_gc_content; Function: Calculates G+C content Returns : A number between 0 and 1 (inclusive) Args : Optional: # if true, counts missing (usually the '?' symbol) as a state # in the final tallies. Otherwise, missing states are ignored -missing => 1 # if true, counts gaps (usually the '-' symbol) as a state # in the final tallies. Otherwise, gap states are ignored -gap => 1 Comments: Throws 'BadArgs' exception if matrix holds anything other than DNA or RNA. The calculation also takes the IUPAC symbol S (which is C|G) into account, but no other symbols (such as V, for A|C|G);
METHODS
- keep_chars()
-
Creates a cloned matrix that only keeps the characters at the supplied (zero-based) indices.
Type : Utility method Title : keep_chars Usage : my $clone = $object->keep_chars([6,3,4,1]); Function: Creates spliced clone. Returns : A spliced clone of the invocant. Args : Required, an array ref of integers Comments: The columns are retained in the order in which they were supplied. - prune_chars()
-
Creates a cloned matrix that omits the characters at the supplied (zero-based) indices.
Type : Utility method Title : prune_chars Usage : my $clone = $object->prune_chars([6,3,4,1]); Function: Creates spliced clone. Returns : A spliced clone of the invocant. Args : Required, an array ref of integers Comments: The columns are retained in the order in which they were supplied. - bootstrap()
-
Creates bootstrapped clone.
Type : Utility method Title : bootstrap Usage : my $bootstrap = $object->bootstrap; Function: Creates bootstrapped clone. Returns : A bootstrapped clone of the invocant. Args : Optional, a subroutine reference that returns a random integer between 0 (inclusive) and the argument provided to it (exclusive). The default implementation is to use sub { int( rand( shift ) ) }, a user might override this by providing an implementation with a better random number generator. Comments: The bootstrapping algorithm uses perl's random number generator to create a new series of indices (without replacement) of the same length as the original matrix. These indices are first sorted, then applied to the cloned sequences. Annotations (if present) stay connected to the resampled cells. - jackknife()
-
Creates jackknifed clone.
Type : Utility method Title : jackknife Usage : my $bootstrap = $object->jackknife(0.5); Function: Creates jackknifed clone. Returns : A jackknifed clone of the invocant. Args : * Required, a number between 0 and 1, representing the fraction of characters to jackknife. * Optional, a subroutine reference that returns a random integer between 0 (inclusive) and the argument provided to it (exclusive). The default implementation is to use sub { int( rand( shift ) ) }, a user might override this by providing an implementation with a better random number generator. Comments: The jackknife algorithm uses perl's random number generator to create a new series of indices of cells to keep. These indices are first sorted, then applied to the cloned sequences. Annotations (if present) stay connected to the resampled cells. - clone()
-
Clones invocant.
Type : Utility method Title : clone Usage : my $clone = $object->clone; Function: Creates a copy of the invocant object. Returns : A copy of the invocant. Args : NONE - insert()
-
Insert argument in invocant.
Type : Listable method Title : insert Usage : $matrix->insert($datum); Function: Inserts $datum in $matrix. Returns : Modified object Args : A datum object Comments: This method re-implements the method by the same name in Bio::Phylo::Listable - compress_lookup()
-
Removes unused states from lookup table
Type : Method Title : validate Usage : $obj->compress_lookup Function: Removes unused states from lookup table Returns : $self Args : None - check_taxa()
-
Validates taxa associations.
Type : Method Title : check_taxa Usage : $obj->check_taxa Function: Validates relation between matrix and taxa block Returns : Modified object Args : None Comments: This method implements the interface method by the same name in Bio::Phylo::Taxa::TaxaLinker - make_taxa()
-
Creates a taxa block from the objects contents if none exists yet.
Type : Method Title : make_taxa Usage : my $taxa = $obj->make_taxa Function: Creates a taxa block from the objects contents if none exists yet. Returns : $taxa Args : NONE
SERIALIZERS
- to_xml()
-
Serializes matrix to nexml format.
Type : Format convertor Title : to_xml Usage : my $data_block = $matrix->to_xml; Function: Converts matrix object into a nexml element structure. Returns : Nexml block (SCALAR). Args : Optional: -compact => 1 (for compact representation of matrix) - to_nexus()
-
Serializes matrix to nexus format.
Type : Format convertor Title : to_nexus Usage : my $data_block = $matrix->to_nexus; Function: Converts matrix object into a nexus data block. Returns : Nexus data block (SCALAR). Args : The following options are available: # if set, writes TITLE & LINK tokens '-links' => 1 # if set, writes block as a "data" block (deprecated, but used by mrbayes), # otherwise writes "characters" block (default) -data_block => 1 # if set, writes "RESPECTCASE" token -respectcase => 1 # if set, writes "GAPMODE=(NEWSTATE or MISSING)" token -gapmode => 1 # if set, writes "MSTAXA=(POLYMORPH or UNCERTAIN)" token -polymorphism => 1 # if set, writes character labels -charlabels => 1 # if set, writes state labels -statelabels => 1 # if set, writes mesquite-style charstatelabels -charstatelabels => 1 # by default, names for sequences are derived from $datum->get_name, if # 'internal' is specified, uses $datum->get_internal_name, if 'taxon' # uses $datum->get_taxon->get_name, if 'taxon_internal' uses # $datum->get_taxon->get_internal_name, if $key, uses $datum->get_generic($key) -seqnames => one of (internal|taxon|taxon_internal|$key) - to_dom()
-
Analog to to_xml.
Type : Serializer Title : to_dom Usage : $matrix->to_dom Function: Generates a DOM subtree from the invocant and its contained objects Returns : an Element object Args : Optional: -compact => 1 : renders characters as sequences, not individual cells
SEE ALSO
- Bio::Phylo::Taxa::TaxaLinker
-
This object inherits from Bio::Phylo::Taxa::TaxaLinker, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix objects.
- Bio::Phylo::Matrices::TypeSafeData
-
This object inherits from Bio::Phylo::Matrices::TypeSafeData, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix objects.
- Bio::Phylo::Manual
-
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
CITATION
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
REVISION
$Id: Matrix.pm 1660 2011-04-02 18:29:40Z rvos $