flock 0.1.0
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- data/README.rdoc +79 -0
- data/Rakefile +18 -0
- data/VERSION +1 -0
- data/examples/example.rb +39 -0
- data/ext/cluster.c +4598 -0
- data/ext/cluster.h +93 -0
- data/ext/extconf.rb +5 -0
- data/ext/flock.c +118 -0
- metadata +72 -0
data/README.rdoc
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= Flock
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Ruby bindings to Cluster 3.0, http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm
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== Description
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Provides bindings to K-Means clustering in Cluster 3.0
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== Synopsis
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require 'flock'
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data = Array.new(13) {[]}
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mask = Array.new(13) {[]}
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weights = Array.new(13) {1.0}
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clusters = Array.new(13)
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data[ 0][ 0]=0.1; data[ 0][ 1]=0.0; data[ 0][ 2]=9.6; data[ 0][ 3] = 5.6;
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data[ 1][ 0]=1.4; data[ 1][ 1]=1.3; data[ 1][ 2]=0.0; data[ 1][ 3] = 3.8;
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data[ 2][ 0]=1.2; data[ 2][ 1]=2.5; data[ 2][ 2]=0.0; data[ 2][ 3] = 4.8;
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data[ 3][ 0]=2.3; data[ 3][ 1]=1.5; data[ 3][ 2]=9.2; data[ 3][ 3] = 4.3;
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data[ 4][ 0]=1.7; data[ 4][ 1]=0.7; data[ 4][ 2]=9.6; data[ 4][ 3] = 3.4;
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data[ 5][ 0]=0.0; data[ 5][ 1]=3.9; data[ 5][ 2]=9.8; data[ 5][ 3] = 5.1;
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data[ 6][ 0]=6.7; data[ 6][ 1]=3.9; data[ 6][ 2]=5.5; data[ 6][ 3] = 4.8;
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data[ 7][ 0]=0.0; data[ 7][ 1]=6.3; data[ 7][ 2]=5.7; data[ 7][ 3] = 4.3;
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data[ 8][ 0]=5.7; data[ 8][ 1]=6.9; data[ 8][ 2]=5.6; data[ 8][ 3] = 4.3;
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data[ 9][ 0]=0.0; data[ 9][ 1]=2.2; data[ 9][ 2]=5.4; data[ 9][ 3] = 0.0;
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data[10][ 0]=3.8; data[10][ 1]=3.5; data[10][ 2]=5.5; data[10][ 3] = 9.6;
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data[11][ 0]=0.0; data[11][ 1]=2.3; data[11][ 2]=3.6; data[11][ 3] = 8.5;
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data[12][ 0]=4.1; data[12][ 1]=4.5; data[12][ 2]=5.8; data[12][ 3] = 7.6;
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mask[ 0][ 0]=1; mask[ 0][ 1]=1; mask[ 0][ 2]=1; mask[ 0][ 3] = 1;
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mask[ 1][ 0]=1; mask[ 1][ 1]=1; mask[ 1][ 2]=0; mask[ 1][ 3] = 1;
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mask[ 2][ 0]=1; mask[ 2][ 1]=1; mask[ 2][ 2]=0; mask[ 2][ 3] = 1;
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mask[ 3][ 0]=1; mask[ 3][ 1]=1; mask[ 3][ 2]=1; mask[ 3][ 3] = 1;
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mask[ 4][ 0]=1; mask[ 4][ 1]=1; mask[ 4][ 2]=1; mask[ 4][ 3] = 1;
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mask[ 5][ 0]=0; mask[ 5][ 1]=1; mask[ 5][ 2]=1; mask[ 5][ 3] = 1;
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mask[ 6][ 0]=1; mask[ 6][ 1]=1; mask[ 6][ 2]=1; mask[ 6][ 3] = 1;
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mask[ 7][ 0]=0; mask[ 7][ 1]=1; mask[ 7][ 2]=1; mask[ 7][ 3] = 1;
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mask[ 8][ 0]=1; mask[ 8][ 1]=1; mask[ 8][ 2]=1; mask[ 8][ 3] = 1;
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mask[ 9][ 0]=1; mask[ 9][ 1]=1; mask[ 9][ 2]=1; mask[ 9][ 3] = 0;
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mask[10][ 0]=1; mask[10][ 1]=1; mask[10][ 2]=1; mask[10][ 3] = 1;
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mask[11][ 0]=0; mask[11][ 1]=1; mask[11][ 2]=1; mask[11][ 3] = 1;
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mask[12][ 0]=1; mask[12][ 1]=1; mask[12][ 2]=1; mask[12][ 3] = 1;
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p Flock.kmeans(6, data, mask)
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# method:
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# - Flock::METHOD_AVERAGE (default)
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# - Flock::METHOD_MEDIAN
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# metric:
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# - Flock::METRIC_EUCLIDIAN (default)
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# - Flock::METRIC_CITY_BLOCK
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# - Flock::METRIC_CORRELATION
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# - Flock::METRIC_ABSOLUTE_CORRELATION
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# - Flock::METRIC_UNCENTERED_CORRELATION
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# - Flock::METRIC_ABSOLUTE_UNCENTERED_CORRELATION
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# - Flock::METRIC_SPEARMAN
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# - Flock::METRIC_KENDALL
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Flock.kmeans(
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6,
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data,
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mask,
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method: Flock::METHOD_KMEANS,
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metric: Flock::METRIC_EUCLIDIAN,
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transpose: 0,
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weights: Array.new(13) {1.0},
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)
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== TODO
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Bindings to,
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* Self Organizing Maps (SOM)
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* Hierarchical clustering (treecluster)
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= License
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{Creative Commons Attribution - CC BY}[http://creativecommons.org/licenses/by/3.0]
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data/Rakefile
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require 'rake'
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begin
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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gem.name = 'flock'
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gem.summary = %q{Ruby bindings to Cluster 3.0.}
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gem.description = %q{A thin ruby binding to Cluster 3.0}
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gem.email = %w{deepfryed@gmail.com}
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gem.homepage = 'http://github.com/deepfryed/flock'
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gem.authors = ["Bharanee Rathna"]
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gem.extensions = FileList['ext/extconf.rb']
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gem.files.reject!{|f| f =~ %r{\.gitignore|examples/.*}}
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end
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Jeweler::GemcutterTasks.new
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rescue LoadError
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puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
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end
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data/VERSION
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1
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0.1.0
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data/examples/example.rb
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#!/usr/bin/ruby
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require 'flock'
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data = Array.new(13) {[]}
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mask = Array.new(13) {[]}
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weights = Array.new(13) {1.0}
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clusters = Array.new(13)
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data[ 0][ 0]=0.1; data[ 0][ 1]=0.0; data[ 0][ 2]=9.6; data[ 0][ 3] = 5.6;
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data[ 1][ 0]=1.4; data[ 1][ 1]=1.3; data[ 1][ 2]=0.0; data[ 1][ 3] = 3.8;
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data[ 2][ 0]=1.2; data[ 2][ 1]=2.5; data[ 2][ 2]=0.0; data[ 2][ 3] = 4.8;
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data[ 3][ 0]=2.3; data[ 3][ 1]=1.5; data[ 3][ 2]=9.2; data[ 3][ 3] = 4.3;
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data[ 4][ 0]=1.7; data[ 4][ 1]=0.7; data[ 4][ 2]=9.6; data[ 4][ 3] = 3.4;
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data[ 5][ 0]=0.0; data[ 5][ 1]=3.9; data[ 5][ 2]=9.8; data[ 5][ 3] = 5.1;
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data[ 6][ 0]=6.7; data[ 6][ 1]=3.9; data[ 6][ 2]=5.5; data[ 6][ 3] = 4.8;
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data[ 7][ 0]=0.0; data[ 7][ 1]=6.3; data[ 7][ 2]=5.7; data[ 7][ 3] = 4.3;
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data[ 8][ 0]=5.7; data[ 8][ 1]=6.9; data[ 8][ 2]=5.6; data[ 8][ 3] = 4.3;
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data[ 9][ 0]=0.0; data[ 9][ 1]=2.2; data[ 9][ 2]=5.4; data[ 9][ 3] = 0.0;
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data[10][ 0]=3.8; data[10][ 1]=3.5; data[10][ 2]=5.5; data[10][ 3] = 9.6;
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data[11][ 0]=0.0; data[11][ 1]=2.3; data[11][ 2]=3.6; data[11][ 3] = 8.5;
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data[12][ 0]=4.1; data[12][ 1]=4.5; data[12][ 2]=5.8; data[12][ 3] = 7.6;
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mask[ 0][ 0]=1; mask[ 0][ 1]=1; mask[ 0][ 2]=1; mask[ 0][ 3] = 1;
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mask[ 1][ 0]=1; mask[ 1][ 1]=1; mask[ 1][ 2]=0; mask[ 1][ 3] = 1;
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mask[ 2][ 0]=1; mask[ 2][ 1]=1; mask[ 2][ 2]=0; mask[ 2][ 3] = 1;
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mask[ 3][ 0]=1; mask[ 3][ 1]=1; mask[ 3][ 2]=1; mask[ 3][ 3] = 1;
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mask[ 4][ 0]=1; mask[ 4][ 1]=1; mask[ 4][ 2]=1; mask[ 4][ 3] = 1;
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mask[ 5][ 0]=0; mask[ 5][ 1]=1; mask[ 5][ 2]=1; mask[ 5][ 3] = 1;
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mask[ 6][ 0]=1; mask[ 6][ 1]=1; mask[ 6][ 2]=1; mask[ 6][ 3] = 1;
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mask[ 7][ 0]=0; mask[ 7][ 1]=1; mask[ 7][ 2]=1; mask[ 7][ 3] = 1;
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mask[ 8][ 0]=1; mask[ 8][ 1]=1; mask[ 8][ 2]=1; mask[ 8][ 3] = 1;
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mask[ 9][ 0]=1; mask[ 9][ 1]=1; mask[ 9][ 2]=1; mask[ 9][ 3] = 0;
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mask[10][ 0]=1; mask[10][ 1]=1; mask[10][ 2]=1; mask[10][ 3] = 1;
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mask[11][ 0]=0; mask[11][ 1]=1; mask[11][ 2]=1; mask[11][ 3] = 1;
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mask[12][ 0]=1; mask[12][ 1]=1; mask[12][ 2]=1; mask[12][ 3] = 1;
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require 'pp'
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pp Flock.kmeans(6, data, mask)
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data/ext/cluster.c
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/* The C clustering library.
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* Copyright (C) 2002 Michiel Jan Laurens de Hoon.
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*
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* This library was written at the Laboratory of DNA Information Analysis,
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* Human Genome Center, Institute of Medical Science, University of Tokyo,
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* 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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* Contact: mdehoon 'AT' gsc.riken.jp
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*
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* Permission to use, copy, modify, and distribute this software and its
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* documentation with or without modifications and for any purpose and
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* without fee is hereby granted, provided that any copyright notices
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* appear in all copies and that both those copyright notices and this
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* permission notice appear in supporting documentation, and that the
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* names of the contributors or copyright holders not be used in
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* advertising or publicity pertaining to distribution of the software
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* without specific prior permission.
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*
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* THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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* WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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* WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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* CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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* OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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* OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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* OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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* OR PERFORMANCE OF THIS SOFTWARE.
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*
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*/
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#include <time.h>
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#include <stdlib.h>
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#include <math.h>
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#include <float.h>
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#include <limits.h>
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#include <string.h>
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#include "cluster.h"
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#ifdef WINDOWS
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# include <windows.h>
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#endif
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/* ************************************************************************ */
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#ifdef WINDOWS
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/* Then we make a Windows DLL */
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int WINAPI
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clusterdll_init (HANDLE h, DWORD reason, void* foo)
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{
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return 1;
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}
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#endif
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/* ************************************************************************ */
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double mean(int n, double x[])
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{ double result = 0.;
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int i;
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for (i = 0; i < n; i++) result += x[i];
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result /= n;
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return result;
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}
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/* ************************************************************************ */
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double median (int n, double x[])
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/*
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Find the median of X(1), ... , X(N), using as much of the quicksort
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algorithm as is needed to isolate it.
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N.B. On exit, the array X is partially ordered.
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Based on Alan J. Miller's median.f90 routine.
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*/
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{ int i, j;
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int nr = n / 2;
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int nl = nr - 1;
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int even = 0;
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/* hi & lo are position limits encompassing the median. */
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int lo = 0;
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int hi = n-1;
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if (n==2*nr) even = 1;
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if (n<3)
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{ if (n<1) return 0.;
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if (n == 1) return x[0];
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return 0.5*(x[0]+x[1]);
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}
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/* Find median of 1st, middle & last values. */
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do
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{ int loop;
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int mid = (lo + hi)/2;
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double result = x[mid];
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double xlo = x[lo];
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double xhi = x[hi];
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if (xhi<xlo)
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{ double temp = xlo;
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xlo = xhi;
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xhi = temp;
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}
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if (result>xhi) result = xhi;
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else if (result<xlo) result = xlo;
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/* The basic quicksort algorithm to move all values <= the sort key (XMED)
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* to the left-hand end, and all higher values to the other end.
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*/
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i = lo;
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j = hi;
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do
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{ while (x[i]<result) i++;
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while (x[j]>result) j--;
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loop = 0;
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if (i<j)
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{ double temp = x[i];
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x[i] = x[j];
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x[j] = temp;
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i++;
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j--;
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if (i<=j) loop = 1;
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}
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} while (loop); /* Decide which half the median is in. */
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if (even)
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{ if (j==nl && i==nr)
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/* Special case, n even, j = n/2 & i = j + 1, so the median is
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* between the two halves of the series. Find max. of the first
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* half & min. of the second half, then average.
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*/
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{ int k;
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double xmax = x[0];
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double xmin = x[n-1];
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for (k = lo; k <= j; k++) xmax = max(xmax,x[k]);
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for (k = i; k <= hi; k++) xmin = min(xmin,x[k]);
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return 0.5*(xmin + xmax);
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}
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if (j<nl) lo = i;
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if (i>nr) hi = j;
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if (i==j)
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{ if (i==nl) lo = nl;
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if (j==nr) hi = nr;
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}
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}
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else
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{ if (j<nr) lo = i;
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if (i>nr) hi = j;
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/* Test whether median has been isolated. */
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if (i==j && i==nr) return result;
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}
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}
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while (lo<hi-1);
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if (even) return (0.5*(x[nl]+x[nr]));
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if (x[lo]>x[hi])
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{ double temp = x[lo];
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x[lo] = x[hi];
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x[hi] = temp;
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}
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return x[nr];
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}
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+
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/* ********************************************************************** */
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static const double* sortdata = NULL; /* used in the quicksort algorithm */
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/* ---------------------------------------------------------------------- */
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static
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+
int compare(const void* a, const void* b)
|
165
|
+
/* Helper function for sort. Previously, this was a nested function under
|
166
|
+
* sort, which is not allowed under ANSI C.
|
167
|
+
*/
|
168
|
+
{ const int i1 = *(const int*)a;
|
169
|
+
const int i2 = *(const int*)b;
|
170
|
+
const double term1 = sortdata[i1];
|
171
|
+
const double term2 = sortdata[i2];
|
172
|
+
if (term1 < term2) return -1;
|
173
|
+
if (term1 > term2) return +1;
|
174
|
+
return 0;
|
175
|
+
}
|
176
|
+
|
177
|
+
/* ---------------------------------------------------------------------- */
|
178
|
+
|
179
|
+
void sort(int n, const double data[], int index[])
|
180
|
+
/* Sets up an index table given the data, such that data[index[]] is in
|
181
|
+
* increasing order. Sorting is done on the indices; the array data
|
182
|
+
* is unchanged.
|
183
|
+
*/
|
184
|
+
{ int i;
|
185
|
+
sortdata = data;
|
186
|
+
for (i = 0; i < n; i++) index[i] = i;
|
187
|
+
qsort(index, n, sizeof(int), compare);
|
188
|
+
}
|
189
|
+
|
190
|
+
/* ********************************************************************** */
|
191
|
+
|
192
|
+
static double* getrank (int n, double data[])
|
193
|
+
/* Calculates the ranks of the elements in the array data. Two elements with
|
194
|
+
* the same value get the same rank, equal to the average of the ranks had the
|
195
|
+
* elements different values. The ranks are returned as a newly allocated
|
196
|
+
* array that should be freed by the calling routine. If getrank fails due to
|
197
|
+
* a memory allocation error, it returns NULL.
|
198
|
+
*/
|
199
|
+
{ int i;
|
200
|
+
double* rank;
|
201
|
+
int* index;
|
202
|
+
rank = malloc(n*sizeof(double));
|
203
|
+
if (!rank) return NULL;
|
204
|
+
index = malloc(n*sizeof(int));
|
205
|
+
if (!index)
|
206
|
+
{ free(rank);
|
207
|
+
return NULL;
|
208
|
+
}
|
209
|
+
/* Call sort to get an index table */
|
210
|
+
sort (n, data, index);
|
211
|
+
/* Build a rank table */
|
212
|
+
for (i = 0; i < n; i++) rank[index[i]] = i;
|
213
|
+
/* Fix for equal ranks */
|
214
|
+
i = 0;
|
215
|
+
while (i < n)
|
216
|
+
{ int m;
|
217
|
+
double value = data[index[i]];
|
218
|
+
int j = i + 1;
|
219
|
+
while (j < n && data[index[j]] == value) j++;
|
220
|
+
m = j - i; /* number of equal ranks found */
|
221
|
+
value = rank[index[i]] + (m-1)/2.;
|
222
|
+
for (j = i; j < i + m; j++) rank[index[j]] = value;
|
223
|
+
i += m;
|
224
|
+
}
|
225
|
+
free (index);
|
226
|
+
return rank;
|
227
|
+
}
|
228
|
+
|
229
|
+
/* ---------------------------------------------------------------------- */
|
230
|
+
|
231
|
+
static int
|
232
|
+
makedatamask(int nrows, int ncols, double*** pdata, int*** pmask)
|
233
|
+
{ int i;
|
234
|
+
double** data;
|
235
|
+
int** mask;
|
236
|
+
data = malloc(nrows*sizeof(double*));
|
237
|
+
if(!data) return 0;
|
238
|
+
mask = malloc(nrows*sizeof(int*));
|
239
|
+
if(!mask)
|
240
|
+
{ free(data);
|
241
|
+
return 0;
|
242
|
+
}
|
243
|
+
for (i = 0; i < nrows; i++)
|
244
|
+
{ data[i] = malloc(ncols*sizeof(double));
|
245
|
+
if(!data[i]) break;
|
246
|
+
mask[i] = malloc(ncols*sizeof(int));
|
247
|
+
if(!mask[i])
|
248
|
+
{ free(data[i]);
|
249
|
+
break;
|
250
|
+
}
|
251
|
+
}
|
252
|
+
if (i==nrows) /* break not encountered */
|
253
|
+
{ *pdata = data;
|
254
|
+
*pmask = mask;
|
255
|
+
return 1;
|
256
|
+
}
|
257
|
+
*pdata = NULL;
|
258
|
+
*pmask = NULL;
|
259
|
+
nrows = i;
|
260
|
+
for (i = 0; i < nrows; i++)
|
261
|
+
{ free(data[i]);
|
262
|
+
free(mask[i]);
|
263
|
+
}
|
264
|
+
free(data);
|
265
|
+
free(mask);
|
266
|
+
return 0;
|
267
|
+
}
|
268
|
+
|
269
|
+
/* ---------------------------------------------------------------------- */
|
270
|
+
|
271
|
+
static void
|
272
|
+
freedatamask(int n, double** data, int** mask)
|
273
|
+
{ int i;
|
274
|
+
for (i = 0; i < n; i++)
|
275
|
+
{ free(mask[i]);
|
276
|
+
free(data[i]);
|
277
|
+
}
|
278
|
+
free(mask);
|
279
|
+
free(data);
|
280
|
+
}
|
281
|
+
|
282
|
+
/* ---------------------------------------------------------------------- */
|
283
|
+
|
284
|
+
static
|
285
|
+
double find_closest_pair(int n, double** distmatrix, int* ip, int* jp)
|
286
|
+
/*
|
287
|
+
This function searches the distance matrix to find the pair with the shortest
|
288
|
+
distance between them. The indices of the pair are returned in ip and jp; the
|
289
|
+
distance itself is returned by the function.
|
290
|
+
|
291
|
+
n (input) int
|
292
|
+
The number of elements in the distance matrix.
|
293
|
+
|
294
|
+
distmatrix (input) double**
|
295
|
+
A ragged array containing the distance matrix. The number of columns in each
|
296
|
+
row is one less than the row index.
|
297
|
+
|
298
|
+
ip (output) int*
|
299
|
+
A pointer to the integer that is to receive the first index of the pair with
|
300
|
+
the shortest distance.
|
301
|
+
|
302
|
+
jp (output) int*
|
303
|
+
A pointer to the integer that is to receive the second index of the pair with
|
304
|
+
the shortest distance.
|
305
|
+
*/
|
306
|
+
{ int i, j;
|
307
|
+
double temp;
|
308
|
+
double distance = distmatrix[1][0];
|
309
|
+
*ip = 1;
|
310
|
+
*jp = 0;
|
311
|
+
for (i = 1; i < n; i++)
|
312
|
+
{ for (j = 0; j < i; j++)
|
313
|
+
{ temp = distmatrix[i][j];
|
314
|
+
if (temp<distance)
|
315
|
+
{ distance = temp;
|
316
|
+
*ip = i;
|
317
|
+
*jp = j;
|
318
|
+
}
|
319
|
+
}
|
320
|
+
}
|
321
|
+
return distance;
|
322
|
+
}
|
323
|
+
|
324
|
+
/* ********************************************************************* */
|
325
|
+
|
326
|
+
static int svd(int m, int n, double** u, double w[], double** vt)
|
327
|
+
/*
|
328
|
+
* This subroutine is a translation of the Algol procedure svd,
|
329
|
+
* Num. Math. 14, 403-420(1970) by Golub and Reinsch.
|
330
|
+
* Handbook for Auto. Comp., Vol II-Linear Algebra, 134-151(1971).
|
331
|
+
*
|
332
|
+
* This subroutine determines the singular value decomposition
|
333
|
+
* t
|
334
|
+
* A=usv of a real m by n rectangular matrix, where m is greater
|
335
|
+
* than or equal to n. Householder bidiagonalization and a variant
|
336
|
+
* of the QR algorithm are used.
|
337
|
+
*
|
338
|
+
*
|
339
|
+
* On input.
|
340
|
+
*
|
341
|
+
* m is the number of rows of A (and u).
|
342
|
+
*
|
343
|
+
* n is the number of columns of A (and u) and the order of v.
|
344
|
+
*
|
345
|
+
* u contains the rectangular input matrix A to be decomposed.
|
346
|
+
*
|
347
|
+
* On output.
|
348
|
+
*
|
349
|
+
* the routine returns an integer ierr equal to
|
350
|
+
* 0 to indicate a normal return,
|
351
|
+
* k if the k-th singular value has not been
|
352
|
+
* determined after 30 iterations,
|
353
|
+
* -1 if memory allocation fails.
|
354
|
+
*
|
355
|
+
*
|
356
|
+
* w contains the n (non-negative) singular values of a (the
|
357
|
+
* diagonal elements of s). they are unordered. if an
|
358
|
+
* error exit is made, the singular values should be correct
|
359
|
+
* for indices ierr+1,ierr+2,...,n.
|
360
|
+
*
|
361
|
+
*
|
362
|
+
* u contains the matrix u (orthogonal column vectors) of the
|
363
|
+
* decomposition.
|
364
|
+
* if an error exit is made, the columns of u corresponding
|
365
|
+
* to indices of correct singular values should be correct.
|
366
|
+
*
|
367
|
+
* t
|
368
|
+
* vt contains the matrix v (orthogonal) of the decomposition.
|
369
|
+
* if an error exit is made, the columns of v corresponding
|
370
|
+
* to indices of correct singular values should be correct.
|
371
|
+
*
|
372
|
+
*
|
373
|
+
* Questions and comments should be directed to B. S. Garbow,
|
374
|
+
* Applied Mathematics division, Argonne National Laboratory
|
375
|
+
*
|
376
|
+
* Modified to eliminate machep
|
377
|
+
*
|
378
|
+
* Translated to C by Michiel de Hoon, Human Genome Center,
|
379
|
+
* University of Tokyo, for inclusion in the C Clustering Library.
|
380
|
+
* This routine is less general than the original svd routine, as
|
381
|
+
* it focuses on the singular value decomposition as needed for
|
382
|
+
* clustering. In particular,
|
383
|
+
* - We calculate both u and v in all cases
|
384
|
+
* - We pass the input array A via u; this array is subsequently
|
385
|
+
* overwritten.
|
386
|
+
* - We allocate for the array rv1, used as a working space,
|
387
|
+
* internally in this routine, instead of passing it as an
|
388
|
+
* argument. If the allocation fails, svd returns -1.
|
389
|
+
* 2003.06.05
|
390
|
+
*/
|
391
|
+
{ int i, j, k, i1, k1, l1, its;
|
392
|
+
double c,f,h,s,x,y,z;
|
393
|
+
int l = 0;
|
394
|
+
int ierr = 0;
|
395
|
+
double g = 0.0;
|
396
|
+
double scale = 0.0;
|
397
|
+
double anorm = 0.0;
|
398
|
+
double* rv1 = malloc(n*sizeof(double));
|
399
|
+
if (!rv1) return -1;
|
400
|
+
if (m >= n)
|
401
|
+
{ /* Householder reduction to bidiagonal form */
|
402
|
+
for (i = 0; i < n; i++)
|
403
|
+
{ l = i + 1;
|
404
|
+
rv1[i] = scale * g;
|
405
|
+
g = 0.0;
|
406
|
+
s = 0.0;
|
407
|
+
scale = 0.0;
|
408
|
+
for (k = i; k < m; k++) scale += fabs(u[k][i]);
|
409
|
+
if (scale != 0.0)
|
410
|
+
{ for (k = i; k < m; k++)
|
411
|
+
{ u[k][i] /= scale;
|
412
|
+
s += u[k][i]*u[k][i];
|
413
|
+
}
|
414
|
+
f = u[i][i];
|
415
|
+
g = (f >= 0) ? -sqrt(s) : sqrt(s);
|
416
|
+
h = f * g - s;
|
417
|
+
u[i][i] = f - g;
|
418
|
+
if (i < n-1)
|
419
|
+
{ for (j = l; j < n; j++)
|
420
|
+
{ s = 0.0;
|
421
|
+
for (k = i; k < m; k++) s += u[k][i] * u[k][j];
|
422
|
+
f = s / h;
|
423
|
+
for (k = i; k < m; k++) u[k][j] += f * u[k][i];
|
424
|
+
}
|
425
|
+
}
|
426
|
+
for (k = i; k < m; k++) u[k][i] *= scale;
|
427
|
+
}
|
428
|
+
w[i] = scale * g;
|
429
|
+
g = 0.0;
|
430
|
+
s = 0.0;
|
431
|
+
scale = 0.0;
|
432
|
+
if (i<n-1)
|
433
|
+
{ for (k = l; k < n; k++) scale += fabs(u[i][k]);
|
434
|
+
if (scale != 0.0)
|
435
|
+
{ for (k = l; k < n; k++)
|
436
|
+
{ u[i][k] /= scale;
|
437
|
+
s += u[i][k] * u[i][k];
|
438
|
+
}
|
439
|
+
f = u[i][l];
|
440
|
+
g = (f >= 0) ? -sqrt(s) : sqrt(s);
|
441
|
+
h = f * g - s;
|
442
|
+
u[i][l] = f - g;
|
443
|
+
for (k = l; k < n; k++) rv1[k] = u[i][k] / h;
|
444
|
+
for (j = l; j < m; j++)
|
445
|
+
{ s = 0.0;
|
446
|
+
for (k = l; k < n; k++) s += u[j][k] * u[i][k];
|
447
|
+
for (k = l; k < n; k++) u[j][k] += s * rv1[k];
|
448
|
+
}
|
449
|
+
for (k = l; k < n; k++) u[i][k] *= scale;
|
450
|
+
}
|
451
|
+
}
|
452
|
+
anorm = max(anorm,fabs(w[i])+fabs(rv1[i]));
|
453
|
+
}
|
454
|
+
/* accumulation of right-hand transformations */
|
455
|
+
for (i = n-1; i>=0; i--)
|
456
|
+
{ if (i < n-1)
|
457
|
+
{ if (g != 0.0)
|
458
|
+
{ for (j = l; j < n; j++) vt[i][j] = (u[i][j] / u[i][l]) / g;
|
459
|
+
/* double division avoids possible underflow */
|
460
|
+
for (j = l; j < n; j++)
|
461
|
+
{ s = 0.0;
|
462
|
+
for (k = l; k < n; k++) s += u[i][k] * vt[j][k];
|
463
|
+
for (k = l; k < n; k++) vt[j][k] += s * vt[i][k];
|
464
|
+
}
|
465
|
+
}
|
466
|
+
}
|
467
|
+
for (j = l; j < n; j++)
|
468
|
+
{ vt[j][i] = 0.0;
|
469
|
+
vt[i][j] = 0.0;
|
470
|
+
}
|
471
|
+
vt[i][i] = 1.0;
|
472
|
+
g = rv1[i];
|
473
|
+
l = i;
|
474
|
+
}
|
475
|
+
/* accumulation of left-hand transformations */
|
476
|
+
for (i = n-1; i >= 0; i--)
|
477
|
+
{ l = i + 1;
|
478
|
+
g = w[i];
|
479
|
+
if (i!=n-1)
|
480
|
+
for (j = l; j < n; j++) u[i][j] = 0.0;
|
481
|
+
if (g!=0.0)
|
482
|
+
{ if (i!=n-1)
|
483
|
+
{ for (j = l; j < n; j++)
|
484
|
+
{ s = 0.0;
|
485
|
+
for (k = l; k < m; k++) s += u[k][i] * u[k][j];
|
486
|
+
/* double division avoids possible underflow */
|
487
|
+
f = (s / u[i][i]) / g;
|
488
|
+
for (k = i; k < m; k++) u[k][j] += f * u[k][i];
|
489
|
+
}
|
490
|
+
}
|
491
|
+
for (j = i; j < m; j++) u[j][i] /= g;
|
492
|
+
}
|
493
|
+
else
|
494
|
+
for (j = i; j < m; j++) u[j][i] = 0.0;
|
495
|
+
u[i][i] += 1.0;
|
496
|
+
}
|
497
|
+
/* diagonalization of the bidiagonal form */
|
498
|
+
for (k = n-1; k >= 0; k--)
|
499
|
+
{ k1 = k-1;
|
500
|
+
its = 0;
|
501
|
+
while(1)
|
502
|
+
/* test for splitting */
|
503
|
+
{ for (l = k; l >= 0; l--)
|
504
|
+
{ l1 = l-1;
|
505
|
+
if (fabs(rv1[l]) + anorm == anorm) break;
|
506
|
+
/* rv1[0] is always zero, so there is no exit
|
507
|
+
* through the bottom of the loop */
|
508
|
+
if (fabs(w[l1]) + anorm == anorm)
|
509
|
+
/* cancellation of rv1[l] if l greater than 0 */
|
510
|
+
{ c = 0.0;
|
511
|
+
s = 1.0;
|
512
|
+
for (i = l; i <= k; i++)
|
513
|
+
{ f = s * rv1[i];
|
514
|
+
rv1[i] *= c;
|
515
|
+
if (fabs(f) + anorm == anorm) break;
|
516
|
+
g = w[i];
|
517
|
+
h = sqrt(f*f+g*g);
|
518
|
+
w[i] = h;
|
519
|
+
c = g / h;
|
520
|
+
s = -f / h;
|
521
|
+
for (j = 0; j < m; j++)
|
522
|
+
{ y = u[j][l1];
|
523
|
+
z = u[j][i];
|
524
|
+
u[j][l1] = y * c + z * s;
|
525
|
+
u[j][i] = -y * s + z * c;
|
526
|
+
}
|
527
|
+
}
|
528
|
+
break;
|
529
|
+
}
|
530
|
+
}
|
531
|
+
/* test for convergence */
|
532
|
+
z = w[k];
|
533
|
+
if (l==k) /* convergence */
|
534
|
+
{ if (z < 0.0)
|
535
|
+
/* w[k] is made non-negative */
|
536
|
+
{ w[k] = -z;
|
537
|
+
for (j = 0; j < n; j++) vt[k][j] = -vt[k][j];
|
538
|
+
}
|
539
|
+
break;
|
540
|
+
}
|
541
|
+
else if (its==30)
|
542
|
+
{ ierr = k;
|
543
|
+
break;
|
544
|
+
}
|
545
|
+
else
|
546
|
+
/* shift from bottom 2 by 2 minor */
|
547
|
+
{ its++;
|
548
|
+
x = w[l];
|
549
|
+
y = w[k1];
|
550
|
+
g = rv1[k1];
|
551
|
+
h = rv1[k];
|
552
|
+
f = ((y - z) * (y + z) + (g - h) * (g + h)) / (2.0 * h * y);
|
553
|
+
g = sqrt(f*f+1.0);
|
554
|
+
f = ((x - z) * (x + z) + h * (y / (f + (f >= 0 ? g : -g)) - h)) / x;
|
555
|
+
/* next qr transformation */
|
556
|
+
c = 1.0;
|
557
|
+
s = 1.0;
|
558
|
+
for (i1 = l; i1 <= k1; i1++)
|
559
|
+
{ i = i1 + 1;
|
560
|
+
g = rv1[i];
|
561
|
+
y = w[i];
|
562
|
+
h = s * g;
|
563
|
+
g = c * g;
|
564
|
+
z = sqrt(f*f+h*h);
|
565
|
+
rv1[i1] = z;
|
566
|
+
c = f / z;
|
567
|
+
s = h / z;
|
568
|
+
f = x * c + g * s;
|
569
|
+
g = -x * s + g * c;
|
570
|
+
h = y * s;
|
571
|
+
y = y * c;
|
572
|
+
for (j = 0; j < n; j++)
|
573
|
+
{ x = vt[i1][j];
|
574
|
+
z = vt[i][j];
|
575
|
+
vt[i1][j] = x * c + z * s;
|
576
|
+
vt[i][j] = -x * s + z * c;
|
577
|
+
}
|
578
|
+
z = sqrt(f*f+h*h);
|
579
|
+
w[i1] = z;
|
580
|
+
/* rotation can be arbitrary if z is zero */
|
581
|
+
if (z!=0.0)
|
582
|
+
{ c = f / z;
|
583
|
+
s = h / z;
|
584
|
+
}
|
585
|
+
f = c * g + s * y;
|
586
|
+
x = -s * g + c * y;
|
587
|
+
for (j = 0; j < m; j++)
|
588
|
+
{ y = u[j][i1];
|
589
|
+
z = u[j][i];
|
590
|
+
u[j][i1] = y * c + z * s;
|
591
|
+
u[j][i] = -y * s + z * c;
|
592
|
+
}
|
593
|
+
}
|
594
|
+
rv1[l] = 0.0;
|
595
|
+
rv1[k] = f;
|
596
|
+
w[k] = x;
|
597
|
+
}
|
598
|
+
}
|
599
|
+
}
|
600
|
+
}
|
601
|
+
else /* m < n */
|
602
|
+
{ /* Householder reduction to bidiagonal form */
|
603
|
+
for (i = 0; i < m; i++)
|
604
|
+
{ l = i + 1;
|
605
|
+
rv1[i] = scale * g;
|
606
|
+
g = 0.0;
|
607
|
+
s = 0.0;
|
608
|
+
scale = 0.0;
|
609
|
+
for (k = i; k < n; k++) scale += fabs(u[i][k]);
|
610
|
+
if (scale != 0.0)
|
611
|
+
{ for (k = i; k < n; k++)
|
612
|
+
{ u[i][k] /= scale;
|
613
|
+
s += u[i][k]*u[i][k];
|
614
|
+
}
|
615
|
+
f = u[i][i];
|
616
|
+
g = (f >= 0) ? -sqrt(s) : sqrt(s);
|
617
|
+
h = f * g - s;
|
618
|
+
u[i][i] = f - g;
|
619
|
+
if (i < m-1)
|
620
|
+
{ for (j = l; j < m; j++)
|
621
|
+
{ s = 0.0;
|
622
|
+
for (k = i; k < n; k++) s += u[i][k] * u[j][k];
|
623
|
+
f = s / h;
|
624
|
+
for (k = i; k < n; k++) u[j][k] += f * u[i][k];
|
625
|
+
}
|
626
|
+
}
|
627
|
+
for (k = i; k < n; k++) u[i][k] *= scale;
|
628
|
+
}
|
629
|
+
w[i] = scale * g;
|
630
|
+
g = 0.0;
|
631
|
+
s = 0.0;
|
632
|
+
scale = 0.0;
|
633
|
+
if (i<m-1)
|
634
|
+
{ for (k = l; k < m; k++) scale += fabs(u[k][i]);
|
635
|
+
if (scale != 0.0)
|
636
|
+
{ for (k = l; k < m; k++)
|
637
|
+
{ u[k][i] /= scale;
|
638
|
+
s += u[k][i] * u[k][i];
|
639
|
+
}
|
640
|
+
f = u[l][i];
|
641
|
+
g = (f >= 0) ? -sqrt(s) : sqrt(s);
|
642
|
+
h = f * g - s;
|
643
|
+
u[l][i] = f - g;
|
644
|
+
for (k = l; k < m; k++) rv1[k] = u[k][i] / h;
|
645
|
+
for (j = l; j < n; j++)
|
646
|
+
{ s = 0.0;
|
647
|
+
for (k = l; k < m; k++) s += u[k][j] * u[k][i];
|
648
|
+
for (k = l; k < m; k++) u[k][j] += s * rv1[k];
|
649
|
+
}
|
650
|
+
for (k = l; k < m; k++) u[k][i] *= scale;
|
651
|
+
}
|
652
|
+
}
|
653
|
+
anorm = max(anorm,fabs(w[i])+fabs(rv1[i]));
|
654
|
+
}
|
655
|
+
/* accumulation of right-hand transformations */
|
656
|
+
for (i = m-1; i>=0; i--)
|
657
|
+
{ if (i < m-1)
|
658
|
+
{ if (g != 0.0)
|
659
|
+
{ for (j = l; j < m; j++) vt[j][i] = (u[j][i] / u[l][i]) / g;
|
660
|
+
/* double division avoids possible underflow */
|
661
|
+
for (j = l; j < m; j++)
|
662
|
+
{ s = 0.0;
|
663
|
+
for (k = l; k < m; k++) s += u[k][i] * vt[k][j];
|
664
|
+
for (k = l; k < m; k++) vt[k][j] += s * vt[k][i];
|
665
|
+
}
|
666
|
+
}
|
667
|
+
}
|
668
|
+
for (j = l; j < m; j++)
|
669
|
+
{ vt[i][j] = 0.0;
|
670
|
+
vt[j][i] = 0.0;
|
671
|
+
}
|
672
|
+
vt[i][i] = 1.0;
|
673
|
+
g = rv1[i];
|
674
|
+
l = i;
|
675
|
+
}
|
676
|
+
/* accumulation of left-hand transformations */
|
677
|
+
for (i = m-1; i >= 0; i--)
|
678
|
+
{ l = i + 1;
|
679
|
+
g = w[i];
|
680
|
+
if (i!=m-1)
|
681
|
+
for (j = l; j < m; j++) u[j][i] = 0.0;
|
682
|
+
if (g!=0.0)
|
683
|
+
{ if (i!=m-1)
|
684
|
+
{ for (j = l; j < m; j++)
|
685
|
+
{ s = 0.0;
|
686
|
+
for (k = l; k < n; k++) s += u[i][k] * u[j][k];
|
687
|
+
/* double division avoids possible underflow */
|
688
|
+
f = (s / u[i][i]) / g;
|
689
|
+
for (k = i; k < n; k++) u[j][k] += f * u[i][k];
|
690
|
+
}
|
691
|
+
}
|
692
|
+
for (j = i; j < n; j++) u[i][j] /= g;
|
693
|
+
}
|
694
|
+
else
|
695
|
+
for (j = i; j < n; j++) u[i][j] = 0.0;
|
696
|
+
u[i][i] += 1.0;
|
697
|
+
}
|
698
|
+
/* diagonalization of the bidiagonal form */
|
699
|
+
for (k = m-1; k >= 0; k--)
|
700
|
+
{ k1 = k-1;
|
701
|
+
its = 0;
|
702
|
+
while(1)
|
703
|
+
/* test for splitting */
|
704
|
+
{ for (l = k; l >= 0; l--)
|
705
|
+
{ l1 = l-1;
|
706
|
+
if (fabs(rv1[l]) + anorm == anorm) break;
|
707
|
+
/* rv1[0] is always zero, so there is no exit
|
708
|
+
* through the bottom of the loop */
|
709
|
+
if (fabs(w[l1]) + anorm == anorm)
|
710
|
+
/* cancellation of rv1[l] if l greater than 0 */
|
711
|
+
{ c = 0.0;
|
712
|
+
s = 1.0;
|
713
|
+
for (i = l; i <= k; i++)
|
714
|
+
{ f = s * rv1[i];
|
715
|
+
rv1[i] *= c;
|
716
|
+
if (fabs(f) + anorm == anorm) break;
|
717
|
+
g = w[i];
|
718
|
+
h = sqrt(f*f+g*g);
|
719
|
+
w[i] = h;
|
720
|
+
c = g / h;
|
721
|
+
s = -f / h;
|
722
|
+
for (j = 0; j < n; j++)
|
723
|
+
{ y = u[l1][j];
|
724
|
+
z = u[i][j];
|
725
|
+
u[l1][j] = y * c + z * s;
|
726
|
+
u[i][j] = -y * s + z * c;
|
727
|
+
}
|
728
|
+
}
|
729
|
+
break;
|
730
|
+
}
|
731
|
+
}
|
732
|
+
/* test for convergence */
|
733
|
+
z = w[k];
|
734
|
+
if (l==k) /* convergence */
|
735
|
+
{ if (z < 0.0)
|
736
|
+
/* w[k] is made non-negative */
|
737
|
+
{ w[k] = -z;
|
738
|
+
for (j = 0; j < m; j++) vt[j][k] = -vt[j][k];
|
739
|
+
}
|
740
|
+
break;
|
741
|
+
}
|
742
|
+
else if (its==30)
|
743
|
+
{ ierr = k;
|
744
|
+
break;
|
745
|
+
}
|
746
|
+
else
|
747
|
+
/* shift from bottom 2 by 2 minor */
|
748
|
+
{ its++;
|
749
|
+
x = w[l];
|
750
|
+
y = w[k1];
|
751
|
+
g = rv1[k1];
|
752
|
+
h = rv1[k];
|
753
|
+
f = ((y - z) * (y + z) + (g - h) * (g + h)) / (2.0 * h * y);
|
754
|
+
g = sqrt(f*f+1.0);
|
755
|
+
f = ((x - z) * (x + z) + h * (y / (f + (f >= 0 ? g : -g)) - h)) / x;
|
756
|
+
/* next qr transformation */
|
757
|
+
c = 1.0;
|
758
|
+
s = 1.0;
|
759
|
+
for (i1 = l; i1 <= k1; i1++)
|
760
|
+
{ i = i1 + 1;
|
761
|
+
g = rv1[i];
|
762
|
+
y = w[i];
|
763
|
+
h = s * g;
|
764
|
+
g = c * g;
|
765
|
+
z = sqrt(f*f+h*h);
|
766
|
+
rv1[i1] = z;
|
767
|
+
c = f / z;
|
768
|
+
s = h / z;
|
769
|
+
f = x * c + g * s;
|
770
|
+
g = -x * s + g * c;
|
771
|
+
h = y * s;
|
772
|
+
y = y * c;
|
773
|
+
for (j = 0; j < m; j++)
|
774
|
+
{ x = vt[j][i1];
|
775
|
+
z = vt[j][i];
|
776
|
+
vt[j][i1] = x * c + z * s;
|
777
|
+
vt[j][i] = -x * s + z * c;
|
778
|
+
}
|
779
|
+
z = sqrt(f*f+h*h);
|
780
|
+
w[i1] = z;
|
781
|
+
/* rotation can be arbitrary if z is zero */
|
782
|
+
if (z!=0.0)
|
783
|
+
{ c = f / z;
|
784
|
+
s = h / z;
|
785
|
+
}
|
786
|
+
f = c * g + s * y;
|
787
|
+
x = -s * g + c * y;
|
788
|
+
for (j = 0; j < n; j++)
|
789
|
+
{ y = u[i1][j];
|
790
|
+
z = u[i][j];
|
791
|
+
u[i1][j] = y * c + z * s;
|
792
|
+
u[i][j] = -y * s + z * c;
|
793
|
+
}
|
794
|
+
}
|
795
|
+
rv1[l] = 0.0;
|
796
|
+
rv1[k] = f;
|
797
|
+
w[k] = x;
|
798
|
+
}
|
799
|
+
}
|
800
|
+
}
|
801
|
+
}
|
802
|
+
free(rv1);
|
803
|
+
return ierr;
|
804
|
+
}
|
805
|
+
|
806
|
+
/* ********************************************************************* */
|
807
|
+
|
808
|
+
int pca(int nrows, int ncolumns, double** u, double** v, double* w)
|
809
|
+
/*
|
810
|
+
Purpose
|
811
|
+
=======
|
812
|
+
|
813
|
+
This subroutine uses the singular value decomposition to perform principal
|
814
|
+
components analysis of a real nrows by ncolumns rectangular matrix.
|
815
|
+
|
816
|
+
Arguments
|
817
|
+
=========
|
818
|
+
|
819
|
+
nrows (input) int
|
820
|
+
The number of rows in the matrix u.
|
821
|
+
|
822
|
+
ncolumns (input) int
|
823
|
+
The number of columns in the matrix v.
|
824
|
+
|
825
|
+
u (input) double[nrows][ncolumns]
|
826
|
+
On input, the array containing the data to which the principal component
|
827
|
+
analysis should be applied. The function assumes that the mean has already been
|
828
|
+
subtracted of each column, and hence that the mean of each column is zero.
|
829
|
+
On output, see below.
|
830
|
+
|
831
|
+
v (input) double[n][n], where n = min(nrows, ncolumns)
|
832
|
+
Not used on input.
|
833
|
+
|
834
|
+
w (input) double[n], where n = min(nrows, ncolumns)
|
835
|
+
Not used on input.
|
836
|
+
|
837
|
+
|
838
|
+
Return value
|
839
|
+
============
|
840
|
+
|
841
|
+
On output:
|
842
|
+
|
843
|
+
If nrows >= ncolumns, then
|
844
|
+
|
845
|
+
u contains the coordinates with respect to the principal components;
|
846
|
+
v contains the principal component vectors.
|
847
|
+
|
848
|
+
The dot product u . v reproduces the data that were passed in u.
|
849
|
+
|
850
|
+
|
851
|
+
If nrows < ncolumns, then
|
852
|
+
|
853
|
+
u contains the principal component vectors;
|
854
|
+
v contains the coordinates with respect to the principal components.
|
855
|
+
|
856
|
+
The dot product v . u reproduces the data that were passed in u.
|
857
|
+
|
858
|
+
The eigenvalues of the covariance matrix are returned in w.
|
859
|
+
|
860
|
+
The arrays u, v, and w are sorted according to eigenvalue, with the largest
|
861
|
+
eigenvalues appearing first.
|
862
|
+
|
863
|
+
The function returns 0 if successful, -1 if memory allocation fails, and a
|
864
|
+
positive integer if the singular value decomposition fails to converge.
|
865
|
+
*/
|
866
|
+
{
|
867
|
+
int i;
|
868
|
+
int j;
|
869
|
+
int error;
|
870
|
+
int* index = malloc(ncolumns*sizeof(int));
|
871
|
+
double* temp = malloc(ncolumns*sizeof(double));
|
872
|
+
if (!index || !temp)
|
873
|
+
{ if (index) free(index);
|
874
|
+
if (temp) free(temp);
|
875
|
+
return -1;
|
876
|
+
}
|
877
|
+
error = svd(nrows, ncolumns, u, w, v);
|
878
|
+
if (error==0)
|
879
|
+
{
|
880
|
+
if (nrows >= ncolumns)
|
881
|
+
{ for (j = 0; j < ncolumns; j++)
|
882
|
+
{ const double s = w[j];
|
883
|
+
for (i = 0; i < nrows; i++) u[i][j] *= s;
|
884
|
+
}
|
885
|
+
sort(ncolumns, w, index);
|
886
|
+
for (i = 0; i < ncolumns/2; i++)
|
887
|
+
{ j = index[i];
|
888
|
+
index[i] = index[ncolumns-1-i];
|
889
|
+
index[ncolumns-1-i] = j;
|
890
|
+
}
|
891
|
+
for (i = 0; i < nrows; i++)
|
892
|
+
{ for (j = 0; j < ncolumns; j++) temp[j] = u[i][index[j]];
|
893
|
+
for (j = 0; j < ncolumns; j++) u[i][j] = temp[j];
|
894
|
+
}
|
895
|
+
for (i = 0; i < ncolumns; i++)
|
896
|
+
{ for (j = 0; j < ncolumns; j++) temp[j] = v[index[j]][i];
|
897
|
+
for (j = 0; j < ncolumns; j++) v[j][i] = temp[j];
|
898
|
+
}
|
899
|
+
for (i = 0; i < ncolumns; i++) temp[i] = w[index[i]];
|
900
|
+
for (i = 0; i < ncolumns; i++) w[i] = temp[i];
|
901
|
+
}
|
902
|
+
else /* nrows < ncolumns */
|
903
|
+
{ for (j = 0; j < nrows; j++)
|
904
|
+
{ const double s = w[j];
|
905
|
+
for (i = 0; i < nrows; i++) v[i][j] *= s;
|
906
|
+
}
|
907
|
+
sort(nrows, w, index);
|
908
|
+
for (i = 0; i < nrows/2; i++)
|
909
|
+
{ j = index[i];
|
910
|
+
index[i] = index[nrows-1-i];
|
911
|
+
index[nrows-1-i] = j;
|
912
|
+
}
|
913
|
+
for (j = 0; j < ncolumns; j++)
|
914
|
+
{ for (i = 0; i < nrows; i++) temp[i] = u[index[i]][j];
|
915
|
+
for (i = 0; i < nrows; i++) u[i][j] = temp[i];
|
916
|
+
}
|
917
|
+
for (j = 0; j < nrows; j++)
|
918
|
+
{ for (i = 0; i < nrows; i++) temp[i] = v[j][index[i]];
|
919
|
+
for (i = 0; i < nrows; i++) v[j][i] = temp[i];
|
920
|
+
}
|
921
|
+
for (i = 0; i < nrows; i++) temp[i] = w[index[i]];
|
922
|
+
for (i = 0; i < nrows; i++) w[i] = temp[i];
|
923
|
+
}
|
924
|
+
}
|
925
|
+
free(index);
|
926
|
+
free(temp);
|
927
|
+
return error;
|
928
|
+
}
|
929
|
+
|
930
|
+
/* ********************************************************************* */
|
931
|
+
|
932
|
+
static
|
933
|
+
double euclid (int n, double** data1, double** data2, int** mask1, int** mask2,
|
934
|
+
const double weight[], int index1, int index2, int transpose)
|
935
|
+
|
936
|
+
/*
|
937
|
+
Purpose
|
938
|
+
=======
|
939
|
+
|
940
|
+
The euclid routine calculates the weighted Euclidean distance between two
|
941
|
+
rows or columns in a matrix.
|
942
|
+
|
943
|
+
Arguments
|
944
|
+
=========
|
945
|
+
|
946
|
+
n (input) int
|
947
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
948
|
+
of columns; otherwise, n is the number of rows.
|
949
|
+
|
950
|
+
data1 (input) double array
|
951
|
+
The data array containing the first vector.
|
952
|
+
|
953
|
+
data2 (input) double array
|
954
|
+
The data array containing the second vector.
|
955
|
+
|
956
|
+
mask1 (input) int array
|
957
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
958
|
+
data1[i][j] is missing.
|
959
|
+
|
960
|
+
mask2 (input) int array
|
961
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
962
|
+
data2[i][j] is missing.
|
963
|
+
|
964
|
+
weight (input) double[n]
|
965
|
+
The weights that are used to calculate the distance.
|
966
|
+
|
967
|
+
index1 (input) int
|
968
|
+
Index of the first row or column.
|
969
|
+
|
970
|
+
index2 (input) int
|
971
|
+
Index of the second row or column.
|
972
|
+
|
973
|
+
transpose (input) int
|
974
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
975
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
976
|
+
|
977
|
+
============================================================================
|
978
|
+
*/
|
979
|
+
{ double result = 0.;
|
980
|
+
double tweight = 0;
|
981
|
+
int i;
|
982
|
+
if (transpose==0) /* Calculate the distance between two rows */
|
983
|
+
{ for (i = 0; i < n; i++)
|
984
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
985
|
+
{ double term = data1[index1][i] - data2[index2][i];
|
986
|
+
result += weight[i]*term*term;
|
987
|
+
tweight += weight[i];
|
988
|
+
}
|
989
|
+
}
|
990
|
+
}
|
991
|
+
else
|
992
|
+
{ for (i = 0; i < n; i++)
|
993
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
994
|
+
{ double term = data1[i][index1] - data2[i][index2];
|
995
|
+
result += weight[i]*term*term;
|
996
|
+
tweight += weight[i];
|
997
|
+
}
|
998
|
+
}
|
999
|
+
}
|
1000
|
+
if (!tweight) return 0; /* usually due to empty clusters */
|
1001
|
+
result /= tweight;
|
1002
|
+
return result;
|
1003
|
+
}
|
1004
|
+
|
1005
|
+
/* ********************************************************************* */
|
1006
|
+
|
1007
|
+
static
|
1008
|
+
double cityblock (int n, double** data1, double** data2, int** mask1,
|
1009
|
+
int** mask2, const double weight[], int index1, int index2, int transpose)
|
1010
|
+
|
1011
|
+
/*
|
1012
|
+
Purpose
|
1013
|
+
=======
|
1014
|
+
|
1015
|
+
The cityblock routine calculates the weighted "City Block" distance between
|
1016
|
+
two rows or columns in a matrix. City Block distance is defined as the
|
1017
|
+
absolute value of X1-X2 plus the absolute value of Y1-Y2 plus..., which is
|
1018
|
+
equivalent to taking an "up and over" path.
|
1019
|
+
|
1020
|
+
Arguments
|
1021
|
+
=========
|
1022
|
+
|
1023
|
+
n (input) int
|
1024
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
1025
|
+
of columns; otherwise, n is the number of rows.
|
1026
|
+
|
1027
|
+
data1 (input) double array
|
1028
|
+
The data array containing the first vector.
|
1029
|
+
|
1030
|
+
data2 (input) double array
|
1031
|
+
The data array containing the second vector.
|
1032
|
+
|
1033
|
+
mask1 (input) int array
|
1034
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
1035
|
+
data1[i][j] is missing.
|
1036
|
+
|
1037
|
+
mask2 (input) int array
|
1038
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
1039
|
+
data2[i][j] is missing.
|
1040
|
+
|
1041
|
+
weight (input) double[n]
|
1042
|
+
The weights that are used to calculate the distance.
|
1043
|
+
|
1044
|
+
index1 (input) int
|
1045
|
+
Index of the first row or column.
|
1046
|
+
|
1047
|
+
index2 (input) int
|
1048
|
+
Index of the second row or column.
|
1049
|
+
|
1050
|
+
transpose (input) int
|
1051
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
1052
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
1053
|
+
|
1054
|
+
============================================================================ */
|
1055
|
+
{ double result = 0.;
|
1056
|
+
double tweight = 0;
|
1057
|
+
int i;
|
1058
|
+
if (transpose==0) /* Calculate the distance between two rows */
|
1059
|
+
{ for (i = 0; i < n; i++)
|
1060
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
1061
|
+
{ double term = data1[index1][i] - data2[index2][i];
|
1062
|
+
result = result + weight[i]*fabs(term);
|
1063
|
+
tweight += weight[i];
|
1064
|
+
}
|
1065
|
+
}
|
1066
|
+
}
|
1067
|
+
else
|
1068
|
+
{ for (i = 0; i < n; i++)
|
1069
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
1070
|
+
{ double term = data1[i][index1] - data2[i][index2];
|
1071
|
+
result = result + weight[i]*fabs(term);
|
1072
|
+
tweight += weight[i];
|
1073
|
+
}
|
1074
|
+
}
|
1075
|
+
}
|
1076
|
+
if (!tweight) return 0; /* usually due to empty clusters */
|
1077
|
+
result /= tweight;
|
1078
|
+
return result;
|
1079
|
+
}
|
1080
|
+
|
1081
|
+
/* ********************************************************************* */
|
1082
|
+
|
1083
|
+
static
|
1084
|
+
double correlation (int n, double** data1, double** data2, int** mask1,
|
1085
|
+
int** mask2, const double weight[], int index1, int index2, int transpose)
|
1086
|
+
/*
|
1087
|
+
Purpose
|
1088
|
+
=======
|
1089
|
+
|
1090
|
+
The correlation routine calculates the weighted Pearson distance between two
|
1091
|
+
rows or columns in a matrix. We define the Pearson distance as one minus the
|
1092
|
+
Pearson correlation.
|
1093
|
+
This definition yields a semi-metric: d(a,b) >= 0, and d(a,b) = 0 iff a = b.
|
1094
|
+
but the triangular inequality d(a,b) + d(b,c) >= d(a,c) does not hold
|
1095
|
+
(e.g., choose b = a + c).
|
1096
|
+
|
1097
|
+
Arguments
|
1098
|
+
=========
|
1099
|
+
|
1100
|
+
n (input) int
|
1101
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
1102
|
+
of columns; otherwise, n is the number of rows.
|
1103
|
+
|
1104
|
+
data1 (input) double array
|
1105
|
+
The data array containing the first vector.
|
1106
|
+
|
1107
|
+
data2 (input) double array
|
1108
|
+
The data array containing the second vector.
|
1109
|
+
|
1110
|
+
mask1 (input) int array
|
1111
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
1112
|
+
data1[i][j] is missing.
|
1113
|
+
|
1114
|
+
mask2 (input) int array
|
1115
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
1116
|
+
data2[i][j] is missing.
|
1117
|
+
|
1118
|
+
weight (input) double[n]
|
1119
|
+
The weights that are used to calculate the distance.
|
1120
|
+
|
1121
|
+
index1 (input) int
|
1122
|
+
Index of the first row or column.
|
1123
|
+
|
1124
|
+
index2 (input) int
|
1125
|
+
Index of the second row or column.
|
1126
|
+
|
1127
|
+
transpose (input) int
|
1128
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
1129
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
1130
|
+
============================================================================
|
1131
|
+
*/
|
1132
|
+
{ double result = 0.;
|
1133
|
+
double sum1 = 0.;
|
1134
|
+
double sum2 = 0.;
|
1135
|
+
double denom1 = 0.;
|
1136
|
+
double denom2 = 0.;
|
1137
|
+
double tweight = 0.;
|
1138
|
+
if (transpose==0) /* Calculate the distance between two rows */
|
1139
|
+
{ int i;
|
1140
|
+
for (i = 0; i < n; i++)
|
1141
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
1142
|
+
{ double term1 = data1[index1][i];
|
1143
|
+
double term2 = data2[index2][i];
|
1144
|
+
double w = weight[i];
|
1145
|
+
sum1 += w*term1;
|
1146
|
+
sum2 += w*term2;
|
1147
|
+
result += w*term1*term2;
|
1148
|
+
denom1 += w*term1*term1;
|
1149
|
+
denom2 += w*term2*term2;
|
1150
|
+
tweight += w;
|
1151
|
+
}
|
1152
|
+
}
|
1153
|
+
}
|
1154
|
+
else
|
1155
|
+
{ int i;
|
1156
|
+
for (i = 0; i < n; i++)
|
1157
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
1158
|
+
{ double term1 = data1[i][index1];
|
1159
|
+
double term2 = data2[i][index2];
|
1160
|
+
double w = weight[i];
|
1161
|
+
sum1 += w*term1;
|
1162
|
+
sum2 += w*term2;
|
1163
|
+
result += w*term1*term2;
|
1164
|
+
denom1 += w*term1*term1;
|
1165
|
+
denom2 += w*term2*term2;
|
1166
|
+
tweight += w;
|
1167
|
+
}
|
1168
|
+
}
|
1169
|
+
}
|
1170
|
+
if (!tweight) return 0; /* usually due to empty clusters */
|
1171
|
+
result -= sum1 * sum2 / tweight;
|
1172
|
+
denom1 -= sum1 * sum1 / tweight;
|
1173
|
+
denom2 -= sum2 * sum2 / tweight;
|
1174
|
+
if (denom1 <= 0) return 1; /* include '<' to deal with roundoff errors */
|
1175
|
+
if (denom2 <= 0) return 1; /* include '<' to deal with roundoff errors */
|
1176
|
+
result = result / sqrt(denom1*denom2);
|
1177
|
+
result = 1. - result;
|
1178
|
+
return result;
|
1179
|
+
}
|
1180
|
+
|
1181
|
+
/* ********************************************************************* */
|
1182
|
+
|
1183
|
+
static
|
1184
|
+
double acorrelation (int n, double** data1, double** data2, int** mask1,
|
1185
|
+
int** mask2, const double weight[], int index1, int index2, int transpose)
|
1186
|
+
/*
|
1187
|
+
Purpose
|
1188
|
+
=======
|
1189
|
+
|
1190
|
+
The acorrelation routine calculates the weighted Pearson distance between two
|
1191
|
+
rows or columns, using the absolute value of the correlation.
|
1192
|
+
This definition yields a semi-metric: d(a,b) >= 0, and d(a,b) = 0 iff a = b.
|
1193
|
+
but the triangular inequality d(a,b) + d(b,c) >= d(a,c) does not hold
|
1194
|
+
(e.g., choose b = a + c).
|
1195
|
+
|
1196
|
+
Arguments
|
1197
|
+
=========
|
1198
|
+
|
1199
|
+
n (input) int
|
1200
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
1201
|
+
of columns; otherwise, n is the number of rows.
|
1202
|
+
|
1203
|
+
data1 (input) double array
|
1204
|
+
The data array containing the first vector.
|
1205
|
+
|
1206
|
+
data2 (input) double array
|
1207
|
+
The data array containing the second vector.
|
1208
|
+
|
1209
|
+
mask1 (input) int array
|
1210
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
1211
|
+
data1[i][j] is missing.
|
1212
|
+
|
1213
|
+
mask2 (input) int array
|
1214
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
1215
|
+
data2[i][j] is missing.
|
1216
|
+
|
1217
|
+
weight (input) double[n]
|
1218
|
+
The weights that are used to calculate the distance.
|
1219
|
+
|
1220
|
+
index1 (input) int
|
1221
|
+
Index of the first row or column.
|
1222
|
+
|
1223
|
+
index2 (input) int
|
1224
|
+
Index of the second row or column.
|
1225
|
+
|
1226
|
+
transpose (input) int
|
1227
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
1228
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
1229
|
+
============================================================================
|
1230
|
+
*/
|
1231
|
+
{ double result = 0.;
|
1232
|
+
double sum1 = 0.;
|
1233
|
+
double sum2 = 0.;
|
1234
|
+
double denom1 = 0.;
|
1235
|
+
double denom2 = 0.;
|
1236
|
+
double tweight = 0.;
|
1237
|
+
if (transpose==0) /* Calculate the distance between two rows */
|
1238
|
+
{ int i;
|
1239
|
+
for (i = 0; i < n; i++)
|
1240
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
1241
|
+
{ double term1 = data1[index1][i];
|
1242
|
+
double term2 = data2[index2][i];
|
1243
|
+
double w = weight[i];
|
1244
|
+
sum1 += w*term1;
|
1245
|
+
sum2 += w*term2;
|
1246
|
+
result += w*term1*term2;
|
1247
|
+
denom1 += w*term1*term1;
|
1248
|
+
denom2 += w*term2*term2;
|
1249
|
+
tweight += w;
|
1250
|
+
}
|
1251
|
+
}
|
1252
|
+
}
|
1253
|
+
else
|
1254
|
+
{ int i;
|
1255
|
+
for (i = 0; i < n; i++)
|
1256
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
1257
|
+
{ double term1 = data1[i][index1];
|
1258
|
+
double term2 = data2[i][index2];
|
1259
|
+
double w = weight[i];
|
1260
|
+
sum1 += w*term1;
|
1261
|
+
sum2 += w*term2;
|
1262
|
+
result += w*term1*term2;
|
1263
|
+
denom1 += w*term1*term1;
|
1264
|
+
denom2 += w*term2*term2;
|
1265
|
+
tweight += w;
|
1266
|
+
}
|
1267
|
+
}
|
1268
|
+
}
|
1269
|
+
if (!tweight) return 0; /* usually due to empty clusters */
|
1270
|
+
result -= sum1 * sum2 / tweight;
|
1271
|
+
denom1 -= sum1 * sum1 / tweight;
|
1272
|
+
denom2 -= sum2 * sum2 / tweight;
|
1273
|
+
if (denom1 <= 0) return 1; /* include '<' to deal with roundoff errors */
|
1274
|
+
if (denom2 <= 0) return 1; /* include '<' to deal with roundoff errors */
|
1275
|
+
result = fabs(result) / sqrt(denom1*denom2);
|
1276
|
+
result = 1. - result;
|
1277
|
+
return result;
|
1278
|
+
}
|
1279
|
+
|
1280
|
+
/* ********************************************************************* */
|
1281
|
+
|
1282
|
+
static
|
1283
|
+
double ucorrelation (int n, double** data1, double** data2, int** mask1,
|
1284
|
+
int** mask2, const double weight[], int index1, int index2, int transpose)
|
1285
|
+
/*
|
1286
|
+
Purpose
|
1287
|
+
=======
|
1288
|
+
|
1289
|
+
The ucorrelation routine calculates the weighted Pearson distance between two
|
1290
|
+
rows or columns, using the uncentered version of the Pearson correlation. In the
|
1291
|
+
uncentered Pearson correlation, a zero mean is used for both vectors even if
|
1292
|
+
the actual mean is nonzero.
|
1293
|
+
This definition yields a semi-metric: d(a,b) >= 0, and d(a,b) = 0 iff a = b.
|
1294
|
+
but the triangular inequality d(a,b) + d(b,c) >= d(a,c) does not hold
|
1295
|
+
(e.g., choose b = a + c).
|
1296
|
+
|
1297
|
+
Arguments
|
1298
|
+
=========
|
1299
|
+
|
1300
|
+
n (input) int
|
1301
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
1302
|
+
of columns; otherwise, n is the number of rows.
|
1303
|
+
|
1304
|
+
data1 (input) double array
|
1305
|
+
The data array containing the first vector.
|
1306
|
+
|
1307
|
+
data2 (input) double array
|
1308
|
+
The data array containing the second vector.
|
1309
|
+
|
1310
|
+
mask1 (input) int array
|
1311
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
1312
|
+
data1[i][j] is missing.
|
1313
|
+
|
1314
|
+
mask2 (input) int array
|
1315
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
1316
|
+
data2[i][j] is missing.
|
1317
|
+
|
1318
|
+
weight (input) double[n]
|
1319
|
+
The weights that are used to calculate the distance.
|
1320
|
+
|
1321
|
+
index1 (input) int
|
1322
|
+
Index of the first row or column.
|
1323
|
+
|
1324
|
+
index2 (input) int
|
1325
|
+
Index of the second row or column.
|
1326
|
+
|
1327
|
+
transpose (input) int
|
1328
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
1329
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
1330
|
+
============================================================================
|
1331
|
+
*/
|
1332
|
+
{ double result = 0.;
|
1333
|
+
double denom1 = 0.;
|
1334
|
+
double denom2 = 0.;
|
1335
|
+
int flag = 0;
|
1336
|
+
/* flag will remain zero if no nonzero combinations of mask1 and mask2 are
|
1337
|
+
* found.
|
1338
|
+
*/
|
1339
|
+
if (transpose==0) /* Calculate the distance between two rows */
|
1340
|
+
{ int i;
|
1341
|
+
for (i = 0; i < n; i++)
|
1342
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
1343
|
+
{ double term1 = data1[index1][i];
|
1344
|
+
double term2 = data2[index2][i];
|
1345
|
+
double w = weight[i];
|
1346
|
+
result += w*term1*term2;
|
1347
|
+
denom1 += w*term1*term1;
|
1348
|
+
denom2 += w*term2*term2;
|
1349
|
+
flag = 1;
|
1350
|
+
}
|
1351
|
+
}
|
1352
|
+
}
|
1353
|
+
else
|
1354
|
+
{ int i;
|
1355
|
+
for (i = 0; i < n; i++)
|
1356
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
1357
|
+
{ double term1 = data1[i][index1];
|
1358
|
+
double term2 = data2[i][index2];
|
1359
|
+
double w = weight[i];
|
1360
|
+
result += w*term1*term2;
|
1361
|
+
denom1 += w*term1*term1;
|
1362
|
+
denom2 += w*term2*term2;
|
1363
|
+
flag = 1;
|
1364
|
+
}
|
1365
|
+
}
|
1366
|
+
}
|
1367
|
+
if (!flag) return 0.;
|
1368
|
+
if (denom1==0.) return 1.;
|
1369
|
+
if (denom2==0.) return 1.;
|
1370
|
+
result = result / sqrt(denom1*denom2);
|
1371
|
+
result = 1. - result;
|
1372
|
+
return result;
|
1373
|
+
}
|
1374
|
+
|
1375
|
+
/* ********************************************************************* */
|
1376
|
+
|
1377
|
+
static
|
1378
|
+
double uacorrelation (int n, double** data1, double** data2, int** mask1,
|
1379
|
+
int** mask2, const double weight[], int index1, int index2, int transpose)
|
1380
|
+
/*
|
1381
|
+
Purpose
|
1382
|
+
=======
|
1383
|
+
|
1384
|
+
The uacorrelation routine calculates the weighted Pearson distance between two
|
1385
|
+
rows or columns, using the absolute value of the uncentered version of the
|
1386
|
+
Pearson correlation. In the uncentered Pearson correlation, a zero mean is used
|
1387
|
+
for both vectors even if the actual mean is nonzero.
|
1388
|
+
This definition yields a semi-metric: d(a,b) >= 0, and d(a,b) = 0 iff a = b.
|
1389
|
+
but the triangular inequality d(a,b) + d(b,c) >= d(a,c) does not hold
|
1390
|
+
(e.g., choose b = a + c).
|
1391
|
+
|
1392
|
+
Arguments
|
1393
|
+
=========
|
1394
|
+
|
1395
|
+
n (input) int
|
1396
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
1397
|
+
of columns; otherwise, n is the number of rows.
|
1398
|
+
|
1399
|
+
data1 (input) double array
|
1400
|
+
The data array containing the first vector.
|
1401
|
+
|
1402
|
+
data2 (input) double array
|
1403
|
+
The data array containing the second vector.
|
1404
|
+
|
1405
|
+
mask1 (input) int array
|
1406
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
1407
|
+
data1[i][j] is missing.
|
1408
|
+
|
1409
|
+
mask2 (input) int array
|
1410
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
1411
|
+
data2[i][j] is missing.
|
1412
|
+
|
1413
|
+
weight (input) double[n]
|
1414
|
+
The weights that are used to calculate the distance.
|
1415
|
+
|
1416
|
+
index1 (input) int
|
1417
|
+
Index of the first row or column.
|
1418
|
+
|
1419
|
+
index2 (input) int
|
1420
|
+
Index of the second row or column.
|
1421
|
+
|
1422
|
+
transpose (input) int
|
1423
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
1424
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
1425
|
+
============================================================================
|
1426
|
+
*/
|
1427
|
+
{ double result = 0.;
|
1428
|
+
double denom1 = 0.;
|
1429
|
+
double denom2 = 0.;
|
1430
|
+
int flag = 0;
|
1431
|
+
/* flag will remain zero if no nonzero combinations of mask1 and mask2 are
|
1432
|
+
* found.
|
1433
|
+
*/
|
1434
|
+
if (transpose==0) /* Calculate the distance between two rows */
|
1435
|
+
{ int i;
|
1436
|
+
for (i = 0; i < n; i++)
|
1437
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
1438
|
+
{ double term1 = data1[index1][i];
|
1439
|
+
double term2 = data2[index2][i];
|
1440
|
+
double w = weight[i];
|
1441
|
+
result += w*term1*term2;
|
1442
|
+
denom1 += w*term1*term1;
|
1443
|
+
denom2 += w*term2*term2;
|
1444
|
+
flag = 1;
|
1445
|
+
}
|
1446
|
+
}
|
1447
|
+
}
|
1448
|
+
else
|
1449
|
+
{ int i;
|
1450
|
+
for (i = 0; i < n; i++)
|
1451
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
1452
|
+
{ double term1 = data1[i][index1];
|
1453
|
+
double term2 = data2[i][index2];
|
1454
|
+
double w = weight[i];
|
1455
|
+
result += w*term1*term2;
|
1456
|
+
denom1 += w*term1*term1;
|
1457
|
+
denom2 += w*term2*term2;
|
1458
|
+
flag = 1;
|
1459
|
+
}
|
1460
|
+
}
|
1461
|
+
}
|
1462
|
+
if (!flag) return 0.;
|
1463
|
+
if (denom1==0.) return 1.;
|
1464
|
+
if (denom2==0.) return 1.;
|
1465
|
+
result = fabs(result) / sqrt(denom1*denom2);
|
1466
|
+
result = 1. - result;
|
1467
|
+
return result;
|
1468
|
+
}
|
1469
|
+
|
1470
|
+
/* ********************************************************************* */
|
1471
|
+
|
1472
|
+
static
|
1473
|
+
double spearman (int n, double** data1, double** data2, int** mask1,
|
1474
|
+
int** mask2, const double weight[], int index1, int index2, int transpose)
|
1475
|
+
/*
|
1476
|
+
Purpose
|
1477
|
+
=======
|
1478
|
+
|
1479
|
+
The spearman routine calculates the Spearman distance between two rows or
|
1480
|
+
columns. The Spearman distance is defined as one minus the Spearman rank
|
1481
|
+
correlation.
|
1482
|
+
|
1483
|
+
Arguments
|
1484
|
+
=========
|
1485
|
+
|
1486
|
+
n (input) int
|
1487
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
1488
|
+
of columns; otherwise, n is the number of rows.
|
1489
|
+
|
1490
|
+
data1 (input) double array
|
1491
|
+
The data array containing the first vector.
|
1492
|
+
|
1493
|
+
data2 (input) double array
|
1494
|
+
The data array containing the second vector.
|
1495
|
+
|
1496
|
+
mask1 (input) int array
|
1497
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
1498
|
+
data1[i][j] is missing.
|
1499
|
+
|
1500
|
+
mask2 (input) int array
|
1501
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
1502
|
+
data2[i][j] is missing.
|
1503
|
+
|
1504
|
+
weight (input) double[n]
|
1505
|
+
These weights are ignored, but included for consistency with other distance
|
1506
|
+
measures.
|
1507
|
+
|
1508
|
+
index1 (input) int
|
1509
|
+
Index of the first row or column.
|
1510
|
+
|
1511
|
+
index2 (input) int
|
1512
|
+
Index of the second row or column.
|
1513
|
+
|
1514
|
+
transpose (input) int
|
1515
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
1516
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
1517
|
+
============================================================================
|
1518
|
+
*/
|
1519
|
+
{ int i;
|
1520
|
+
int m = 0;
|
1521
|
+
double* rank1;
|
1522
|
+
double* rank2;
|
1523
|
+
double result = 0.;
|
1524
|
+
double denom1 = 0.;
|
1525
|
+
double denom2 = 0.;
|
1526
|
+
double avgrank;
|
1527
|
+
double* tdata1;
|
1528
|
+
double* tdata2;
|
1529
|
+
tdata1 = malloc(n*sizeof(double));
|
1530
|
+
if(!tdata1) return 0.0; /* Memory allocation error */
|
1531
|
+
tdata2 = malloc(n*sizeof(double));
|
1532
|
+
if(!tdata2) /* Memory allocation error */
|
1533
|
+
{ free(tdata1);
|
1534
|
+
return 0.0;
|
1535
|
+
}
|
1536
|
+
if (transpose==0)
|
1537
|
+
{ for (i = 0; i < n; i++)
|
1538
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
1539
|
+
{ tdata1[m] = data1[index1][i];
|
1540
|
+
tdata2[m] = data2[index2][i];
|
1541
|
+
m++;
|
1542
|
+
}
|
1543
|
+
}
|
1544
|
+
}
|
1545
|
+
else
|
1546
|
+
{ for (i = 0; i < n; i++)
|
1547
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
1548
|
+
{ tdata1[m] = data1[i][index1];
|
1549
|
+
tdata2[m] = data2[i][index2];
|
1550
|
+
m++;
|
1551
|
+
}
|
1552
|
+
}
|
1553
|
+
}
|
1554
|
+
if (m==0)
|
1555
|
+
{ free(tdata1);
|
1556
|
+
free(tdata2);
|
1557
|
+
return 0;
|
1558
|
+
}
|
1559
|
+
rank1 = getrank(m, tdata1);
|
1560
|
+
free(tdata1);
|
1561
|
+
if(!rank1)
|
1562
|
+
{ free(tdata2);
|
1563
|
+
return 0.0; /* Memory allocation error */
|
1564
|
+
}
|
1565
|
+
rank2 = getrank(m, tdata2);
|
1566
|
+
free(tdata2);
|
1567
|
+
if(!rank2) /* Memory allocation error */
|
1568
|
+
{ free(rank1);
|
1569
|
+
return 0.0;
|
1570
|
+
}
|
1571
|
+
avgrank = 0.5*(m-1); /* Average rank */
|
1572
|
+
for (i = 0; i < m; i++)
|
1573
|
+
{ const double value1 = rank1[i];
|
1574
|
+
const double value2 = rank2[i];
|
1575
|
+
result += value1 * value2;
|
1576
|
+
denom1 += value1 * value1;
|
1577
|
+
denom2 += value2 * value2;
|
1578
|
+
}
|
1579
|
+
/* Note: denom1 and denom2 cannot be calculated directly from the number
|
1580
|
+
* of elements. If two elements have the same rank, the squared sum of
|
1581
|
+
* their ranks will change.
|
1582
|
+
*/
|
1583
|
+
free(rank1);
|
1584
|
+
free(rank2);
|
1585
|
+
result /= m;
|
1586
|
+
denom1 /= m;
|
1587
|
+
denom2 /= m;
|
1588
|
+
result -= avgrank * avgrank;
|
1589
|
+
denom1 -= avgrank * avgrank;
|
1590
|
+
denom2 -= avgrank * avgrank;
|
1591
|
+
if (denom1 <= 0) return 1; /* include '<' to deal with roundoff errors */
|
1592
|
+
if (denom2 <= 0) return 1; /* include '<' to deal with roundoff errors */
|
1593
|
+
result = result / sqrt(denom1*denom2);
|
1594
|
+
result = 1. - result;
|
1595
|
+
return result;
|
1596
|
+
}
|
1597
|
+
|
1598
|
+
/* ********************************************************************* */
|
1599
|
+
|
1600
|
+
static
|
1601
|
+
double kendall (int n, double** data1, double** data2, int** mask1, int** mask2,
|
1602
|
+
const double weight[], int index1, int index2, int transpose)
|
1603
|
+
/*
|
1604
|
+
Purpose
|
1605
|
+
=======
|
1606
|
+
|
1607
|
+
The kendall routine calculates the Kendall distance between two
|
1608
|
+
rows or columns. The Kendall distance is defined as one minus Kendall's tau.
|
1609
|
+
|
1610
|
+
Arguments
|
1611
|
+
=========
|
1612
|
+
|
1613
|
+
n (input) int
|
1614
|
+
The number of elements in a row or column. If transpose==0, then n is the number
|
1615
|
+
of columns; otherwise, n is the number of rows.
|
1616
|
+
|
1617
|
+
data1 (input) double array
|
1618
|
+
The data array containing the first vector.
|
1619
|
+
|
1620
|
+
data2 (input) double array
|
1621
|
+
The data array containing the second vector.
|
1622
|
+
|
1623
|
+
mask1 (input) int array
|
1624
|
+
This array which elements in data1 are missing. If mask1[i][j]==0, then
|
1625
|
+
data1[i][j] is missing.
|
1626
|
+
|
1627
|
+
mask2 (input) int array
|
1628
|
+
This array which elements in data2 are missing. If mask2[i][j]==0, then
|
1629
|
+
data2[i][j] is missing.
|
1630
|
+
|
1631
|
+
weight (input) double[n]
|
1632
|
+
These weights are ignored, but included for consistency with other distance
|
1633
|
+
measures.
|
1634
|
+
|
1635
|
+
index1 (input) int
|
1636
|
+
Index of the first row or column.
|
1637
|
+
|
1638
|
+
index2 (input) int
|
1639
|
+
Index of the second row or column.
|
1640
|
+
|
1641
|
+
transpose (input) int
|
1642
|
+
If transpose==0, the distance between two rows in the matrix is calculated.
|
1643
|
+
Otherwise, the distance between two columns in the matrix is calculated.
|
1644
|
+
============================================================================
|
1645
|
+
*/
|
1646
|
+
{ int con = 0;
|
1647
|
+
int dis = 0;
|
1648
|
+
int exx = 0;
|
1649
|
+
int exy = 0;
|
1650
|
+
int flag = 0;
|
1651
|
+
/* flag will remain zero if no nonzero combinations of mask1 and mask2 are
|
1652
|
+
* found.
|
1653
|
+
*/
|
1654
|
+
double denomx;
|
1655
|
+
double denomy;
|
1656
|
+
double tau;
|
1657
|
+
int i, j;
|
1658
|
+
if (transpose==0)
|
1659
|
+
{ for (i = 0; i < n; i++)
|
1660
|
+
{ if (mask1[index1][i] && mask2[index2][i])
|
1661
|
+
{ for (j = 0; j < i; j++)
|
1662
|
+
{ if (mask1[index1][j] && mask2[index2][j])
|
1663
|
+
{ double x1 = data1[index1][i];
|
1664
|
+
double x2 = data1[index1][j];
|
1665
|
+
double y1 = data2[index2][i];
|
1666
|
+
double y2 = data2[index2][j];
|
1667
|
+
if (x1 < x2 && y1 < y2) con++;
|
1668
|
+
if (x1 > x2 && y1 > y2) con++;
|
1669
|
+
if (x1 < x2 && y1 > y2) dis++;
|
1670
|
+
if (x1 > x2 && y1 < y2) dis++;
|
1671
|
+
if (x1 == x2 && y1 != y2) exx++;
|
1672
|
+
if (x1 != x2 && y1 == y2) exy++;
|
1673
|
+
flag = 1;
|
1674
|
+
}
|
1675
|
+
}
|
1676
|
+
}
|
1677
|
+
}
|
1678
|
+
}
|
1679
|
+
else
|
1680
|
+
{ for (i = 0; i < n; i++)
|
1681
|
+
{ if (mask1[i][index1] && mask2[i][index2])
|
1682
|
+
{ for (j = 0; j < i; j++)
|
1683
|
+
{ if (mask1[j][index1] && mask2[j][index2])
|
1684
|
+
{ double x1 = data1[i][index1];
|
1685
|
+
double x2 = data1[j][index1];
|
1686
|
+
double y1 = data2[i][index2];
|
1687
|
+
double y2 = data2[j][index2];
|
1688
|
+
if (x1 < x2 && y1 < y2) con++;
|
1689
|
+
if (x1 > x2 && y1 > y2) con++;
|
1690
|
+
if (x1 < x2 && y1 > y2) dis++;
|
1691
|
+
if (x1 > x2 && y1 < y2) dis++;
|
1692
|
+
if (x1 == x2 && y1 != y2) exx++;
|
1693
|
+
if (x1 != x2 && y1 == y2) exy++;
|
1694
|
+
flag = 1;
|
1695
|
+
}
|
1696
|
+
}
|
1697
|
+
}
|
1698
|
+
}
|
1699
|
+
}
|
1700
|
+
if (!flag) return 0.;
|
1701
|
+
denomx = con + dis + exx;
|
1702
|
+
denomy = con + dis + exy;
|
1703
|
+
if (denomx==0) return 1;
|
1704
|
+
if (denomy==0) return 1;
|
1705
|
+
tau = (con-dis)/sqrt(denomx*denomy);
|
1706
|
+
return 1.-tau;
|
1707
|
+
}
|
1708
|
+
|
1709
|
+
/* ********************************************************************* */
|
1710
|
+
|
1711
|
+
static double(*setmetric(char dist))
|
1712
|
+
(int, double**, double**, int**, int**, const double[], int, int, int)
|
1713
|
+
{ switch(dist)
|
1714
|
+
{ case 'e': return &euclid;
|
1715
|
+
case 'b': return &cityblock;
|
1716
|
+
case 'c': return &correlation;
|
1717
|
+
case 'a': return &acorrelation;
|
1718
|
+
case 'u': return &ucorrelation;
|
1719
|
+
case 'x': return &uacorrelation;
|
1720
|
+
case 's': return &spearman;
|
1721
|
+
case 'k': return &kendall;
|
1722
|
+
default: return &euclid;
|
1723
|
+
}
|
1724
|
+
return NULL; /* Never get here */
|
1725
|
+
}
|
1726
|
+
|
1727
|
+
/* ********************************************************************* */
|
1728
|
+
|
1729
|
+
static double uniform(void)
|
1730
|
+
/*
|
1731
|
+
Purpose
|
1732
|
+
=======
|
1733
|
+
|
1734
|
+
This routine returns a uniform random number between 0.0 and 1.0. Both 0.0
|
1735
|
+
and 1.0 are excluded. This random number generator is described in:
|
1736
|
+
|
1737
|
+
Pierre l'Ecuyer
|
1738
|
+
Efficient and Portable Combined Random Number Generators
|
1739
|
+
Communications of the ACM, Volume 31, Number 6, June 1988, pages 742-749,774.
|
1740
|
+
|
1741
|
+
The first time this routine is called, it initializes the random number
|
1742
|
+
generator using the current time. First, the current epoch time in seconds is
|
1743
|
+
used as a seed for the random number generator in the C library. The first two
|
1744
|
+
random numbers generated by this generator are used to initialize the random
|
1745
|
+
number generator implemented in this routine.
|
1746
|
+
|
1747
|
+
|
1748
|
+
Arguments
|
1749
|
+
=========
|
1750
|
+
|
1751
|
+
None.
|
1752
|
+
|
1753
|
+
|
1754
|
+
Return value
|
1755
|
+
============
|
1756
|
+
|
1757
|
+
A double-precison number between 0.0 and 1.0.
|
1758
|
+
============================================================================
|
1759
|
+
*/
|
1760
|
+
{ int z;
|
1761
|
+
static const int m1 = 2147483563;
|
1762
|
+
static const int m2 = 2147483399;
|
1763
|
+
const double scale = 1.0/m1;
|
1764
|
+
|
1765
|
+
static int s1 = 0;
|
1766
|
+
static int s2 = 0;
|
1767
|
+
|
1768
|
+
if (s1==0 || s2==0) /* initialize */
|
1769
|
+
{ unsigned int initseed = (unsigned int) time(0);
|
1770
|
+
srand(initseed);
|
1771
|
+
s1 = rand();
|
1772
|
+
s2 = rand();
|
1773
|
+
}
|
1774
|
+
|
1775
|
+
do
|
1776
|
+
{ int k;
|
1777
|
+
k = s1/53668;
|
1778
|
+
s1 = 40014*(s1-k*53668)-k*12211;
|
1779
|
+
if (s1 < 0) s1+=m1;
|
1780
|
+
k = s2/52774;
|
1781
|
+
s2 = 40692*(s2-k*52774)-k*3791;
|
1782
|
+
if(s2 < 0) s2+=m2;
|
1783
|
+
z = s1-s2;
|
1784
|
+
if(z < 1) z+=(m1-1);
|
1785
|
+
} while (z==m1); /* To avoid returning 1.0 */
|
1786
|
+
|
1787
|
+
return z*scale;
|
1788
|
+
}
|
1789
|
+
|
1790
|
+
/* ************************************************************************ */
|
1791
|
+
|
1792
|
+
static int binomial(int n, double p)
|
1793
|
+
/*
|
1794
|
+
Purpose
|
1795
|
+
=======
|
1796
|
+
|
1797
|
+
This routine generates a random number between 0 and n inclusive, following
|
1798
|
+
the binomial distribution with probability p and n trials. The routine is
|
1799
|
+
based on the BTPE algorithm, described in:
|
1800
|
+
|
1801
|
+
Voratas Kachitvichyanukul and Bruce W. Schmeiser:
|
1802
|
+
Binomial Random Variate Generation
|
1803
|
+
Communications of the ACM, Volume 31, Number 2, February 1988, pages 216-222.
|
1804
|
+
|
1805
|
+
|
1806
|
+
Arguments
|
1807
|
+
=========
|
1808
|
+
|
1809
|
+
p (input) double
|
1810
|
+
The probability of a single event. This probability should be less than or
|
1811
|
+
equal to 0.5.
|
1812
|
+
|
1813
|
+
n (input) int
|
1814
|
+
The number of trials.
|
1815
|
+
|
1816
|
+
|
1817
|
+
Return value
|
1818
|
+
============
|
1819
|
+
|
1820
|
+
An integer drawn from a binomial distribution with parameters (p, n).
|
1821
|
+
|
1822
|
+
============================================================================
|
1823
|
+
*/
|
1824
|
+
{ const double q = 1 - p;
|
1825
|
+
if (n*p < 30.0) /* Algorithm BINV */
|
1826
|
+
{ const double s = p/q;
|
1827
|
+
const double a = (n+1)*s;
|
1828
|
+
double r = exp(n*log(q)); /* pow() causes a crash on AIX */
|
1829
|
+
int x = 0;
|
1830
|
+
double u = uniform();
|
1831
|
+
while(1)
|
1832
|
+
{ if (u < r) return x;
|
1833
|
+
u-=r;
|
1834
|
+
x++;
|
1835
|
+
r *= (a/x)-s;
|
1836
|
+
}
|
1837
|
+
}
|
1838
|
+
else /* Algorithm BTPE */
|
1839
|
+
{ /* Step 0 */
|
1840
|
+
const double fm = n*p + p;
|
1841
|
+
const int m = (int) fm;
|
1842
|
+
const double p1 = floor(2.195*sqrt(n*p*q) -4.6*q) + 0.5;
|
1843
|
+
const double xm = m + 0.5;
|
1844
|
+
const double xl = xm - p1;
|
1845
|
+
const double xr = xm + p1;
|
1846
|
+
const double c = 0.134 + 20.5/(15.3+m);
|
1847
|
+
const double a = (fm-xl)/(fm-xl*p);
|
1848
|
+
const double b = (xr-fm)/(xr*q);
|
1849
|
+
const double lambdal = a*(1.0+0.5*a);
|
1850
|
+
const double lambdar = b*(1.0+0.5*b);
|
1851
|
+
const double p2 = p1*(1+2*c);
|
1852
|
+
const double p3 = p2 + c/lambdal;
|
1853
|
+
const double p4 = p3 + c/lambdar;
|
1854
|
+
while (1)
|
1855
|
+
{ /* Step 1 */
|
1856
|
+
int y;
|
1857
|
+
int k;
|
1858
|
+
double u = uniform();
|
1859
|
+
double v = uniform();
|
1860
|
+
u *= p4;
|
1861
|
+
if (u <= p1) return (int)(xm-p1*v+u);
|
1862
|
+
/* Step 2 */
|
1863
|
+
if (u > p2)
|
1864
|
+
{ /* Step 3 */
|
1865
|
+
if (u > p3)
|
1866
|
+
{ /* Step 4 */
|
1867
|
+
y = (int)(xr-log(v)/lambdar);
|
1868
|
+
if (y > n) continue;
|
1869
|
+
/* Go to step 5 */
|
1870
|
+
v = v*(u-p3)*lambdar;
|
1871
|
+
}
|
1872
|
+
else
|
1873
|
+
{ y = (int)(xl+log(v)/lambdal);
|
1874
|
+
if (y < 0) continue;
|
1875
|
+
/* Go to step 5 */
|
1876
|
+
v = v*(u-p2)*lambdal;
|
1877
|
+
}
|
1878
|
+
}
|
1879
|
+
else
|
1880
|
+
{ const double x = xl + (u-p1)/c;
|
1881
|
+
v = v*c + 1.0 - fabs(m-x+0.5)/p1;
|
1882
|
+
if (v > 1) continue;
|
1883
|
+
/* Go to step 5 */
|
1884
|
+
y = (int)x;
|
1885
|
+
}
|
1886
|
+
/* Step 5 */
|
1887
|
+
/* Step 5.0 */
|
1888
|
+
k = abs(y-m);
|
1889
|
+
if (k > 20 && k < 0.5*n*p*q-1.0)
|
1890
|
+
{ /* Step 5.2 */
|
1891
|
+
double rho = (k/(n*p*q))*((k*(k/3.0 + 0.625) + 0.1666666666666)/(n*p*q)+0.5);
|
1892
|
+
double t = -k*k/(2*n*p*q);
|
1893
|
+
double A = log(v);
|
1894
|
+
if (A < t-rho) return y;
|
1895
|
+
else if (A > t+rho) continue;
|
1896
|
+
else
|
1897
|
+
{ /* Step 5.3 */
|
1898
|
+
double x1 = y+1;
|
1899
|
+
double f1 = m+1;
|
1900
|
+
double z = n+1-m;
|
1901
|
+
double w = n-y+1;
|
1902
|
+
double x2 = x1*x1;
|
1903
|
+
double f2 = f1*f1;
|
1904
|
+
double z2 = z*z;
|
1905
|
+
double w2 = w*w;
|
1906
|
+
if (A > xm * log(f1/x1) + (n-m+0.5)*log(z/w)
|
1907
|
+
+ (y-m)*log(w*p/(x1*q))
|
1908
|
+
+ (13860.-(462.-(132.-(99.-140./f2)/f2)/f2)/f2)/f1/166320.
|
1909
|
+
+ (13860.-(462.-(132.-(99.-140./z2)/z2)/z2)/z2)/z/166320.
|
1910
|
+
+ (13860.-(462.-(132.-(99.-140./x2)/x2)/x2)/x2)/x1/166320.
|
1911
|
+
+ (13860.-(462.-(132.-(99.-140./w2)/w2)/w2)/w2)/w/166320.)
|
1912
|
+
continue;
|
1913
|
+
return y;
|
1914
|
+
}
|
1915
|
+
}
|
1916
|
+
else
|
1917
|
+
{ /* Step 5.1 */
|
1918
|
+
int i;
|
1919
|
+
const double s = p/q;
|
1920
|
+
const double aa = s*(n+1);
|
1921
|
+
double f = 1.0;
|
1922
|
+
for (i = m; i < y; f *= (aa/(++i)-s));
|
1923
|
+
for (i = y; i < m; f /= (aa/(++i)-s));
|
1924
|
+
if (v > f) continue;
|
1925
|
+
return y;
|
1926
|
+
}
|
1927
|
+
}
|
1928
|
+
}
|
1929
|
+
/* Never get here */
|
1930
|
+
return -1;
|
1931
|
+
}
|
1932
|
+
|
1933
|
+
/* ************************************************************************ */
|
1934
|
+
|
1935
|
+
static void randomassign (int nclusters, int nelements, int clusterid[])
|
1936
|
+
/*
|
1937
|
+
Purpose
|
1938
|
+
=======
|
1939
|
+
|
1940
|
+
The randomassign routine performs an initial random clustering, needed for
|
1941
|
+
k-means or k-median clustering. Elements (genes or microarrays) are randomly
|
1942
|
+
assigned to clusters. The number of elements in each cluster is chosen
|
1943
|
+
randomly, making sure that each cluster will receive at least one element.
|
1944
|
+
|
1945
|
+
|
1946
|
+
Arguments
|
1947
|
+
=========
|
1948
|
+
|
1949
|
+
nclusters (input) int
|
1950
|
+
The number of clusters.
|
1951
|
+
|
1952
|
+
nelements (input) int
|
1953
|
+
The number of elements to be clustered (i.e., the number of genes or microarrays
|
1954
|
+
to be clustered).
|
1955
|
+
|
1956
|
+
clusterid (output) int[nelements]
|
1957
|
+
The cluster number to which an element was assigned.
|
1958
|
+
|
1959
|
+
============================================================================
|
1960
|
+
*/
|
1961
|
+
{ int i, j;
|
1962
|
+
int k = 0;
|
1963
|
+
double p;
|
1964
|
+
int n = nelements-nclusters;
|
1965
|
+
/* Draw the number of elements in each cluster from a multinomial
|
1966
|
+
* distribution, reserving ncluster elements to set independently
|
1967
|
+
* in order to guarantee that none of the clusters are empty.
|
1968
|
+
*/
|
1969
|
+
for (i = 0; i < nclusters-1; i++)
|
1970
|
+
{ p = 1.0/(nclusters-i);
|
1971
|
+
j = binomial(n, p);
|
1972
|
+
n -= j;
|
1973
|
+
j += k+1; /* Assign at least one element to cluster i */
|
1974
|
+
for ( ; k < j; k++) clusterid[k] = i;
|
1975
|
+
}
|
1976
|
+
/* Assign the remaining elements to the last cluster */
|
1977
|
+
for ( ; k < nelements; k++) clusterid[k] = i;
|
1978
|
+
|
1979
|
+
/* Create a random permutation of the cluster assignments */
|
1980
|
+
for (i = 0; i < nelements; i++)
|
1981
|
+
{ j = (int) (i + (nelements-i)*uniform());
|
1982
|
+
k = clusterid[j];
|
1983
|
+
clusterid[j] = clusterid[i];
|
1984
|
+
clusterid[i] = k;
|
1985
|
+
}
|
1986
|
+
|
1987
|
+
return;
|
1988
|
+
}
|
1989
|
+
|
1990
|
+
/* ********************************************************************* */
|
1991
|
+
|
1992
|
+
static void getclustermeans(int nclusters, int nrows, int ncolumns,
|
1993
|
+
double** data, int** mask, int clusterid[], double** cdata, int** cmask,
|
1994
|
+
int transpose)
|
1995
|
+
/*
|
1996
|
+
Purpose
|
1997
|
+
=======
|
1998
|
+
|
1999
|
+
The getclustermeans routine calculates the cluster centroids, given to which
|
2000
|
+
cluster each element belongs. The centroid is defined as the mean over all
|
2001
|
+
elements for each dimension.
|
2002
|
+
|
2003
|
+
Arguments
|
2004
|
+
=========
|
2005
|
+
|
2006
|
+
nclusters (input) int
|
2007
|
+
The number of clusters.
|
2008
|
+
|
2009
|
+
nrows (input) int
|
2010
|
+
The number of rows in the gene expression data matrix, equal to the number of
|
2011
|
+
genes.
|
2012
|
+
|
2013
|
+
ncolumns (input) int
|
2014
|
+
The number of columns in the gene expression data matrix, equal to the number of
|
2015
|
+
microarrays.
|
2016
|
+
|
2017
|
+
data (input) double[nrows][ncolumns]
|
2018
|
+
The array containing the gene expression data.
|
2019
|
+
|
2020
|
+
mask (input) int[nrows][ncolumns]
|
2021
|
+
This array shows which data values are missing. If mask[i][j]==0, then
|
2022
|
+
data[i][j] is missing.
|
2023
|
+
|
2024
|
+
clusterid (output) int[nrows] if transpose==0
|
2025
|
+
int[ncolumns] if transpose==1
|
2026
|
+
The cluster number to which each element belongs. If transpose==0, then the
|
2027
|
+
dimension of clusterid is equal to nrows (the number of genes). Otherwise, it
|
2028
|
+
is equal to ncolumns (the number of microarrays).
|
2029
|
+
|
2030
|
+
cdata (output) double[nclusters][ncolumns] if transpose==0
|
2031
|
+
double[nrows][nclusters] if transpose==1
|
2032
|
+
On exit of getclustermeans, this array contains the cluster centroids.
|
2033
|
+
|
2034
|
+
cmask (output) int[nclusters][ncolumns] if transpose==0
|
2035
|
+
int[nrows][nclusters] if transpose==1
|
2036
|
+
This array shows which data values of are missing for each centroid. If
|
2037
|
+
cmask[i][j]==0, then cdata[i][j] is missing. A data value is missing for
|
2038
|
+
a centroid if all corresponding data values of the cluster members are missing.
|
2039
|
+
|
2040
|
+
transpose (input) int
|
2041
|
+
If transpose==0, clusters of rows (genes) are specified. Otherwise, clusters of
|
2042
|
+
columns (microarrays) are specified.
|
2043
|
+
|
2044
|
+
========================================================================
|
2045
|
+
*/
|
2046
|
+
{ int i, j, k;
|
2047
|
+
if (transpose==0)
|
2048
|
+
{ for (i = 0; i < nclusters; i++)
|
2049
|
+
{ for (j = 0; j < ncolumns; j++)
|
2050
|
+
{ cmask[i][j] = 0;
|
2051
|
+
cdata[i][j] = 0.;
|
2052
|
+
}
|
2053
|
+
}
|
2054
|
+
for (k = 0; k < nrows; k++)
|
2055
|
+
{ i = clusterid[k];
|
2056
|
+
for (j = 0; j < ncolumns; j++)
|
2057
|
+
{ if (mask[k][j] != 0)
|
2058
|
+
{ cdata[i][j]+=data[k][j];
|
2059
|
+
cmask[i][j]++;
|
2060
|
+
}
|
2061
|
+
}
|
2062
|
+
}
|
2063
|
+
for (i = 0; i < nclusters; i++)
|
2064
|
+
{ for (j = 0; j < ncolumns; j++)
|
2065
|
+
{ if (cmask[i][j]>0)
|
2066
|
+
{ cdata[i][j] /= cmask[i][j];
|
2067
|
+
cmask[i][j] = 1;
|
2068
|
+
}
|
2069
|
+
}
|
2070
|
+
}
|
2071
|
+
}
|
2072
|
+
else
|
2073
|
+
{ for (i = 0; i < nrows; i++)
|
2074
|
+
{ for (j = 0; j < nclusters; j++)
|
2075
|
+
{ cdata[i][j] = 0.;
|
2076
|
+
cmask[i][j] = 0;
|
2077
|
+
}
|
2078
|
+
}
|
2079
|
+
for (k = 0; k < ncolumns; k++)
|
2080
|
+
{ i = clusterid[k];
|
2081
|
+
for (j = 0; j < nrows; j++)
|
2082
|
+
{ if (mask[j][k] != 0)
|
2083
|
+
{ cdata[j][i]+=data[j][k];
|
2084
|
+
cmask[j][i]++;
|
2085
|
+
}
|
2086
|
+
}
|
2087
|
+
}
|
2088
|
+
for (i = 0; i < nrows; i++)
|
2089
|
+
{ for (j = 0; j < nclusters; j++)
|
2090
|
+
{ if (cmask[i][j]>0)
|
2091
|
+
{ cdata[i][j] /= cmask[i][j];
|
2092
|
+
cmask[i][j] = 1;
|
2093
|
+
}
|
2094
|
+
}
|
2095
|
+
}
|
2096
|
+
}
|
2097
|
+
}
|
2098
|
+
|
2099
|
+
/* ********************************************************************* */
|
2100
|
+
|
2101
|
+
static void
|
2102
|
+
getclustermedians(int nclusters, int nrows, int ncolumns,
|
2103
|
+
double** data, int** mask, int clusterid[], double** cdata, int** cmask,
|
2104
|
+
int transpose, double cache[])
|
2105
|
+
/*
|
2106
|
+
Purpose
|
2107
|
+
=======
|
2108
|
+
|
2109
|
+
The getclustermedians routine calculates the cluster centroids, given to which
|
2110
|
+
cluster each element belongs. The centroid is defined as the median over all
|
2111
|
+
elements for each dimension.
|
2112
|
+
|
2113
|
+
Arguments
|
2114
|
+
=========
|
2115
|
+
|
2116
|
+
nclusters (input) int
|
2117
|
+
The number of clusters.
|
2118
|
+
|
2119
|
+
nrows (input) int
|
2120
|
+
The number of rows in the gene expression data matrix, equal to the number of
|
2121
|
+
genes.
|
2122
|
+
|
2123
|
+
ncolumns (input) int
|
2124
|
+
The number of columns in the gene expression data matrix, equal to the number of
|
2125
|
+
microarrays.
|
2126
|
+
|
2127
|
+
data (input) double[nrows][ncolumns]
|
2128
|
+
The array containing the gene expression data.
|
2129
|
+
|
2130
|
+
mask (input) int[nrows][ncolumns]
|
2131
|
+
This array shows which data values are missing. If mask[i][j]==0, then
|
2132
|
+
data[i][j] is missing.
|
2133
|
+
|
2134
|
+
clusterid (output) int[nrows] if transpose==0
|
2135
|
+
int[ncolumns] if transpose==1
|
2136
|
+
The cluster number to which each element belongs. If transpose==0, then the
|
2137
|
+
dimension of clusterid is equal to nrows (the number of genes). Otherwise, it
|
2138
|
+
is equal to ncolumns (the number of microarrays).
|
2139
|
+
|
2140
|
+
cdata (output) double[nclusters][ncolumns] if transpose==0
|
2141
|
+
double[nrows][nclusters] if transpose==1
|
2142
|
+
On exit of getclustermedians, this array contains the cluster centroids.
|
2143
|
+
|
2144
|
+
cmask (output) int[nclusters][ncolumns] if transpose==0
|
2145
|
+
int[nrows][nclusters] if transpose==1
|
2146
|
+
This array shows which data values of are missing for each centroid. If
|
2147
|
+
cmask[i][j]==0, then cdata[i][j] is missing. A data value is missing for
|
2148
|
+
a centroid if all corresponding data values of the cluster members are missing.
|
2149
|
+
|
2150
|
+
transpose (input) int
|
2151
|
+
If transpose==0, clusters of rows (genes) are specified. Otherwise, clusters of
|
2152
|
+
columns (microarrays) are specified.
|
2153
|
+
|
2154
|
+
cache (input) double[nrows] if transpose==0
|
2155
|
+
double[ncolumns] if transpose==1
|
2156
|
+
This array should be allocated before calling getclustermedians; its contents
|
2157
|
+
on input is not relevant. This array is used as a temporary storage space when
|
2158
|
+
calculating the medians.
|
2159
|
+
|
2160
|
+
========================================================================
|
2161
|
+
*/
|
2162
|
+
{ int i, j, k;
|
2163
|
+
if (transpose==0)
|
2164
|
+
{ for (i = 0; i < nclusters; i++)
|
2165
|
+
{ for (j = 0; j < ncolumns; j++)
|
2166
|
+
{ int count = 0;
|
2167
|
+
for (k = 0; k < nrows; k++)
|
2168
|
+
{ if (i==clusterid[k] && mask[k][j])
|
2169
|
+
{ cache[count] = data[k][j];
|
2170
|
+
count++;
|
2171
|
+
}
|
2172
|
+
}
|
2173
|
+
if (count>0)
|
2174
|
+
{ cdata[i][j] = median(count,cache);
|
2175
|
+
cmask[i][j] = 1;
|
2176
|
+
}
|
2177
|
+
else
|
2178
|
+
{ cdata[i][j] = 0.;
|
2179
|
+
cmask[i][j] = 0;
|
2180
|
+
}
|
2181
|
+
}
|
2182
|
+
}
|
2183
|
+
}
|
2184
|
+
else
|
2185
|
+
{ for (i = 0; i < nclusters; i++)
|
2186
|
+
{ for (j = 0; j < nrows; j++)
|
2187
|
+
{ int count = 0;
|
2188
|
+
for (k = 0; k < ncolumns; k++)
|
2189
|
+
{ if (i==clusterid[k] && mask[j][k])
|
2190
|
+
{ cache[count] = data[j][k];
|
2191
|
+
count++;
|
2192
|
+
}
|
2193
|
+
}
|
2194
|
+
if (count>0)
|
2195
|
+
{ cdata[j][i] = median(count,cache);
|
2196
|
+
cmask[j][i] = 1;
|
2197
|
+
}
|
2198
|
+
else
|
2199
|
+
{ cdata[j][i] = 0.;
|
2200
|
+
cmask[j][i] = 0;
|
2201
|
+
}
|
2202
|
+
}
|
2203
|
+
}
|
2204
|
+
}
|
2205
|
+
}
|
2206
|
+
|
2207
|
+
/* ********************************************************************* */
|
2208
|
+
|
2209
|
+
int getclustercentroids(int nclusters, int nrows, int ncolumns,
|
2210
|
+
double** data, int** mask, int clusterid[], double** cdata, int** cmask,
|
2211
|
+
int transpose, char method)
|
2212
|
+
/*
|
2213
|
+
Purpose
|
2214
|
+
=======
|
2215
|
+
|
2216
|
+
The getclustercentroids routine calculates the cluster centroids, given to
|
2217
|
+
which cluster each element belongs. Depending on the argument method, the
|
2218
|
+
centroid is defined as either the mean or the median for each dimension over
|
2219
|
+
all elements belonging to a cluster.
|
2220
|
+
|
2221
|
+
Arguments
|
2222
|
+
=========
|
2223
|
+
|
2224
|
+
nclusters (input) int
|
2225
|
+
The number of clusters.
|
2226
|
+
|
2227
|
+
nrows (input) int
|
2228
|
+
The number of rows in the gene expression data matrix, equal to the number of
|
2229
|
+
genes.
|
2230
|
+
|
2231
|
+
ncolumns (input) int
|
2232
|
+
The number of columns in the gene expression data matrix, equal to the number of
|
2233
|
+
microarrays.
|
2234
|
+
|
2235
|
+
data (input) double[nrows][ncolumns]
|
2236
|
+
The array containing the gene expression data.
|
2237
|
+
|
2238
|
+
mask (input) int[nrows][ncolumns]
|
2239
|
+
This array shows which data values are missing. If mask[i][j]==0, then
|
2240
|
+
data[i][j] is missing.
|
2241
|
+
|
2242
|
+
clusterid (output) int[nrows] if transpose==0
|
2243
|
+
int[ncolumns] if transpose==1
|
2244
|
+
The cluster number to which each element belongs. If transpose==0, then the
|
2245
|
+
dimension of clusterid is equal to nrows (the number of genes). Otherwise, it
|
2246
|
+
is equal to ncolumns (the number of microarrays).
|
2247
|
+
|
2248
|
+
cdata (output) double[nclusters][ncolumns] if transpose==0
|
2249
|
+
double[nrows][nclusters] if transpose==1
|
2250
|
+
On exit of getclustercentroids, this array contains the cluster centroids.
|
2251
|
+
|
2252
|
+
cmask (output) int[nclusters][ncolumns] if transpose==0
|
2253
|
+
int[nrows][nclusters] if transpose==1
|
2254
|
+
This array shows which data values of are missing for each centroid. If
|
2255
|
+
cmask[i][j]==0, then cdata[i][j] is missing. A data value is missing for
|
2256
|
+
a centroid if all corresponding data values of the cluster members are missing.
|
2257
|
+
|
2258
|
+
transpose (input) int
|
2259
|
+
If transpose==0, clusters of rows (genes) are specified. Otherwise, clusters of
|
2260
|
+
columns (microarrays) are specified.
|
2261
|
+
|
2262
|
+
method (input) char
|
2263
|
+
For method=='a', the centroid is defined as the mean over all elements
|
2264
|
+
belonging to a cluster for each dimension.
|
2265
|
+
For method=='m', the centroid is defined as the median over all elements
|
2266
|
+
belonging to a cluster for each dimension.
|
2267
|
+
|
2268
|
+
Return value
|
2269
|
+
============
|
2270
|
+
|
2271
|
+
The function returns an integer to indicate success or failure. If a
|
2272
|
+
memory error occurs, or if method is not 'm' or 'a', getclustercentroids
|
2273
|
+
returns 0. If successful, getclustercentroids returns 1.
|
2274
|
+
========================================================================
|
2275
|
+
*/
|
2276
|
+
{ switch(method)
|
2277
|
+
{ case 'm':
|
2278
|
+
{ const int nelements = (transpose==0) ? nrows : ncolumns;
|
2279
|
+
double* cache = malloc(nelements*sizeof(double));
|
2280
|
+
if (!cache) return 0;
|
2281
|
+
getclustermedians(nclusters, nrows, ncolumns, data, mask, clusterid,
|
2282
|
+
cdata, cmask, transpose, cache);
|
2283
|
+
free(cache);
|
2284
|
+
return 1;
|
2285
|
+
}
|
2286
|
+
case 'a':
|
2287
|
+
{ getclustermeans(nclusters, nrows, ncolumns, data, mask, clusterid,
|
2288
|
+
cdata, cmask, transpose);
|
2289
|
+
return 1;
|
2290
|
+
}
|
2291
|
+
}
|
2292
|
+
return 0;
|
2293
|
+
}
|
2294
|
+
|
2295
|
+
/* ********************************************************************* */
|
2296
|
+
|
2297
|
+
void getclustermedoids(int nclusters, int nelements, double** distance,
|
2298
|
+
int clusterid[], int centroids[], double errors[])
|
2299
|
+
/*
|
2300
|
+
Purpose
|
2301
|
+
=======
|
2302
|
+
|
2303
|
+
The getclustermedoids routine calculates the cluster centroids, given to which
|
2304
|
+
cluster each element belongs. The centroid is defined as the element with the
|
2305
|
+
smallest sum of distances to the other elements.
|
2306
|
+
|
2307
|
+
Arguments
|
2308
|
+
=========
|
2309
|
+
|
2310
|
+
nclusters (input) int
|
2311
|
+
The number of clusters.
|
2312
|
+
|
2313
|
+
nelements (input) int
|
2314
|
+
The total number of elements.
|
2315
|
+
|
2316
|
+
distmatrix (input) double array, ragged
|
2317
|
+
(number of rows is nelements, number of columns is equal to the row number)
|
2318
|
+
The distance matrix. To save space, the distance matrix is given in the
|
2319
|
+
form of a ragged array. The distance matrix is symmetric and has zeros
|
2320
|
+
on the diagonal. See distancematrix for a description of the content.
|
2321
|
+
|
2322
|
+
clusterid (output) int[nelements]
|
2323
|
+
The cluster number to which each element belongs.
|
2324
|
+
|
2325
|
+
centroid (output) int[nclusters]
|
2326
|
+
The index of the element that functions as the centroid for each cluster.
|
2327
|
+
|
2328
|
+
errors (output) double[nclusters]
|
2329
|
+
The within-cluster sum of distances between the items and the cluster
|
2330
|
+
centroid.
|
2331
|
+
|
2332
|
+
========================================================================
|
2333
|
+
*/
|
2334
|
+
{ int i, j, k;
|
2335
|
+
for (j = 0; j < nclusters; j++) errors[j] = DBL_MAX;
|
2336
|
+
for (i = 0; i < nelements; i++)
|
2337
|
+
{ double d = 0.0;
|
2338
|
+
j = clusterid[i];
|
2339
|
+
for (k = 0; k < nelements; k++)
|
2340
|
+
{ if (i==k || clusterid[k]!=j) continue;
|
2341
|
+
d += (i < k ? distance[k][i] : distance[i][k]);
|
2342
|
+
if (d > errors[j]) break;
|
2343
|
+
}
|
2344
|
+
if (d < errors[j])
|
2345
|
+
{ errors[j] = d;
|
2346
|
+
centroids[j] = i;
|
2347
|
+
}
|
2348
|
+
}
|
2349
|
+
}
|
2350
|
+
|
2351
|
+
/* ********************************************************************* */
|
2352
|
+
|
2353
|
+
static int
|
2354
|
+
kmeans(int nclusters, int nrows, int ncolumns, double** data, int** mask,
|
2355
|
+
double weight[], int transpose, int npass, char dist,
|
2356
|
+
double** cdata, int** cmask, int clusterid[], double* error,
|
2357
|
+
int tclusterid[], int counts[], int mapping[])
|
2358
|
+
{ int i, j, k;
|
2359
|
+
const int nelements = (transpose==0) ? nrows : ncolumns;
|
2360
|
+
const int ndata = (transpose==0) ? ncolumns : nrows;
|
2361
|
+
int ifound = 1;
|
2362
|
+
int ipass = 0;
|
2363
|
+
/* Set the metric function as indicated by dist */
|
2364
|
+
double (*metric)
|
2365
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
2366
|
+
setmetric(dist);
|
2367
|
+
|
2368
|
+
/* We save the clustering solution periodically and check if it reappears */
|
2369
|
+
int* saved = malloc(nelements*sizeof(int));
|
2370
|
+
if (saved==NULL) return -1;
|
2371
|
+
|
2372
|
+
*error = DBL_MAX;
|
2373
|
+
|
2374
|
+
do
|
2375
|
+
{ double total = DBL_MAX;
|
2376
|
+
int counter = 0;
|
2377
|
+
int period = 10;
|
2378
|
+
|
2379
|
+
/* Perform the EM algorithm. First, randomly assign elements to clusters. */
|
2380
|
+
if (npass!=0) randomassign (nclusters, nelements, tclusterid);
|
2381
|
+
|
2382
|
+
for (i = 0; i < nclusters; i++) counts[i] = 0;
|
2383
|
+
for (i = 0; i < nelements; i++) counts[tclusterid[i]]++;
|
2384
|
+
|
2385
|
+
/* Start the loop */
|
2386
|
+
while(1)
|
2387
|
+
{ double previous = total;
|
2388
|
+
total = 0.0;
|
2389
|
+
|
2390
|
+
if (counter % period == 0) /* Save the current cluster assignments */
|
2391
|
+
{ for (i = 0; i < nelements; i++) saved[i] = tclusterid[i];
|
2392
|
+
if (period < INT_MAX / 2) period *= 2;
|
2393
|
+
}
|
2394
|
+
counter++;
|
2395
|
+
|
2396
|
+
/* Find the center */
|
2397
|
+
getclustermeans(nclusters, nrows, ncolumns, data, mask, tclusterid,
|
2398
|
+
cdata, cmask, transpose);
|
2399
|
+
|
2400
|
+
for (i = 0; i < nelements; i++)
|
2401
|
+
/* Calculate the distances */
|
2402
|
+
{ double distance;
|
2403
|
+
k = tclusterid[i];
|
2404
|
+
if (counts[k]==1) continue;
|
2405
|
+
/* No reassignment if that would lead to an empty cluster */
|
2406
|
+
/* Treat the present cluster as a special case */
|
2407
|
+
distance = metric(ndata,data,cdata,mask,cmask,weight,i,k,transpose);
|
2408
|
+
for (j = 0; j < nclusters; j++)
|
2409
|
+
{ double tdistance;
|
2410
|
+
if (j==k) continue;
|
2411
|
+
tdistance = metric(ndata,data,cdata,mask,cmask,weight,i,j,transpose);
|
2412
|
+
if (tdistance < distance)
|
2413
|
+
{ distance = tdistance;
|
2414
|
+
counts[tclusterid[i]]--;
|
2415
|
+
tclusterid[i] = j;
|
2416
|
+
counts[j]++;
|
2417
|
+
}
|
2418
|
+
}
|
2419
|
+
total += distance;
|
2420
|
+
}
|
2421
|
+
if (total>=previous) break;
|
2422
|
+
/* total>=previous is FALSE on some machines even if total and previous
|
2423
|
+
* are bitwise identical. */
|
2424
|
+
for (i = 0; i < nelements; i++)
|
2425
|
+
if (saved[i]!=tclusterid[i]) break;
|
2426
|
+
if (i==nelements)
|
2427
|
+
break; /* Identical solution found; break out of this loop */
|
2428
|
+
}
|
2429
|
+
|
2430
|
+
if (npass<=1)
|
2431
|
+
{ *error = total;
|
2432
|
+
break;
|
2433
|
+
}
|
2434
|
+
|
2435
|
+
for (i = 0; i < nclusters; i++) mapping[i] = -1;
|
2436
|
+
for (i = 0; i < nelements; i++)
|
2437
|
+
{ j = tclusterid[i];
|
2438
|
+
k = clusterid[i];
|
2439
|
+
if (mapping[k] == -1) mapping[k] = j;
|
2440
|
+
else if (mapping[k] != j)
|
2441
|
+
{ if (total < *error)
|
2442
|
+
{ ifound = 1;
|
2443
|
+
*error = total;
|
2444
|
+
for (j = 0; j < nelements; j++) clusterid[j] = tclusterid[j];
|
2445
|
+
}
|
2446
|
+
break;
|
2447
|
+
}
|
2448
|
+
}
|
2449
|
+
if (i==nelements) ifound++; /* break statement not encountered */
|
2450
|
+
} while (++ipass < npass);
|
2451
|
+
|
2452
|
+
free(saved);
|
2453
|
+
return ifound;
|
2454
|
+
}
|
2455
|
+
|
2456
|
+
/* ---------------------------------------------------------------------- */
|
2457
|
+
|
2458
|
+
static int
|
2459
|
+
kmedians(int nclusters, int nrows, int ncolumns, double** data, int** mask,
|
2460
|
+
double weight[], int transpose, int npass, char dist,
|
2461
|
+
double** cdata, int** cmask, int clusterid[], double* error,
|
2462
|
+
int tclusterid[], int counts[], int mapping[], double cache[])
|
2463
|
+
{ int i, j, k;
|
2464
|
+
const int nelements = (transpose==0) ? nrows : ncolumns;
|
2465
|
+
const int ndata = (transpose==0) ? ncolumns : nrows;
|
2466
|
+
int ifound = 1;
|
2467
|
+
int ipass = 0;
|
2468
|
+
/* Set the metric function as indicated by dist */
|
2469
|
+
double (*metric)
|
2470
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
2471
|
+
setmetric(dist);
|
2472
|
+
|
2473
|
+
/* We save the clustering solution periodically and check if it reappears */
|
2474
|
+
int* saved = malloc(nelements*sizeof(int));
|
2475
|
+
if (saved==NULL) return -1;
|
2476
|
+
|
2477
|
+
*error = DBL_MAX;
|
2478
|
+
|
2479
|
+
do
|
2480
|
+
{ double total = DBL_MAX;
|
2481
|
+
int counter = 0;
|
2482
|
+
int period = 10;
|
2483
|
+
|
2484
|
+
/* Perform the EM algorithm. First, randomly assign elements to clusters. */
|
2485
|
+
if (npass!=0) randomassign (nclusters, nelements, tclusterid);
|
2486
|
+
|
2487
|
+
for (i = 0; i < nclusters; i++) counts[i]=0;
|
2488
|
+
for (i = 0; i < nelements; i++) counts[tclusterid[i]]++;
|
2489
|
+
|
2490
|
+
/* Start the loop */
|
2491
|
+
while(1)
|
2492
|
+
{ double previous = total;
|
2493
|
+
total = 0.0;
|
2494
|
+
|
2495
|
+
if (counter % period == 0) /* Save the current cluster assignments */
|
2496
|
+
{ for (i = 0; i < nelements; i++) saved[i] = tclusterid[i];
|
2497
|
+
if (period < INT_MAX / 2) period *= 2;
|
2498
|
+
}
|
2499
|
+
counter++;
|
2500
|
+
|
2501
|
+
/* Find the center */
|
2502
|
+
getclustermedians(nclusters, nrows, ncolumns, data, mask, tclusterid,
|
2503
|
+
cdata, cmask, transpose, cache);
|
2504
|
+
|
2505
|
+
for (i = 0; i < nelements; i++)
|
2506
|
+
/* Calculate the distances */
|
2507
|
+
{ double distance;
|
2508
|
+
k = tclusterid[i];
|
2509
|
+
if (counts[k]==1) continue;
|
2510
|
+
/* No reassignment if that would lead to an empty cluster */
|
2511
|
+
/* Treat the present cluster as a special case */
|
2512
|
+
distance = metric(ndata,data,cdata,mask,cmask,weight,i,k,transpose);
|
2513
|
+
for (j = 0; j < nclusters; j++)
|
2514
|
+
{ double tdistance;
|
2515
|
+
if (j==k) continue;
|
2516
|
+
tdistance = metric(ndata,data,cdata,mask,cmask,weight,i,j,transpose);
|
2517
|
+
if (tdistance < distance)
|
2518
|
+
{ distance = tdistance;
|
2519
|
+
counts[tclusterid[i]]--;
|
2520
|
+
tclusterid[i] = j;
|
2521
|
+
counts[j]++;
|
2522
|
+
}
|
2523
|
+
}
|
2524
|
+
total += distance;
|
2525
|
+
}
|
2526
|
+
if (total>=previous) break;
|
2527
|
+
/* total>=previous is FALSE on some machines even if total and previous
|
2528
|
+
* are bitwise identical. */
|
2529
|
+
for (i = 0; i < nelements; i++)
|
2530
|
+
if (saved[i]!=tclusterid[i]) break;
|
2531
|
+
if (i==nelements)
|
2532
|
+
break; /* Identical solution found; break out of this loop */
|
2533
|
+
}
|
2534
|
+
|
2535
|
+
if (npass<=1)
|
2536
|
+
{ *error = total;
|
2537
|
+
break;
|
2538
|
+
}
|
2539
|
+
|
2540
|
+
for (i = 0; i < nclusters; i++) mapping[i] = -1;
|
2541
|
+
for (i = 0; i < nelements; i++)
|
2542
|
+
{ j = tclusterid[i];
|
2543
|
+
k = clusterid[i];
|
2544
|
+
if (mapping[k] == -1) mapping[k] = j;
|
2545
|
+
else if (mapping[k] != j)
|
2546
|
+
{ if (total < *error)
|
2547
|
+
{ ifound = 1;
|
2548
|
+
*error = total;
|
2549
|
+
for (j = 0; j < nelements; j++) clusterid[j] = tclusterid[j];
|
2550
|
+
}
|
2551
|
+
break;
|
2552
|
+
}
|
2553
|
+
}
|
2554
|
+
if (i==nelements) ifound++; /* break statement not encountered */
|
2555
|
+
} while (++ipass < npass);
|
2556
|
+
|
2557
|
+
free(saved);
|
2558
|
+
return ifound;
|
2559
|
+
}
|
2560
|
+
|
2561
|
+
/* ********************************************************************* */
|
2562
|
+
|
2563
|
+
void kcluster (int nclusters, int nrows, int ncolumns,
|
2564
|
+
double** data, int** mask, double weight[], int transpose,
|
2565
|
+
int npass, char method, char dist,
|
2566
|
+
int clusterid[], double* error, int* ifound)
|
2567
|
+
/*
|
2568
|
+
Purpose
|
2569
|
+
=======
|
2570
|
+
|
2571
|
+
The kcluster routine performs k-means or k-median clustering on a given set of
|
2572
|
+
elements, using the specified distance measure. The number of clusters is given
|
2573
|
+
by the user. Multiple passes are being made to find the optimal clustering
|
2574
|
+
solution, each time starting from a different initial clustering.
|
2575
|
+
|
2576
|
+
|
2577
|
+
Arguments
|
2578
|
+
=========
|
2579
|
+
|
2580
|
+
nclusters (input) int
|
2581
|
+
The number of clusters to be found.
|
2582
|
+
|
2583
|
+
data (input) double[nrows][ncolumns]
|
2584
|
+
The array containing the data of the elements to be clustered (i.e., the gene
|
2585
|
+
expression data).
|
2586
|
+
|
2587
|
+
mask (input) int[nrows][ncolumns]
|
2588
|
+
This array shows which data values are missing. If
|
2589
|
+
mask[i][j] == 0, then data[i][j] is missing.
|
2590
|
+
|
2591
|
+
nrows (input) int
|
2592
|
+
The number of rows in the data matrix, equal to the number of genes.
|
2593
|
+
|
2594
|
+
ncolumns (input) int
|
2595
|
+
The number of columns in the data matrix, equal to the number of microarrays.
|
2596
|
+
|
2597
|
+
weight (input) double[n]
|
2598
|
+
The weights that are used to calculate the distance.
|
2599
|
+
|
2600
|
+
transpose (input) int
|
2601
|
+
If transpose==0, the rows of the matrix are clustered. Otherwise, columns
|
2602
|
+
of the matrix are clustered.
|
2603
|
+
|
2604
|
+
npass (input) int
|
2605
|
+
The number of times clustering is performed. Clustering is performed npass
|
2606
|
+
times, each time starting from a different (random) initial assignment of
|
2607
|
+
genes to clusters. The clustering solution with the lowest within-cluster sum
|
2608
|
+
of distances is chosen.
|
2609
|
+
If npass==0, then the clustering algorithm will be run once, where the initial
|
2610
|
+
assignment of elements to clusters is taken from the clusterid array.
|
2611
|
+
|
2612
|
+
method (input) char
|
2613
|
+
Defines whether the arithmetic mean (method=='a') or the median
|
2614
|
+
(method=='m') is used to calculate the cluster center.
|
2615
|
+
|
2616
|
+
dist (input) char
|
2617
|
+
Defines which distance measure is used, as given by the table:
|
2618
|
+
dist=='e': Euclidean distance
|
2619
|
+
dist=='b': City-block distance
|
2620
|
+
dist=='c': correlation
|
2621
|
+
dist=='a': absolute value of the correlation
|
2622
|
+
dist=='u': uncentered correlation
|
2623
|
+
dist=='x': absolute uncentered correlation
|
2624
|
+
dist=='s': Spearman's rank correlation
|
2625
|
+
dist=='k': Kendall's tau
|
2626
|
+
For other values of dist, the default (Euclidean distance) is used.
|
2627
|
+
|
2628
|
+
clusterid (output; input) int[nrows] if transpose==0
|
2629
|
+
int[ncolumns] if transpose==1
|
2630
|
+
The cluster number to which a gene or microarray was assigned. If npass==0,
|
2631
|
+
then on input clusterid contains the initial clustering assignment from which
|
2632
|
+
the clustering algorithm starts. On output, it contains the clustering solution
|
2633
|
+
that was found.
|
2634
|
+
|
2635
|
+
error (output) double*
|
2636
|
+
The sum of distances to the cluster center of each item in the optimal k-means
|
2637
|
+
clustering solution that was found.
|
2638
|
+
|
2639
|
+
ifound (output) int*
|
2640
|
+
The number of times the optimal clustering solution was
|
2641
|
+
found. The value of ifound is at least 1; its maximum value is npass. If the
|
2642
|
+
number of clusters is larger than the number of elements being clustered,
|
2643
|
+
*ifound is set to 0 as an error code. If a memory allocation error occurs,
|
2644
|
+
*ifound is set to -1.
|
2645
|
+
|
2646
|
+
========================================================================
|
2647
|
+
*/
|
2648
|
+
{ const int nelements = (transpose==0) ? nrows : ncolumns;
|
2649
|
+
const int ndata = (transpose==0) ? ncolumns : nrows;
|
2650
|
+
|
2651
|
+
int i;
|
2652
|
+
int ok;
|
2653
|
+
int* tclusterid;
|
2654
|
+
int* mapping = NULL;
|
2655
|
+
double** cdata;
|
2656
|
+
int** cmask;
|
2657
|
+
int* counts;
|
2658
|
+
|
2659
|
+
if (nelements < nclusters)
|
2660
|
+
{ *ifound = 0;
|
2661
|
+
return;
|
2662
|
+
}
|
2663
|
+
/* More clusters asked for than elements available */
|
2664
|
+
|
2665
|
+
*ifound = -1;
|
2666
|
+
|
2667
|
+
/* This will contain the number of elements in each cluster, which is
|
2668
|
+
* needed to check for empty clusters. */
|
2669
|
+
counts = malloc(nclusters*sizeof(int));
|
2670
|
+
if(!counts) return;
|
2671
|
+
|
2672
|
+
/* Find out if the user specified an initial clustering */
|
2673
|
+
if (npass<=1) tclusterid = clusterid;
|
2674
|
+
else
|
2675
|
+
{ tclusterid = malloc(nelements*sizeof(int));
|
2676
|
+
if (!tclusterid)
|
2677
|
+
{ free(counts);
|
2678
|
+
return;
|
2679
|
+
}
|
2680
|
+
mapping = malloc(nclusters*sizeof(int));
|
2681
|
+
if (!mapping)
|
2682
|
+
{ free(counts);
|
2683
|
+
free(tclusterid);
|
2684
|
+
return;
|
2685
|
+
}
|
2686
|
+
for (i = 0; i < nelements; i++) clusterid[i] = 0;
|
2687
|
+
}
|
2688
|
+
|
2689
|
+
/* Allocate space to store the centroid data */
|
2690
|
+
if (transpose==0) ok = makedatamask(nclusters, ndata, &cdata, &cmask);
|
2691
|
+
else ok = makedatamask(ndata, nclusters, &cdata, &cmask);
|
2692
|
+
if(!ok)
|
2693
|
+
{ free(counts);
|
2694
|
+
if(npass>1)
|
2695
|
+
{ free(tclusterid);
|
2696
|
+
free(mapping);
|
2697
|
+
return;
|
2698
|
+
}
|
2699
|
+
}
|
2700
|
+
|
2701
|
+
if (method=='m')
|
2702
|
+
{ double* cache = malloc(nelements*sizeof(double));
|
2703
|
+
if(cache)
|
2704
|
+
{ *ifound = kmedians(nclusters, nrows, ncolumns, data, mask, weight,
|
2705
|
+
transpose, npass, dist, cdata, cmask, clusterid, error,
|
2706
|
+
tclusterid, counts, mapping, cache);
|
2707
|
+
free(cache);
|
2708
|
+
}
|
2709
|
+
}
|
2710
|
+
else
|
2711
|
+
*ifound = kmeans(nclusters, nrows, ncolumns, data, mask, weight,
|
2712
|
+
transpose, npass, dist, cdata, cmask, clusterid, error,
|
2713
|
+
tclusterid, counts, mapping);
|
2714
|
+
|
2715
|
+
/* Deallocate temporarily used space */
|
2716
|
+
if (npass > 1)
|
2717
|
+
{ free(mapping);
|
2718
|
+
free(tclusterid);
|
2719
|
+
}
|
2720
|
+
|
2721
|
+
if (transpose==0) freedatamask(nclusters, cdata, cmask);
|
2722
|
+
else freedatamask(ndata, cdata, cmask);
|
2723
|
+
|
2724
|
+
free(counts);
|
2725
|
+
}
|
2726
|
+
|
2727
|
+
/* *********************************************************************** */
|
2728
|
+
|
2729
|
+
void kmedoids (int nclusters, int nelements, double** distmatrix,
|
2730
|
+
int npass, int clusterid[], double* error, int* ifound)
|
2731
|
+
/*
|
2732
|
+
Purpose
|
2733
|
+
=======
|
2734
|
+
|
2735
|
+
The kmedoids routine performs k-medoids clustering on a given set of elements,
|
2736
|
+
using the distance matrix and the number of clusters passed by the user.
|
2737
|
+
Multiple passes are being made to find the optimal clustering solution, each
|
2738
|
+
time starting from a different initial clustering.
|
2739
|
+
|
2740
|
+
|
2741
|
+
Arguments
|
2742
|
+
=========
|
2743
|
+
|
2744
|
+
nclusters (input) int
|
2745
|
+
The number of clusters to be found.
|
2746
|
+
|
2747
|
+
nelements (input) int
|
2748
|
+
The number of elements to be clustered.
|
2749
|
+
|
2750
|
+
distmatrix (input) double array, ragged
|
2751
|
+
(number of rows is nelements, number of columns is equal to the row number)
|
2752
|
+
The distance matrix. To save space, the distance matrix is given in the
|
2753
|
+
form of a ragged array. The distance matrix is symmetric and has zeros
|
2754
|
+
on the diagonal. See distancematrix for a description of the content.
|
2755
|
+
|
2756
|
+
npass (input) int
|
2757
|
+
The number of times clustering is performed. Clustering is performed npass
|
2758
|
+
times, each time starting from a different (random) initial assignment of genes
|
2759
|
+
to clusters. The clustering solution with the lowest within-cluster sum of
|
2760
|
+
distances is chosen.
|
2761
|
+
If npass==0, then the clustering algorithm will be run once, where the initial
|
2762
|
+
assignment of elements to clusters is taken from the clusterid array.
|
2763
|
+
|
2764
|
+
clusterid (output; input) int[nelements]
|
2765
|
+
On input, if npass==0, then clusterid contains the initial clustering assignment
|
2766
|
+
from which the clustering algorithm starts; all numbers in clusterid should be
|
2767
|
+
between zero and nelements-1 inclusive. If npass!=0, clusterid is ignored on
|
2768
|
+
input.
|
2769
|
+
On output, clusterid contains the clustering solution that was found: clusterid
|
2770
|
+
contains the number of the cluster to which each item was assigned. On output,
|
2771
|
+
the number of a cluster is defined as the item number of the centroid of the
|
2772
|
+
cluster.
|
2773
|
+
|
2774
|
+
error (output) double
|
2775
|
+
The sum of distances to the cluster center of each item in the optimal k-medoids
|
2776
|
+
clustering solution that was found.
|
2777
|
+
|
2778
|
+
ifound (output) int
|
2779
|
+
If kmedoids is successful: the number of times the optimal clustering solution
|
2780
|
+
was found. The value of ifound is at least 1; its maximum value is npass.
|
2781
|
+
If the user requested more clusters than elements available, ifound is set
|
2782
|
+
to 0. If kmedoids fails due to a memory allocation error, ifound is set to -1.
|
2783
|
+
|
2784
|
+
========================================================================
|
2785
|
+
*/
|
2786
|
+
{ int i, j, icluster;
|
2787
|
+
int* tclusterid;
|
2788
|
+
int* saved;
|
2789
|
+
int* centroids;
|
2790
|
+
double* errors;
|
2791
|
+
int ipass = 0;
|
2792
|
+
|
2793
|
+
if (nelements < nclusters)
|
2794
|
+
{ *ifound = 0;
|
2795
|
+
return;
|
2796
|
+
} /* More clusters asked for than elements available */
|
2797
|
+
|
2798
|
+
*ifound = -1;
|
2799
|
+
|
2800
|
+
/* We save the clustering solution periodically and check if it reappears */
|
2801
|
+
saved = malloc(nelements*sizeof(int));
|
2802
|
+
if (saved==NULL) return;
|
2803
|
+
|
2804
|
+
centroids = malloc(nclusters*sizeof(int));
|
2805
|
+
if(!centroids)
|
2806
|
+
{ free(saved);
|
2807
|
+
return;
|
2808
|
+
}
|
2809
|
+
|
2810
|
+
errors = malloc(nclusters*sizeof(double));
|
2811
|
+
if(!errors)
|
2812
|
+
{ free(saved);
|
2813
|
+
free(centroids);
|
2814
|
+
return;
|
2815
|
+
}
|
2816
|
+
|
2817
|
+
/* Find out if the user specified an initial clustering */
|
2818
|
+
if (npass<=1) tclusterid = clusterid;
|
2819
|
+
else
|
2820
|
+
{ tclusterid = malloc(nelements*sizeof(int));
|
2821
|
+
if(!tclusterid)
|
2822
|
+
{ free(saved);
|
2823
|
+
free(centroids);
|
2824
|
+
free(errors);
|
2825
|
+
return;
|
2826
|
+
}
|
2827
|
+
}
|
2828
|
+
|
2829
|
+
*error = DBL_MAX;
|
2830
|
+
do /* Start the loop */
|
2831
|
+
{ double total = DBL_MAX;
|
2832
|
+
int counter = 0;
|
2833
|
+
int period = 10;
|
2834
|
+
|
2835
|
+
if (npass!=0) randomassign (nclusters, nelements, tclusterid);
|
2836
|
+
while(1)
|
2837
|
+
{ double previous = total;
|
2838
|
+
total = 0.0;
|
2839
|
+
|
2840
|
+
if (counter % period == 0) /* Save the current cluster assignments */
|
2841
|
+
{ for (i = 0; i < nelements; i++) saved[i] = tclusterid[i];
|
2842
|
+
if (period < INT_MAX / 2) period *= 2;
|
2843
|
+
}
|
2844
|
+
counter++;
|
2845
|
+
|
2846
|
+
/* Find the center */
|
2847
|
+
getclustermedoids(nclusters, nelements, distmatrix, tclusterid,
|
2848
|
+
centroids, errors);
|
2849
|
+
|
2850
|
+
for (i = 0; i < nelements; i++)
|
2851
|
+
/* Find the closest cluster */
|
2852
|
+
{ double distance = DBL_MAX;
|
2853
|
+
for (icluster = 0; icluster < nclusters; icluster++)
|
2854
|
+
{ double tdistance;
|
2855
|
+
j = centroids[icluster];
|
2856
|
+
if (i==j)
|
2857
|
+
{ distance = 0.0;
|
2858
|
+
tclusterid[i] = icluster;
|
2859
|
+
break;
|
2860
|
+
}
|
2861
|
+
tdistance = (i > j) ? distmatrix[i][j] : distmatrix[j][i];
|
2862
|
+
if (tdistance < distance)
|
2863
|
+
{ distance = tdistance;
|
2864
|
+
tclusterid[i] = icluster;
|
2865
|
+
}
|
2866
|
+
}
|
2867
|
+
total += distance;
|
2868
|
+
}
|
2869
|
+
if (total>=previous) break;
|
2870
|
+
/* total>=previous is FALSE on some machines even if total and previous
|
2871
|
+
* are bitwise identical. */
|
2872
|
+
for (i = 0; i < nelements; i++)
|
2873
|
+
if (saved[i]!=tclusterid[i]) break;
|
2874
|
+
if (i==nelements)
|
2875
|
+
break; /* Identical solution found; break out of this loop */
|
2876
|
+
}
|
2877
|
+
|
2878
|
+
for (i = 0; i < nelements; i++)
|
2879
|
+
{ if (clusterid[i]!=centroids[tclusterid[i]])
|
2880
|
+
{ if (total < *error)
|
2881
|
+
{ *ifound = 1;
|
2882
|
+
*error = total;
|
2883
|
+
/* Replace by the centroid in each cluster. */
|
2884
|
+
for (j = 0; j < nelements; j++)
|
2885
|
+
clusterid[j] = centroids[tclusterid[j]];
|
2886
|
+
}
|
2887
|
+
break;
|
2888
|
+
}
|
2889
|
+
}
|
2890
|
+
if (i==nelements) (*ifound)++; /* break statement not encountered */
|
2891
|
+
} while (++ipass < npass);
|
2892
|
+
|
2893
|
+
/* Deallocate temporarily used space */
|
2894
|
+
if (npass > 1) free(tclusterid);
|
2895
|
+
|
2896
|
+
free(saved);
|
2897
|
+
free(centroids);
|
2898
|
+
free(errors);
|
2899
|
+
|
2900
|
+
return;
|
2901
|
+
}
|
2902
|
+
|
2903
|
+
/* ******************************************************************** */
|
2904
|
+
|
2905
|
+
double** distancematrix (int nrows, int ncolumns, double** data,
|
2906
|
+
int** mask, double weights[], char dist, int transpose)
|
2907
|
+
/*
|
2908
|
+
Purpose
|
2909
|
+
=======
|
2910
|
+
|
2911
|
+
The distancematrix routine calculates the distance matrix between genes or
|
2912
|
+
microarrays using their measured gene expression data. Several distance measures
|
2913
|
+
can be used. The routine returns a pointer to a ragged array containing the
|
2914
|
+
distances between the genes. As the distance matrix is symmetric, with zeros on
|
2915
|
+
the diagonal, only the lower triangular half of the distance matrix is saved.
|
2916
|
+
The distancematrix routine allocates space for the distance matrix. If the
|
2917
|
+
parameter transpose is set to a nonzero value, the distances between the columns
|
2918
|
+
(microarrays) are calculated, otherwise distances between the rows (genes) are
|
2919
|
+
calculated.
|
2920
|
+
If sufficient space in memory cannot be allocated to store the distance matrix,
|
2921
|
+
the routine returns a NULL pointer, and all memory allocated so far for the
|
2922
|
+
distance matrix is freed.
|
2923
|
+
|
2924
|
+
|
2925
|
+
Arguments
|
2926
|
+
=========
|
2927
|
+
|
2928
|
+
nrows (input) int
|
2929
|
+
The number of rows in the gene expression data matrix (i.e., the number of
|
2930
|
+
genes)
|
2931
|
+
|
2932
|
+
ncolumns (input) int
|
2933
|
+
The number of columns in the gene expression data matrix (i.e., the number of
|
2934
|
+
microarrays)
|
2935
|
+
|
2936
|
+
data (input) double[nrows][ncolumns]
|
2937
|
+
The array containing the gene expression data.
|
2938
|
+
|
2939
|
+
mask (input) int[nrows][ncolumns]
|
2940
|
+
This array shows which data values are missing. If mask[i][j]==0, then
|
2941
|
+
data[i][j] is missing.
|
2942
|
+
|
2943
|
+
weight (input) double[n]
|
2944
|
+
The weights that are used to calculate the distance. The length of this vector
|
2945
|
+
is equal to the number of columns if the distances between genes are calculated,
|
2946
|
+
or the number of rows if the distances between microarrays are calculated.
|
2947
|
+
|
2948
|
+
dist (input) char
|
2949
|
+
Defines which distance measure is used, as given by the table:
|
2950
|
+
dist=='e': Euclidean distance
|
2951
|
+
dist=='b': City-block distance
|
2952
|
+
dist=='c': correlation
|
2953
|
+
dist=='a': absolute value of the correlation
|
2954
|
+
dist=='u': uncentered correlation
|
2955
|
+
dist=='x': absolute uncentered correlation
|
2956
|
+
dist=='s': Spearman's rank correlation
|
2957
|
+
dist=='k': Kendall's tau
|
2958
|
+
For other values of dist, the default (Euclidean distance) is used.
|
2959
|
+
|
2960
|
+
transpose (input) int
|
2961
|
+
If transpose is equal to zero, the distances between the rows is
|
2962
|
+
calculated. Otherwise, the distances between the columns is calculated.
|
2963
|
+
The former is needed when genes are being clustered; the latter is used
|
2964
|
+
when microarrays are being clustered.
|
2965
|
+
|
2966
|
+
========================================================================
|
2967
|
+
*/
|
2968
|
+
{ /* First determine the size of the distance matrix */
|
2969
|
+
const int n = (transpose==0) ? nrows : ncolumns;
|
2970
|
+
const int ndata = (transpose==0) ? ncolumns : nrows;
|
2971
|
+
int i,j;
|
2972
|
+
double** matrix;
|
2973
|
+
|
2974
|
+
/* Set the metric function as indicated by dist */
|
2975
|
+
double (*metric)
|
2976
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
2977
|
+
setmetric(dist);
|
2978
|
+
|
2979
|
+
if (n < 2) return NULL;
|
2980
|
+
|
2981
|
+
/* Set up the ragged array */
|
2982
|
+
matrix = malloc(n*sizeof(double*));
|
2983
|
+
if(matrix==NULL) return NULL; /* Not enough memory available */
|
2984
|
+
matrix[0] = NULL;
|
2985
|
+
/* The zeroth row has zero columns. We allocate it anyway for convenience.*/
|
2986
|
+
for (i = 1; i < n; i++)
|
2987
|
+
{ matrix[i] = malloc(i*sizeof(double));
|
2988
|
+
if (matrix[i]==NULL) break; /* Not enough memory available */
|
2989
|
+
}
|
2990
|
+
if (i < n) /* break condition encountered */
|
2991
|
+
{ j = i;
|
2992
|
+
for (i = 1; i < j; i++) free(matrix[i]);
|
2993
|
+
return NULL;
|
2994
|
+
}
|
2995
|
+
|
2996
|
+
/* Calculate the distances and save them in the ragged array */
|
2997
|
+
for (i = 1; i < n; i++)
|
2998
|
+
for (j = 0; j < i; j++)
|
2999
|
+
matrix[i][j]=metric(ndata,data,data,mask,mask,weights,i,j,transpose);
|
3000
|
+
|
3001
|
+
return matrix;
|
3002
|
+
}
|
3003
|
+
|
3004
|
+
/* ******************************************************************** */
|
3005
|
+
|
3006
|
+
double* calculate_weights(int nrows, int ncolumns, double** data, int** mask,
|
3007
|
+
double weights[], int transpose, char dist, double cutoff, double exponent)
|
3008
|
+
|
3009
|
+
/*
|
3010
|
+
Purpose
|
3011
|
+
=======
|
3012
|
+
|
3013
|
+
This function calculates the weights using the weighting scheme proposed by
|
3014
|
+
Michael Eisen:
|
3015
|
+
w[i] = 1.0 / sum_{j where d[i][j]<cutoff} (1 - d[i][j]/cutoff)^exponent
|
3016
|
+
where the cutoff and the exponent are specified by the user.
|
3017
|
+
|
3018
|
+
|
3019
|
+
Arguments
|
3020
|
+
=========
|
3021
|
+
|
3022
|
+
nrows (input) int
|
3023
|
+
The number of rows in the gene expression data matrix, equal to the number of
|
3024
|
+
genes.
|
3025
|
+
|
3026
|
+
ncolumns (input) int
|
3027
|
+
The number of columns in the gene expression data matrix, equal to the number of
|
3028
|
+
microarrays.
|
3029
|
+
|
3030
|
+
data (input) double[nrows][ncolumns]
|
3031
|
+
The array containing the gene expression data.
|
3032
|
+
|
3033
|
+
mask (input) int[nrows][ncolumns]
|
3034
|
+
This array shows which data values are missing. If mask[i][j]==0, then
|
3035
|
+
data[i][j] is missing.
|
3036
|
+
|
3037
|
+
weight (input) int[ncolumns] if transpose==0,
|
3038
|
+
int[nrows] if transpose==1
|
3039
|
+
The weights that are used to calculate the distance. The length of this vector
|
3040
|
+
is ncolumns if gene weights are being clustered, and nrows if microarrays
|
3041
|
+
weights are being clustered.
|
3042
|
+
|
3043
|
+
transpose (input) int
|
3044
|
+
If transpose==0, the weights of the rows of the data matrix are calculated.
|
3045
|
+
Otherwise, the weights of the columns of the data matrix are calculated.
|
3046
|
+
|
3047
|
+
dist (input) char
|
3048
|
+
Defines which distance measure is used, as given by the table:
|
3049
|
+
dist=='e': Euclidean distance
|
3050
|
+
dist=='b': City-block distance
|
3051
|
+
dist=='c': correlation
|
3052
|
+
dist=='a': absolute value of the correlation
|
3053
|
+
dist=='u': uncentered correlation
|
3054
|
+
dist=='x': absolute uncentered correlation
|
3055
|
+
dist=='s': Spearman's rank correlation
|
3056
|
+
dist=='k': Kendall's tau
|
3057
|
+
For other values of dist, the default (Euclidean distance) is used.
|
3058
|
+
|
3059
|
+
cutoff (input) double
|
3060
|
+
The cutoff to be used to calculate the weights.
|
3061
|
+
|
3062
|
+
exponent (input) double
|
3063
|
+
The exponent to be used to calculate the weights.
|
3064
|
+
|
3065
|
+
|
3066
|
+
Return value
|
3067
|
+
============
|
3068
|
+
|
3069
|
+
The function returns a pointer to a newly allocated array containing the
|
3070
|
+
calculated weights for the rows (if transpose==0) or columns (if
|
3071
|
+
transpose==1). If not enough memory could be allocated to store the
|
3072
|
+
weights array, the function returns NULL.
|
3073
|
+
|
3074
|
+
========================================================================
|
3075
|
+
*/
|
3076
|
+
{ int i,j;
|
3077
|
+
const int ndata = (transpose==0) ? ncolumns : nrows;
|
3078
|
+
const int nelements = (transpose==0) ? nrows : ncolumns;
|
3079
|
+
|
3080
|
+
/* Set the metric function as indicated by dist */
|
3081
|
+
double (*metric)
|
3082
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
3083
|
+
setmetric(dist);
|
3084
|
+
|
3085
|
+
double* result = malloc(nelements*sizeof(double));
|
3086
|
+
if (!result) return NULL;
|
3087
|
+
memset(result, 0, nelements*sizeof(double));
|
3088
|
+
|
3089
|
+
for (i = 0; i < nelements; i++)
|
3090
|
+
{ result[i] += 1.0;
|
3091
|
+
for (j = 0; j < i; j++)
|
3092
|
+
{ const double distance = metric(ndata, data, data, mask, mask, weights,
|
3093
|
+
i, j, transpose);
|
3094
|
+
if (distance < cutoff)
|
3095
|
+
{ const double dweight = exp(exponent*log(1-distance/cutoff));
|
3096
|
+
/* pow() causes a crash on AIX */
|
3097
|
+
result[i] += dweight;
|
3098
|
+
result[j] += dweight;
|
3099
|
+
}
|
3100
|
+
}
|
3101
|
+
}
|
3102
|
+
for (i = 0; i < nelements; i++) result[i] = 1.0/result[i];
|
3103
|
+
return result;
|
3104
|
+
}
|
3105
|
+
|
3106
|
+
/* ******************************************************************** */
|
3107
|
+
|
3108
|
+
void cuttree (int nelements, Node* tree, int nclusters, int clusterid[])
|
3109
|
+
|
3110
|
+
/*
|
3111
|
+
Purpose
|
3112
|
+
=======
|
3113
|
+
|
3114
|
+
The cuttree routine takes the output of a hierarchical clustering routine, and
|
3115
|
+
divides the elements in the tree structure into clusters based on the
|
3116
|
+
hierarchical clustering result. The number of clusters is specified by the user.
|
3117
|
+
|
3118
|
+
Arguments
|
3119
|
+
=========
|
3120
|
+
|
3121
|
+
nelements (input) int
|
3122
|
+
The number of elements that were clustered.
|
3123
|
+
|
3124
|
+
tree (input) Node[nelements-1]
|
3125
|
+
The clustering solution. Each node in the array describes one linking event,
|
3126
|
+
with tree[i].left and tree[i].right representig the elements that were joined.
|
3127
|
+
The original elements are numbered 0..nelements-1, nodes are numbered
|
3128
|
+
-1..-(nelements-1).
|
3129
|
+
|
3130
|
+
nclusters (input) int
|
3131
|
+
The number of clusters to be formed.
|
3132
|
+
|
3133
|
+
clusterid (output) int[nelements]
|
3134
|
+
The number of the cluster to which each element was assigned. Space for this
|
3135
|
+
array should be allocated before calling the cuttree routine. If a memory
|
3136
|
+
error occured, all elements in clusterid are set to -1.
|
3137
|
+
|
3138
|
+
========================================================================
|
3139
|
+
*/
|
3140
|
+
{ int i, j, k;
|
3141
|
+
int icluster = 0;
|
3142
|
+
const int n = nelements-nclusters; /* number of nodes to join */
|
3143
|
+
int* nodeid;
|
3144
|
+
for (i = nelements-2; i >= n; i--)
|
3145
|
+
{ k = tree[i].left;
|
3146
|
+
if (k>=0)
|
3147
|
+
{ clusterid[k] = icluster;
|
3148
|
+
icluster++;
|
3149
|
+
}
|
3150
|
+
k = tree[i].right;
|
3151
|
+
if (k>=0)
|
3152
|
+
{ clusterid[k] = icluster;
|
3153
|
+
icluster++;
|
3154
|
+
}
|
3155
|
+
}
|
3156
|
+
nodeid = malloc(n*sizeof(int));
|
3157
|
+
if(!nodeid)
|
3158
|
+
{ for (i = 0; i < nelements; i++) clusterid[i] = -1;
|
3159
|
+
return;
|
3160
|
+
}
|
3161
|
+
for (i = 0; i < n; i++) nodeid[i] = -1;
|
3162
|
+
for (i = n-1; i >= 0; i--)
|
3163
|
+
{ if(nodeid[i]<0)
|
3164
|
+
{ j = icluster;
|
3165
|
+
nodeid[i] = j;
|
3166
|
+
icluster++;
|
3167
|
+
}
|
3168
|
+
else j = nodeid[i];
|
3169
|
+
k = tree[i].left;
|
3170
|
+
if (k<0) nodeid[-k-1] = j; else clusterid[k] = j;
|
3171
|
+
k = tree[i].right;
|
3172
|
+
if (k<0) nodeid[-k-1] = j; else clusterid[k] = j;
|
3173
|
+
}
|
3174
|
+
free(nodeid);
|
3175
|
+
return;
|
3176
|
+
}
|
3177
|
+
|
3178
|
+
/* ******************************************************************** */
|
3179
|
+
|
3180
|
+
static
|
3181
|
+
Node* pclcluster (int nrows, int ncolumns, double** data, int** mask,
|
3182
|
+
double weight[], double** distmatrix, char dist, int transpose)
|
3183
|
+
|
3184
|
+
/*
|
3185
|
+
|
3186
|
+
Purpose
|
3187
|
+
=======
|
3188
|
+
|
3189
|
+
The pclcluster routine performs clustering using pairwise centroid-linking
|
3190
|
+
on a given set of gene expression data, using the distance metric given by dist.
|
3191
|
+
|
3192
|
+
Arguments
|
3193
|
+
=========
|
3194
|
+
|
3195
|
+
nrows (input) int
|
3196
|
+
The number of rows in the gene expression data matrix, equal to the number of
|
3197
|
+
genes.
|
3198
|
+
|
3199
|
+
ncolumns (input) int
|
3200
|
+
The number of columns in the gene expression data matrix, equal to the number of
|
3201
|
+
microarrays.
|
3202
|
+
|
3203
|
+
data (input) double[nrows][ncolumns]
|
3204
|
+
The array containing the gene expression data.
|
3205
|
+
|
3206
|
+
mask (input) int[nrows][ncolumns]
|
3207
|
+
This array shows which data values are missing. If
|
3208
|
+
mask[i][j] == 0, then data[i][j] is missing.
|
3209
|
+
|
3210
|
+
weight (input) double[ncolumns] if transpose==0;
|
3211
|
+
double[nrows] if transpose==1
|
3212
|
+
The weights that are used to calculate the distance. The length of this vector
|
3213
|
+
is ncolumns if genes are being clustered, and nrows if microarrays are being
|
3214
|
+
clustered.
|
3215
|
+
|
3216
|
+
transpose (input) int
|
3217
|
+
If transpose==0, the rows of the matrix are clustered. Otherwise, columns
|
3218
|
+
of the matrix are clustered.
|
3219
|
+
|
3220
|
+
dist (input) char
|
3221
|
+
Defines which distance measure is used, as given by the table:
|
3222
|
+
dist=='e': Euclidean distance
|
3223
|
+
dist=='b': City-block distance
|
3224
|
+
dist=='c': correlation
|
3225
|
+
dist=='a': absolute value of the correlation
|
3226
|
+
dist=='u': uncentered correlation
|
3227
|
+
dist=='x': absolute uncentered correlation
|
3228
|
+
dist=='s': Spearman's rank correlation
|
3229
|
+
dist=='k': Kendall's tau
|
3230
|
+
For other values of dist, the default (Euclidean distance) is used.
|
3231
|
+
|
3232
|
+
distmatrix (input) double**
|
3233
|
+
The distance matrix. This matrix is precalculated by the calling routine
|
3234
|
+
treecluster. The pclcluster routine modifies the contents of distmatrix, but
|
3235
|
+
does not deallocate it.
|
3236
|
+
|
3237
|
+
Return value
|
3238
|
+
============
|
3239
|
+
|
3240
|
+
A pointer to a newly allocated array of Node structs, describing the
|
3241
|
+
hierarchical clustering solution consisting of nelements-1 nodes. Depending on
|
3242
|
+
whether genes (rows) or microarrays (columns) were clustered, nelements is
|
3243
|
+
equal to nrows or ncolumns. See src/cluster.h for a description of the Node
|
3244
|
+
structure.
|
3245
|
+
If a memory error occurs, pclcluster returns NULL.
|
3246
|
+
========================================================================
|
3247
|
+
*/
|
3248
|
+
{ int i, j;
|
3249
|
+
const int nelements = (transpose==0) ? nrows : ncolumns;
|
3250
|
+
int inode;
|
3251
|
+
const int ndata = transpose ? nrows : ncolumns;
|
3252
|
+
const int nnodes = nelements - 1;
|
3253
|
+
|
3254
|
+
/* Set the metric function as indicated by dist */
|
3255
|
+
double (*metric)
|
3256
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
3257
|
+
setmetric(dist);
|
3258
|
+
|
3259
|
+
Node* result;
|
3260
|
+
double** newdata;
|
3261
|
+
int** newmask;
|
3262
|
+
int* distid = malloc(nelements*sizeof(int));
|
3263
|
+
if(!distid) return NULL;
|
3264
|
+
result = malloc(nnodes*sizeof(Node));
|
3265
|
+
if(!result)
|
3266
|
+
{ free(distid);
|
3267
|
+
return NULL;
|
3268
|
+
}
|
3269
|
+
if(!makedatamask(nelements, ndata, &newdata, &newmask))
|
3270
|
+
{ free(result);
|
3271
|
+
free(distid);
|
3272
|
+
return NULL;
|
3273
|
+
}
|
3274
|
+
|
3275
|
+
for (i = 0; i < nelements; i++) distid[i] = i;
|
3276
|
+
/* To remember which row/column in the distance matrix contains what */
|
3277
|
+
|
3278
|
+
/* Storage for node data */
|
3279
|
+
if (transpose)
|
3280
|
+
{ for (i = 0; i < nelements; i++)
|
3281
|
+
{ for (j = 0; j < ndata; j++)
|
3282
|
+
{ newdata[i][j] = data[j][i];
|
3283
|
+
newmask[i][j] = mask[j][i];
|
3284
|
+
}
|
3285
|
+
}
|
3286
|
+
data = newdata;
|
3287
|
+
mask = newmask;
|
3288
|
+
}
|
3289
|
+
else
|
3290
|
+
{ for (i = 0; i < nelements; i++)
|
3291
|
+
{ memcpy(newdata[i], data[i], ndata*sizeof(double));
|
3292
|
+
memcpy(newmask[i], mask[i], ndata*sizeof(int));
|
3293
|
+
}
|
3294
|
+
data = newdata;
|
3295
|
+
mask = newmask;
|
3296
|
+
}
|
3297
|
+
|
3298
|
+
for (inode = 0; inode < nnodes; inode++)
|
3299
|
+
{ /* Find the pair with the shortest distance */
|
3300
|
+
int is = 1;
|
3301
|
+
int js = 0;
|
3302
|
+
result[inode].distance = find_closest_pair(nelements-inode, distmatrix, &is, &js);
|
3303
|
+
result[inode].left = distid[js];
|
3304
|
+
result[inode].right = distid[is];
|
3305
|
+
|
3306
|
+
/* Make node js the new node */
|
3307
|
+
for (i = 0; i < ndata; i++)
|
3308
|
+
{ data[js][i] = data[js][i]*mask[js][i] + data[is][i]*mask[is][i];
|
3309
|
+
mask[js][i] += mask[is][i];
|
3310
|
+
if (mask[js][i]) data[js][i] /= mask[js][i];
|
3311
|
+
}
|
3312
|
+
free(data[is]);
|
3313
|
+
free(mask[is]);
|
3314
|
+
data[is] = data[nnodes-inode];
|
3315
|
+
mask[is] = mask[nnodes-inode];
|
3316
|
+
|
3317
|
+
/* Fix the distances */
|
3318
|
+
distid[is] = distid[nnodes-inode];
|
3319
|
+
for (i = 0; i < is; i++)
|
3320
|
+
distmatrix[is][i] = distmatrix[nnodes-inode][i];
|
3321
|
+
for (i = is + 1; i < nnodes-inode; i++)
|
3322
|
+
distmatrix[i][is] = distmatrix[nnodes-inode][i];
|
3323
|
+
|
3324
|
+
distid[js] = -inode-1;
|
3325
|
+
for (i = 0; i < js; i++)
|
3326
|
+
distmatrix[js][i] = metric(ndata,data,data,mask,mask,weight,js,i,0);
|
3327
|
+
for (i = js + 1; i < nnodes-inode; i++)
|
3328
|
+
distmatrix[i][js] = metric(ndata,data,data,mask,mask,weight,js,i,0);
|
3329
|
+
}
|
3330
|
+
|
3331
|
+
/* Free temporarily allocated space */
|
3332
|
+
free(data[0]);
|
3333
|
+
free(mask[0]);
|
3334
|
+
free(data);
|
3335
|
+
free(mask);
|
3336
|
+
free(distid);
|
3337
|
+
|
3338
|
+
return result;
|
3339
|
+
}
|
3340
|
+
|
3341
|
+
/* ******************************************************************** */
|
3342
|
+
|
3343
|
+
static
|
3344
|
+
int nodecompare(const void* a, const void* b)
|
3345
|
+
/* Helper function for qsort. */
|
3346
|
+
{ const Node* node1 = (const Node*)a;
|
3347
|
+
const Node* node2 = (const Node*)b;
|
3348
|
+
const double term1 = node1->distance;
|
3349
|
+
const double term2 = node2->distance;
|
3350
|
+
if (term1 < term2) return -1;
|
3351
|
+
if (term1 > term2) return +1;
|
3352
|
+
return 0;
|
3353
|
+
}
|
3354
|
+
|
3355
|
+
/* ---------------------------------------------------------------------- */
|
3356
|
+
|
3357
|
+
static
|
3358
|
+
Node* pslcluster (int nrows, int ncolumns, double** data, int** mask,
|
3359
|
+
double weight[], double** distmatrix, char dist, int transpose)
|
3360
|
+
|
3361
|
+
/*
|
3362
|
+
|
3363
|
+
Purpose
|
3364
|
+
=======
|
3365
|
+
|
3366
|
+
The pslcluster routine performs single-linkage hierarchical clustering, using
|
3367
|
+
either the distance matrix directly, if available, or by calculating the
|
3368
|
+
distances from the data array. This implementation is based on the SLINK
|
3369
|
+
algorithm, described in:
|
3370
|
+
Sibson, R. (1973). SLINK: An optimally efficient algorithm for the single-link
|
3371
|
+
cluster method. The Computer Journal, 16(1): 30-34.
|
3372
|
+
The output of this algorithm is identical to conventional single-linkage
|
3373
|
+
hierarchical clustering, but is much more memory-efficient and faster. Hence,
|
3374
|
+
it can be applied to large data sets, for which the conventional single-
|
3375
|
+
linkage algorithm fails due to lack of memory.
|
3376
|
+
|
3377
|
+
|
3378
|
+
Arguments
|
3379
|
+
=========
|
3380
|
+
|
3381
|
+
nrows (input) int
|
3382
|
+
The number of rows in the gene expression data matrix, equal to the number of
|
3383
|
+
genes.
|
3384
|
+
|
3385
|
+
ncolumns (input) int
|
3386
|
+
The number of columns in the gene expression data matrix, equal to the number of
|
3387
|
+
microarrays.
|
3388
|
+
|
3389
|
+
data (input) double[nrows][ncolumns]
|
3390
|
+
The array containing the gene expression data.
|
3391
|
+
|
3392
|
+
mask (input) int[nrows][ncolumns]
|
3393
|
+
This array shows which data values are missing. If
|
3394
|
+
mask[i][j] == 0, then data[i][j] is missing.
|
3395
|
+
|
3396
|
+
weight (input) double[n]
|
3397
|
+
The weights that are used to calculate the distance. The length of this vector
|
3398
|
+
is ncolumns if genes are being clustered, and nrows if microarrays are being
|
3399
|
+
clustered.
|
3400
|
+
|
3401
|
+
transpose (input) int
|
3402
|
+
If transpose==0, the rows of the matrix are clustered. Otherwise, columns
|
3403
|
+
of the matrix are clustered.
|
3404
|
+
|
3405
|
+
dist (input) char
|
3406
|
+
Defines which distance measure is used, as given by the table:
|
3407
|
+
dist=='e': Euclidean distance
|
3408
|
+
dist=='b': City-block distance
|
3409
|
+
dist=='c': correlation
|
3410
|
+
dist=='a': absolute value of the correlation
|
3411
|
+
dist=='u': uncentered correlation
|
3412
|
+
dist=='x': absolute uncentered correlation
|
3413
|
+
dist=='s': Spearman's rank correlation
|
3414
|
+
dist=='k': Kendall's tau
|
3415
|
+
For other values of dist, the default (Euclidean distance) is used.
|
3416
|
+
|
3417
|
+
distmatrix (input) double**
|
3418
|
+
The distance matrix. If the distance matrix is passed by the calling routine
|
3419
|
+
treecluster, it is used by pslcluster to speed up the clustering calculation.
|
3420
|
+
The pslcluster routine does not modify the contents of distmatrix, and does
|
3421
|
+
not deallocate it. If distmatrix is NULL, the pairwise distances are calculated
|
3422
|
+
by the pslcluster routine from the gene expression data (the data and mask
|
3423
|
+
arrays) and stored in temporary arrays. If distmatrix is passed, the original
|
3424
|
+
gene expression data (specified by the data and mask arguments) are not needed
|
3425
|
+
and are therefore ignored.
|
3426
|
+
|
3427
|
+
|
3428
|
+
Return value
|
3429
|
+
============
|
3430
|
+
|
3431
|
+
A pointer to a newly allocated array of Node structs, describing the
|
3432
|
+
hierarchical clustering solution consisting of nelements-1 nodes. Depending on
|
3433
|
+
whether genes (rows) or microarrays (columns) were clustered, nelements is
|
3434
|
+
equal to nrows or ncolumns. See src/cluster.h for a description of the Node
|
3435
|
+
structure.
|
3436
|
+
If a memory error occurs, pslcluster returns NULL.
|
3437
|
+
|
3438
|
+
========================================================================
|
3439
|
+
*/
|
3440
|
+
{ int i, j, k;
|
3441
|
+
const int nelements = transpose ? ncolumns : nrows;
|
3442
|
+
const int nnodes = nelements - 1;
|
3443
|
+
int* vector;
|
3444
|
+
double* temp;
|
3445
|
+
int* index;
|
3446
|
+
Node* result;
|
3447
|
+
temp = malloc(nnodes*sizeof(double));
|
3448
|
+
if(!temp) return NULL;
|
3449
|
+
index = malloc(nelements*sizeof(int));
|
3450
|
+
if(!index)
|
3451
|
+
{ free(temp);
|
3452
|
+
return NULL;
|
3453
|
+
}
|
3454
|
+
vector = malloc(nnodes*sizeof(int));
|
3455
|
+
if(!vector)
|
3456
|
+
{ free(index);
|
3457
|
+
free(temp);
|
3458
|
+
return NULL;
|
3459
|
+
}
|
3460
|
+
result = malloc(nelements*sizeof(Node));
|
3461
|
+
if(!result)
|
3462
|
+
{ free(vector);
|
3463
|
+
free(index);
|
3464
|
+
free(temp);
|
3465
|
+
return NULL;
|
3466
|
+
}
|
3467
|
+
|
3468
|
+
for (i = 0; i < nnodes; i++) vector[i] = i;
|
3469
|
+
|
3470
|
+
if(distmatrix)
|
3471
|
+
{ for (i = 0; i < nrows; i++)
|
3472
|
+
{ result[i].distance = DBL_MAX;
|
3473
|
+
for (j = 0; j < i; j++) temp[j] = distmatrix[i][j];
|
3474
|
+
for (j = 0; j < i; j++)
|
3475
|
+
{ k = vector[j];
|
3476
|
+
if (result[j].distance >= temp[j])
|
3477
|
+
{ if (result[j].distance < temp[k]) temp[k] = result[j].distance;
|
3478
|
+
result[j].distance = temp[j];
|
3479
|
+
vector[j] = i;
|
3480
|
+
}
|
3481
|
+
else if (temp[j] < temp[k]) temp[k] = temp[j];
|
3482
|
+
}
|
3483
|
+
for (j = 0; j < i; j++)
|
3484
|
+
{
|
3485
|
+
if (result[j].distance >= result[vector[j]].distance) vector[j] = i;
|
3486
|
+
}
|
3487
|
+
}
|
3488
|
+
}
|
3489
|
+
else
|
3490
|
+
{ const int ndata = transpose ? nrows : ncolumns;
|
3491
|
+
/* Set the metric function as indicated by dist */
|
3492
|
+
double (*metric)
|
3493
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
3494
|
+
setmetric(dist);
|
3495
|
+
|
3496
|
+
for (i = 0; i < nelements; i++)
|
3497
|
+
{ result[i].distance = DBL_MAX;
|
3498
|
+
for (j = 0; j < i; j++) temp[j] =
|
3499
|
+
metric(ndata, data, data, mask, mask, weight, i, j, transpose);
|
3500
|
+
for (j = 0; j < i; j++)
|
3501
|
+
{ k = vector[j];
|
3502
|
+
if (result[j].distance >= temp[j])
|
3503
|
+
{ if (result[j].distance < temp[k]) temp[k] = result[j].distance;
|
3504
|
+
result[j].distance = temp[j];
|
3505
|
+
vector[j] = i;
|
3506
|
+
}
|
3507
|
+
else if (temp[j] < temp[k]) temp[k] = temp[j];
|
3508
|
+
}
|
3509
|
+
for (j = 0; j < i; j++)
|
3510
|
+
if (result[j].distance >= result[vector[j]].distance) vector[j] = i;
|
3511
|
+
}
|
3512
|
+
}
|
3513
|
+
free(temp);
|
3514
|
+
|
3515
|
+
for (i = 0; i < nnodes; i++) result[i].left = i;
|
3516
|
+
qsort(result, nnodes, sizeof(Node), nodecompare);
|
3517
|
+
|
3518
|
+
for (i = 0; i < nelements; i++) index[i] = i;
|
3519
|
+
for (i = 0; i < nnodes; i++)
|
3520
|
+
{ j = result[i].left;
|
3521
|
+
k = vector[j];
|
3522
|
+
result[i].left = index[j];
|
3523
|
+
result[i].right = index[k];
|
3524
|
+
index[k] = -i-1;
|
3525
|
+
}
|
3526
|
+
free(vector);
|
3527
|
+
free(index);
|
3528
|
+
|
3529
|
+
result = realloc(result, nnodes*sizeof(Node));
|
3530
|
+
|
3531
|
+
return result;
|
3532
|
+
}
|
3533
|
+
/* ******************************************************************** */
|
3534
|
+
|
3535
|
+
static Node* pmlcluster (int nelements, double** distmatrix)
|
3536
|
+
/*
|
3537
|
+
|
3538
|
+
Purpose
|
3539
|
+
=======
|
3540
|
+
|
3541
|
+
The pmlcluster routine performs clustering using pairwise maximum- (complete-)
|
3542
|
+
linking on the given distance matrix.
|
3543
|
+
|
3544
|
+
Arguments
|
3545
|
+
=========
|
3546
|
+
|
3547
|
+
nelements (input) int
|
3548
|
+
The number of elements to be clustered.
|
3549
|
+
|
3550
|
+
distmatrix (input) double**
|
3551
|
+
The distance matrix, with nelements rows, each row being filled up to the
|
3552
|
+
diagonal. The elements on the diagonal are not used, as they are assumed to be
|
3553
|
+
zero. The distance matrix will be modified by this routine.
|
3554
|
+
|
3555
|
+
Return value
|
3556
|
+
============
|
3557
|
+
|
3558
|
+
A pointer to a newly allocated array of Node structs, describing the
|
3559
|
+
hierarchical clustering solution consisting of nelements-1 nodes. Depending on
|
3560
|
+
whether genes (rows) or microarrays (columns) were clustered, nelements is
|
3561
|
+
equal to nrows or ncolumns. See src/cluster.h for a description of the Node
|
3562
|
+
structure.
|
3563
|
+
If a memory error occurs, pmlcluster returns NULL.
|
3564
|
+
========================================================================
|
3565
|
+
*/
|
3566
|
+
{ int j;
|
3567
|
+
int n;
|
3568
|
+
int* clusterid;
|
3569
|
+
Node* result;
|
3570
|
+
|
3571
|
+
clusterid = malloc(nelements*sizeof(int));
|
3572
|
+
if(!clusterid) return NULL;
|
3573
|
+
result = malloc((nelements-1)*sizeof(Node));
|
3574
|
+
if (!result)
|
3575
|
+
{ free(clusterid);
|
3576
|
+
return NULL;
|
3577
|
+
}
|
3578
|
+
|
3579
|
+
/* Setup a list specifying to which cluster a gene belongs */
|
3580
|
+
for (j = 0; j < nelements; j++) clusterid[j] = j;
|
3581
|
+
|
3582
|
+
for (n = nelements; n > 1; n--)
|
3583
|
+
{ int is = 1;
|
3584
|
+
int js = 0;
|
3585
|
+
result[nelements-n].distance = find_closest_pair(n, distmatrix, &is, &js);
|
3586
|
+
|
3587
|
+
/* Fix the distances */
|
3588
|
+
for (j = 0; j < js; j++)
|
3589
|
+
distmatrix[js][j] = max(distmatrix[is][j],distmatrix[js][j]);
|
3590
|
+
for (j = js+1; j < is; j++)
|
3591
|
+
distmatrix[j][js] = max(distmatrix[is][j],distmatrix[j][js]);
|
3592
|
+
for (j = is+1; j < n; j++)
|
3593
|
+
distmatrix[j][js] = max(distmatrix[j][is],distmatrix[j][js]);
|
3594
|
+
|
3595
|
+
for (j = 0; j < is; j++) distmatrix[is][j] = distmatrix[n-1][j];
|
3596
|
+
for (j = is+1; j < n-1; j++) distmatrix[j][is] = distmatrix[n-1][j];
|
3597
|
+
|
3598
|
+
/* Update clusterids */
|
3599
|
+
result[nelements-n].left = clusterid[is];
|
3600
|
+
result[nelements-n].right = clusterid[js];
|
3601
|
+
clusterid[js] = n-nelements-1;
|
3602
|
+
clusterid[is] = clusterid[n-1];
|
3603
|
+
}
|
3604
|
+
free(clusterid);
|
3605
|
+
|
3606
|
+
return result;
|
3607
|
+
}
|
3608
|
+
|
3609
|
+
/* ******************************************************************* */
|
3610
|
+
|
3611
|
+
static Node* palcluster (int nelements, double** distmatrix)
|
3612
|
+
/*
|
3613
|
+
Purpose
|
3614
|
+
=======
|
3615
|
+
|
3616
|
+
The palcluster routine performs clustering using pairwise average
|
3617
|
+
linking on the given distance matrix.
|
3618
|
+
|
3619
|
+
Arguments
|
3620
|
+
=========
|
3621
|
+
|
3622
|
+
nelements (input) int
|
3623
|
+
The number of elements to be clustered.
|
3624
|
+
|
3625
|
+
distmatrix (input) double**
|
3626
|
+
The distance matrix, with nelements rows, each row being filled up to the
|
3627
|
+
diagonal. The elements on the diagonal are not used, as they are assumed to be
|
3628
|
+
zero. The distance matrix will be modified by this routine.
|
3629
|
+
|
3630
|
+
Return value
|
3631
|
+
============
|
3632
|
+
|
3633
|
+
A pointer to a newly allocated array of Node structs, describing the
|
3634
|
+
hierarchical clustering solution consisting of nelements-1 nodes. Depending on
|
3635
|
+
whether genes (rows) or microarrays (columns) were clustered, nelements is
|
3636
|
+
equal to nrows or ncolumns. See src/cluster.h for a description of the Node
|
3637
|
+
structure.
|
3638
|
+
If a memory error occurs, palcluster returns NULL.
|
3639
|
+
========================================================================
|
3640
|
+
*/
|
3641
|
+
{ int j;
|
3642
|
+
int n;
|
3643
|
+
int* clusterid;
|
3644
|
+
int* number;
|
3645
|
+
Node* result;
|
3646
|
+
|
3647
|
+
clusterid = malloc(nelements*sizeof(int));
|
3648
|
+
if(!clusterid) return NULL;
|
3649
|
+
number = malloc(nelements*sizeof(int));
|
3650
|
+
if(!number)
|
3651
|
+
{ free(clusterid);
|
3652
|
+
return NULL;
|
3653
|
+
}
|
3654
|
+
result = malloc((nelements-1)*sizeof(Node));
|
3655
|
+
if (!result)
|
3656
|
+
{ free(clusterid);
|
3657
|
+
free(number);
|
3658
|
+
return NULL;
|
3659
|
+
}
|
3660
|
+
|
3661
|
+
/* Setup a list specifying to which cluster a gene belongs, and keep track
|
3662
|
+
* of the number of elements in each cluster (needed to calculate the
|
3663
|
+
* average). */
|
3664
|
+
for (j = 0; j < nelements; j++)
|
3665
|
+
{ number[j] = 1;
|
3666
|
+
clusterid[j] = j;
|
3667
|
+
}
|
3668
|
+
|
3669
|
+
for (n = nelements; n > 1; n--)
|
3670
|
+
{ int sum;
|
3671
|
+
int is = 1;
|
3672
|
+
int js = 0;
|
3673
|
+
result[nelements-n].distance = find_closest_pair(n, distmatrix, &is, &js);
|
3674
|
+
|
3675
|
+
/* Save result */
|
3676
|
+
result[nelements-n].left = clusterid[is];
|
3677
|
+
result[nelements-n].right = clusterid[js];
|
3678
|
+
|
3679
|
+
/* Fix the distances */
|
3680
|
+
sum = number[is] + number[js];
|
3681
|
+
for (j = 0; j < js; j++)
|
3682
|
+
{ distmatrix[js][j] = distmatrix[is][j]*number[is]
|
3683
|
+
+ distmatrix[js][j]*number[js];
|
3684
|
+
distmatrix[js][j] /= sum;
|
3685
|
+
}
|
3686
|
+
for (j = js+1; j < is; j++)
|
3687
|
+
{ distmatrix[j][js] = distmatrix[is][j]*number[is]
|
3688
|
+
+ distmatrix[j][js]*number[js];
|
3689
|
+
distmatrix[j][js] /= sum;
|
3690
|
+
}
|
3691
|
+
for (j = is+1; j < n; j++)
|
3692
|
+
{ distmatrix[j][js] = distmatrix[j][is]*number[is]
|
3693
|
+
+ distmatrix[j][js]*number[js];
|
3694
|
+
distmatrix[j][js] /= sum;
|
3695
|
+
}
|
3696
|
+
|
3697
|
+
for (j = 0; j < is; j++) distmatrix[is][j] = distmatrix[n-1][j];
|
3698
|
+
for (j = is+1; j < n-1; j++) distmatrix[j][is] = distmatrix[n-1][j];
|
3699
|
+
|
3700
|
+
/* Update number of elements in the clusters */
|
3701
|
+
number[js] = sum;
|
3702
|
+
number[is] = number[n-1];
|
3703
|
+
|
3704
|
+
/* Update clusterids */
|
3705
|
+
clusterid[js] = n-nelements-1;
|
3706
|
+
clusterid[is] = clusterid[n-1];
|
3707
|
+
}
|
3708
|
+
free(clusterid);
|
3709
|
+
free(number);
|
3710
|
+
|
3711
|
+
return result;
|
3712
|
+
}
|
3713
|
+
|
3714
|
+
/* ******************************************************************* */
|
3715
|
+
|
3716
|
+
Node* treecluster (int nrows, int ncolumns, double** data, int** mask,
|
3717
|
+
double weight[], int transpose, char dist, char method, double** distmatrix)
|
3718
|
+
/*
|
3719
|
+
Purpose
|
3720
|
+
=======
|
3721
|
+
|
3722
|
+
The treecluster routine performs hierarchical clustering using pairwise
|
3723
|
+
single-, maximum-, centroid-, or average-linkage, as defined by method, on a
|
3724
|
+
given set of gene expression data, using the distance metric given by dist.
|
3725
|
+
If successful, the function returns a pointer to a newly allocated Tree struct
|
3726
|
+
containing the hierarchical clustering solution, and NULL if a memory error
|
3727
|
+
occurs. The pointer should be freed by the calling routine to prevent memory
|
3728
|
+
leaks.
|
3729
|
+
|
3730
|
+
Arguments
|
3731
|
+
=========
|
3732
|
+
|
3733
|
+
nrows (input) int
|
3734
|
+
The number of rows in the data matrix, equal to the number of genes.
|
3735
|
+
|
3736
|
+
ncolumns (input) int
|
3737
|
+
The number of columns in the data matrix, equal to the number of microarrays.
|
3738
|
+
|
3739
|
+
data (input) double[nrows][ncolumns]
|
3740
|
+
The array containing the data of the vectors to be clustered.
|
3741
|
+
|
3742
|
+
mask (input) int[nrows][ncolumns]
|
3743
|
+
This array shows which data values are missing. If mask[i][j]==0, then
|
3744
|
+
data[i][j] is missing.
|
3745
|
+
|
3746
|
+
weight (input) double array[n]
|
3747
|
+
The weights that are used to calculate the distance.
|
3748
|
+
|
3749
|
+
transpose (input) int
|
3750
|
+
If transpose==0, the rows of the matrix are clustered. Otherwise, columns
|
3751
|
+
of the matrix are clustered.
|
3752
|
+
|
3753
|
+
dist (input) char
|
3754
|
+
Defines which distance measure is used, as given by the table:
|
3755
|
+
dist=='e': Euclidean distance
|
3756
|
+
dist=='b': City-block distance
|
3757
|
+
dist=='c': correlation
|
3758
|
+
dist=='a': absolute value of the correlation
|
3759
|
+
dist=='u': uncentered correlation
|
3760
|
+
dist=='x': absolute uncentered correlation
|
3761
|
+
dist=='s': Spearman's rank correlation
|
3762
|
+
dist=='k': Kendall's tau
|
3763
|
+
For other values of dist, the default (Euclidean distance) is used.
|
3764
|
+
|
3765
|
+
method (input) char
|
3766
|
+
Defines which hierarchical clustering method is used:
|
3767
|
+
method=='s': pairwise single-linkage clustering
|
3768
|
+
method=='m': pairwise maximum- (or complete-) linkage clustering
|
3769
|
+
method=='a': pairwise average-linkage clustering
|
3770
|
+
method=='c': pairwise centroid-linkage clustering
|
3771
|
+
For the first three, either the distance matrix or the gene expression data is
|
3772
|
+
sufficient to perform the clustering algorithm. For pairwise centroid-linkage
|
3773
|
+
clustering, however, the gene expression data are always needed, even if the
|
3774
|
+
distance matrix itself is available.
|
3775
|
+
|
3776
|
+
distmatrix (input) double**
|
3777
|
+
The distance matrix. If the distance matrix is zero initially, the distance
|
3778
|
+
matrix will be allocated and calculated from the data by treecluster, and
|
3779
|
+
deallocated before treecluster returns. If the distance matrix is passed by the
|
3780
|
+
calling routine, treecluster will modify the contents of the distance matrix as
|
3781
|
+
part of the clustering algorithm, but will not deallocate it. The calling
|
3782
|
+
routine should deallocate the distance matrix after the return from treecluster.
|
3783
|
+
|
3784
|
+
Return value
|
3785
|
+
============
|
3786
|
+
|
3787
|
+
A pointer to a newly allocated array of Node structs, describing the
|
3788
|
+
hierarchical clustering solution consisting of nelements-1 nodes. Depending on
|
3789
|
+
whether genes (rows) or microarrays (columns) were clustered, nelements is
|
3790
|
+
equal to nrows or ncolumns. See src/cluster.h for a description of the Node
|
3791
|
+
structure.
|
3792
|
+
If a memory error occurs, treecluster returns NULL.
|
3793
|
+
|
3794
|
+
========================================================================
|
3795
|
+
*/
|
3796
|
+
{ Node* result = NULL;
|
3797
|
+
const int nelements = (transpose==0) ? nrows : ncolumns;
|
3798
|
+
const int ldistmatrix = (distmatrix==NULL && method!='s') ? 1 : 0;
|
3799
|
+
|
3800
|
+
if (nelements < 2) return NULL;
|
3801
|
+
|
3802
|
+
/* Calculate the distance matrix if the user didn't give it */
|
3803
|
+
if(ldistmatrix)
|
3804
|
+
{ distmatrix =
|
3805
|
+
distancematrix(nrows, ncolumns, data, mask, weight, dist, transpose);
|
3806
|
+
if (!distmatrix) return NULL; /* Insufficient memory */
|
3807
|
+
}
|
3808
|
+
|
3809
|
+
switch(method)
|
3810
|
+
{ case 's':
|
3811
|
+
result = pslcluster(nrows, ncolumns, data, mask, weight, distmatrix,
|
3812
|
+
dist, transpose);
|
3813
|
+
break;
|
3814
|
+
case 'm':
|
3815
|
+
result = pmlcluster(nelements, distmatrix);
|
3816
|
+
break;
|
3817
|
+
case 'a':
|
3818
|
+
result = palcluster(nelements, distmatrix);
|
3819
|
+
break;
|
3820
|
+
case 'c':
|
3821
|
+
result = pclcluster(nrows, ncolumns, data, mask, weight, distmatrix,
|
3822
|
+
dist, transpose);
|
3823
|
+
break;
|
3824
|
+
}
|
3825
|
+
|
3826
|
+
/* Deallocate space for distance matrix, if it was allocated by treecluster */
|
3827
|
+
if(ldistmatrix)
|
3828
|
+
{ int i;
|
3829
|
+
for (i = 1; i < nelements; i++) free(distmatrix[i]);
|
3830
|
+
free (distmatrix);
|
3831
|
+
}
|
3832
|
+
|
3833
|
+
return result;
|
3834
|
+
}
|
3835
|
+
|
3836
|
+
/* ******************************************************************* */
|
3837
|
+
|
3838
|
+
static
|
3839
|
+
void somworker (int nrows, int ncolumns, double** data, int** mask,
|
3840
|
+
const double weights[], int transpose, int nxgrid, int nygrid,
|
3841
|
+
double inittau, double*** celldata, int niter, char dist)
|
3842
|
+
|
3843
|
+
{ const int nelements = (transpose==0) ? nrows : ncolumns;
|
3844
|
+
const int ndata = (transpose==0) ? ncolumns : nrows;
|
3845
|
+
int i, j;
|
3846
|
+
double* stddata = calloc(nelements,sizeof(double));
|
3847
|
+
int** dummymask;
|
3848
|
+
int ix, iy;
|
3849
|
+
int* index;
|
3850
|
+
int iter;
|
3851
|
+
/* Maximum radius in which nodes are adjusted */
|
3852
|
+
double maxradius = sqrt(nxgrid*nxgrid+nygrid*nygrid);
|
3853
|
+
|
3854
|
+
/* Set the metric function as indicated by dist */
|
3855
|
+
double (*metric)
|
3856
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
3857
|
+
setmetric(dist);
|
3858
|
+
|
3859
|
+
/* Calculate the standard deviation for each row or column */
|
3860
|
+
if (transpose==0)
|
3861
|
+
{ for (i = 0; i < nelements; i++)
|
3862
|
+
{ int n = 0;
|
3863
|
+
for (j = 0; j < ndata; j++)
|
3864
|
+
{ if (mask[i][j])
|
3865
|
+
{ double term = data[i][j];
|
3866
|
+
term = term * term;
|
3867
|
+
stddata[i] += term;
|
3868
|
+
n++;
|
3869
|
+
}
|
3870
|
+
}
|
3871
|
+
if (stddata[i] > 0) stddata[i] = sqrt(stddata[i]/n);
|
3872
|
+
else stddata[i] = 1;
|
3873
|
+
}
|
3874
|
+
}
|
3875
|
+
else
|
3876
|
+
{ for (i = 0; i < nelements; i++)
|
3877
|
+
{ int n = 0;
|
3878
|
+
for (j = 0; j < ndata; j++)
|
3879
|
+
{ if (mask[j][i])
|
3880
|
+
{ double term = data[j][i];
|
3881
|
+
term = term * term;
|
3882
|
+
stddata[i] += term;
|
3883
|
+
n++;
|
3884
|
+
}
|
3885
|
+
}
|
3886
|
+
if (stddata[i] > 0) stddata[i] = sqrt(stddata[i]/n);
|
3887
|
+
else stddata[i] = 1;
|
3888
|
+
}
|
3889
|
+
}
|
3890
|
+
|
3891
|
+
if (transpose==0)
|
3892
|
+
{ dummymask = malloc(nygrid*sizeof(int*));
|
3893
|
+
for (i = 0; i < nygrid; i++)
|
3894
|
+
{ dummymask[i] = malloc(ndata*sizeof(int));
|
3895
|
+
for (j = 0; j < ndata; j++) dummymask[i][j] = 1;
|
3896
|
+
}
|
3897
|
+
}
|
3898
|
+
else
|
3899
|
+
{ dummymask = malloc(ndata*sizeof(int*));
|
3900
|
+
for (i = 0; i < ndata; i++)
|
3901
|
+
{ dummymask[i] = malloc(sizeof(int));
|
3902
|
+
dummymask[i][0] = 1;
|
3903
|
+
}
|
3904
|
+
}
|
3905
|
+
|
3906
|
+
/* Randomly initialize the nodes */
|
3907
|
+
for (ix = 0; ix < nxgrid; ix++)
|
3908
|
+
{ for (iy = 0; iy < nygrid; iy++)
|
3909
|
+
{ double sum = 0.;
|
3910
|
+
for (i = 0; i < ndata; i++)
|
3911
|
+
{ double term = -1.0 + 2.0*uniform();
|
3912
|
+
celldata[ix][iy][i] = term;
|
3913
|
+
sum += term * term;
|
3914
|
+
}
|
3915
|
+
sum = sqrt(sum/ndata);
|
3916
|
+
for (i = 0; i < ndata; i++) celldata[ix][iy][i] /= sum;
|
3917
|
+
}
|
3918
|
+
}
|
3919
|
+
|
3920
|
+
/* Randomize the order in which genes or arrays will be used */
|
3921
|
+
index = malloc(nelements*sizeof(int));
|
3922
|
+
for (i = 0; i < nelements; i++) index[i] = i;
|
3923
|
+
for (i = 0; i < nelements; i++)
|
3924
|
+
{ j = (int) (i + (nelements-i)*uniform());
|
3925
|
+
ix = index[j];
|
3926
|
+
index[j] = index[i];
|
3927
|
+
index[i] = ix;
|
3928
|
+
}
|
3929
|
+
|
3930
|
+
/* Start the iteration */
|
3931
|
+
for (iter = 0; iter < niter; iter++)
|
3932
|
+
{ int ixbest = 0;
|
3933
|
+
int iybest = 0;
|
3934
|
+
int iobject = iter % nelements;
|
3935
|
+
iobject = index[iobject];
|
3936
|
+
if (transpose==0)
|
3937
|
+
{ double closest = metric(ndata,data,celldata[ixbest],
|
3938
|
+
mask,dummymask,weights,iobject,iybest,transpose);
|
3939
|
+
double radius = maxradius * (1. - ((double)iter)/((double)niter));
|
3940
|
+
double tau = inittau * (1. - ((double)iter)/((double)niter));
|
3941
|
+
|
3942
|
+
for (ix = 0; ix < nxgrid; ix++)
|
3943
|
+
{ for (iy = 0; iy < nygrid; iy++)
|
3944
|
+
{ double distance =
|
3945
|
+
metric (ndata,data,celldata[ix],
|
3946
|
+
mask,dummymask,weights,iobject,iy,transpose);
|
3947
|
+
if (distance < closest)
|
3948
|
+
{ ixbest = ix;
|
3949
|
+
iybest = iy;
|
3950
|
+
closest = distance;
|
3951
|
+
}
|
3952
|
+
}
|
3953
|
+
}
|
3954
|
+
for (ix = 0; ix < nxgrid; ix++)
|
3955
|
+
{ for (iy = 0; iy < nygrid; iy++)
|
3956
|
+
{ if (sqrt((ix-ixbest)*(ix-ixbest)+(iy-iybest)*(iy-iybest))<radius)
|
3957
|
+
{ double sum = 0.;
|
3958
|
+
for (i = 0; i < ndata; i++)
|
3959
|
+
{ if (mask[iobject][i]==0) continue;
|
3960
|
+
celldata[ix][iy][i] +=
|
3961
|
+
tau * (data[iobject][i]/stddata[iobject]-celldata[ix][iy][i]);
|
3962
|
+
}
|
3963
|
+
for (i = 0; i < ndata; i++)
|
3964
|
+
{ double term = celldata[ix][iy][i];
|
3965
|
+
term = term * term;
|
3966
|
+
sum += term;
|
3967
|
+
}
|
3968
|
+
if (sum>0)
|
3969
|
+
{ sum = sqrt(sum/ndata);
|
3970
|
+
for (i = 0; i < ndata; i++) celldata[ix][iy][i] /= sum;
|
3971
|
+
}
|
3972
|
+
}
|
3973
|
+
}
|
3974
|
+
}
|
3975
|
+
}
|
3976
|
+
else
|
3977
|
+
{ double closest;
|
3978
|
+
double** celldatavector = malloc(ndata*sizeof(double*));
|
3979
|
+
double radius = maxradius * (1. - ((double)iter)/((double)niter));
|
3980
|
+
double tau = inittau * (1. - ((double)iter)/((double)niter));
|
3981
|
+
|
3982
|
+
for (i = 0; i < ndata; i++)
|
3983
|
+
celldatavector[i] = &(celldata[ixbest][iybest][i]);
|
3984
|
+
closest = metric(ndata,data,celldatavector,
|
3985
|
+
mask,dummymask,weights,iobject,0,transpose);
|
3986
|
+
for (ix = 0; ix < nxgrid; ix++)
|
3987
|
+
{ for (iy = 0; iy < nygrid; iy++)
|
3988
|
+
{ double distance;
|
3989
|
+
for (i = 0; i < ndata; i++)
|
3990
|
+
celldatavector[i] = &(celldata[ixbest][iybest][i]);
|
3991
|
+
distance =
|
3992
|
+
metric (ndata,data,celldatavector,
|
3993
|
+
mask,dummymask,weights,iobject,0,transpose);
|
3994
|
+
if (distance < closest)
|
3995
|
+
{ ixbest = ix;
|
3996
|
+
iybest = iy;
|
3997
|
+
closest = distance;
|
3998
|
+
}
|
3999
|
+
}
|
4000
|
+
}
|
4001
|
+
free(celldatavector);
|
4002
|
+
for (ix = 0; ix < nxgrid; ix++)
|
4003
|
+
{ for (iy = 0; iy < nygrid; iy++)
|
4004
|
+
{ if (sqrt((ix-ixbest)*(ix-ixbest)+(iy-iybest)*(iy-iybest))<radius)
|
4005
|
+
{ double sum = 0.;
|
4006
|
+
for (i = 0; i < ndata; i++)
|
4007
|
+
{ if (mask[i][iobject]==0) continue;
|
4008
|
+
celldata[ix][iy][i] +=
|
4009
|
+
tau * (data[i][iobject]/stddata[iobject]-celldata[ix][iy][i]);
|
4010
|
+
}
|
4011
|
+
for (i = 0; i < ndata; i++)
|
4012
|
+
{ double term = celldata[ix][iy][i];
|
4013
|
+
term = term * term;
|
4014
|
+
sum += term;
|
4015
|
+
}
|
4016
|
+
if (sum>0)
|
4017
|
+
{ sum = sqrt(sum/ndata);
|
4018
|
+
for (i = 0; i < ndata; i++) celldata[ix][iy][i] /= sum;
|
4019
|
+
}
|
4020
|
+
}
|
4021
|
+
}
|
4022
|
+
}
|
4023
|
+
}
|
4024
|
+
}
|
4025
|
+
if (transpose==0)
|
4026
|
+
for (i = 0; i < nygrid; i++) free(dummymask[i]);
|
4027
|
+
else
|
4028
|
+
for (i = 0; i < ndata; i++) free(dummymask[i]);
|
4029
|
+
free(dummymask);
|
4030
|
+
free(stddata);
|
4031
|
+
free(index);
|
4032
|
+
return;
|
4033
|
+
}
|
4034
|
+
|
4035
|
+
/* ******************************************************************* */
|
4036
|
+
|
4037
|
+
static
|
4038
|
+
void somassign (int nrows, int ncolumns, double** data, int** mask,
|
4039
|
+
const double weights[], int transpose, int nxgrid, int nygrid,
|
4040
|
+
double*** celldata, char dist, int clusterid[][2])
|
4041
|
+
/* Collect clusterids */
|
4042
|
+
{ const int ndata = (transpose==0) ? ncolumns : nrows;
|
4043
|
+
int i,j;
|
4044
|
+
|
4045
|
+
/* Set the metric function as indicated by dist */
|
4046
|
+
double (*metric)
|
4047
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
4048
|
+
setmetric(dist);
|
4049
|
+
|
4050
|
+
if (transpose==0)
|
4051
|
+
{ int** dummymask = malloc(nygrid*sizeof(int*));
|
4052
|
+
for (i = 0; i < nygrid; i++)
|
4053
|
+
{ dummymask[i] = malloc(ncolumns*sizeof(int));
|
4054
|
+
for (j = 0; j < ncolumns; j++) dummymask[i][j] = 1;
|
4055
|
+
}
|
4056
|
+
for (i = 0; i < nrows; i++)
|
4057
|
+
{ int ixbest = 0;
|
4058
|
+
int iybest = 0;
|
4059
|
+
double closest = metric(ndata,data,celldata[ixbest],
|
4060
|
+
mask,dummymask,weights,i,iybest,transpose);
|
4061
|
+
int ix, iy;
|
4062
|
+
for (ix = 0; ix < nxgrid; ix++)
|
4063
|
+
{ for (iy = 0; iy < nygrid; iy++)
|
4064
|
+
{ double distance =
|
4065
|
+
metric (ndata,data,celldata[ix],
|
4066
|
+
mask,dummymask,weights,i,iy,transpose);
|
4067
|
+
if (distance < closest)
|
4068
|
+
{ ixbest = ix;
|
4069
|
+
iybest = iy;
|
4070
|
+
closest = distance;
|
4071
|
+
}
|
4072
|
+
}
|
4073
|
+
}
|
4074
|
+
clusterid[i][0] = ixbest;
|
4075
|
+
clusterid[i][1] = iybest;
|
4076
|
+
}
|
4077
|
+
for (i = 0; i < nygrid; i++) free(dummymask[i]);
|
4078
|
+
free(dummymask);
|
4079
|
+
}
|
4080
|
+
else
|
4081
|
+
{ double** celldatavector = malloc(ndata*sizeof(double*));
|
4082
|
+
int** dummymask = malloc(nrows*sizeof(int*));
|
4083
|
+
int ixbest = 0;
|
4084
|
+
int iybest = 0;
|
4085
|
+
for (i = 0; i < nrows; i++)
|
4086
|
+
{ dummymask[i] = malloc(sizeof(int));
|
4087
|
+
dummymask[i][0] = 1;
|
4088
|
+
}
|
4089
|
+
for (i = 0; i < ncolumns; i++)
|
4090
|
+
{ double closest;
|
4091
|
+
int ix, iy;
|
4092
|
+
for (j = 0; j < ndata; j++)
|
4093
|
+
celldatavector[j] = &(celldata[ixbest][iybest][j]);
|
4094
|
+
closest = metric(ndata,data,celldatavector,
|
4095
|
+
mask,dummymask,weights,i,0,transpose);
|
4096
|
+
for (ix = 0; ix < nxgrid; ix++)
|
4097
|
+
{ for (iy = 0; iy < nygrid; iy++)
|
4098
|
+
{ double distance;
|
4099
|
+
for(j = 0; j < ndata; j++)
|
4100
|
+
celldatavector[j] = &(celldata[ix][iy][j]);
|
4101
|
+
distance = metric(ndata,data,celldatavector,
|
4102
|
+
mask,dummymask,weights,i,0,transpose);
|
4103
|
+
if (distance < closest)
|
4104
|
+
{ ixbest = ix;
|
4105
|
+
iybest = iy;
|
4106
|
+
closest = distance;
|
4107
|
+
}
|
4108
|
+
}
|
4109
|
+
}
|
4110
|
+
clusterid[i][0] = ixbest;
|
4111
|
+
clusterid[i][1] = iybest;
|
4112
|
+
}
|
4113
|
+
free(celldatavector);
|
4114
|
+
for (i = 0; i < nrows; i++) free(dummymask[i]);
|
4115
|
+
free(dummymask);
|
4116
|
+
}
|
4117
|
+
return;
|
4118
|
+
}
|
4119
|
+
|
4120
|
+
/* ******************************************************************* */
|
4121
|
+
|
4122
|
+
void somcluster (int nrows, int ncolumns, double** data, int** mask,
|
4123
|
+
const double weight[], int transpose, int nxgrid, int nygrid,
|
4124
|
+
double inittau, int niter, char dist, double*** celldata, int clusterid[][2])
|
4125
|
+
/*
|
4126
|
+
|
4127
|
+
Purpose
|
4128
|
+
=======
|
4129
|
+
|
4130
|
+
The somcluster routine implements a self-organizing map (Kohonen) on a
|
4131
|
+
rectangular grid, using a given set of vectors. The distance measure to be
|
4132
|
+
used to find the similarity between genes and nodes is given by dist.
|
4133
|
+
|
4134
|
+
Arguments
|
4135
|
+
=========
|
4136
|
+
|
4137
|
+
nrows (input) int
|
4138
|
+
The number of rows in the data matrix, equal to the number of genes.
|
4139
|
+
|
4140
|
+
ncolumns (input) int
|
4141
|
+
The number of columns in the data matrix, equal to the number of microarrays.
|
4142
|
+
|
4143
|
+
data (input) double[nrows][ncolumns]
|
4144
|
+
The array containing the gene expression data.
|
4145
|
+
|
4146
|
+
mask (input) int[nrows][ncolumns]
|
4147
|
+
This array shows which data values are missing. If
|
4148
|
+
mask[i][j] == 0, then data[i][j] is missing.
|
4149
|
+
|
4150
|
+
weights (input) double[ncolumns] if transpose==0;
|
4151
|
+
double[nrows] if transpose==1
|
4152
|
+
The weights that are used to calculate the distance. The length of this vector
|
4153
|
+
is ncolumns if genes are being clustered, or nrows if microarrays are being
|
4154
|
+
clustered.
|
4155
|
+
|
4156
|
+
transpose (input) int
|
4157
|
+
If transpose==0, the rows (genes) of the matrix are clustered. Otherwise,
|
4158
|
+
columns (microarrays) of the matrix are clustered.
|
4159
|
+
|
4160
|
+
nxgrid (input) int
|
4161
|
+
The number of grid cells horizontally in the rectangular topology of clusters.
|
4162
|
+
|
4163
|
+
nygrid (input) int
|
4164
|
+
The number of grid cells horizontally in the rectangular topology of clusters.
|
4165
|
+
|
4166
|
+
inittau (input) double
|
4167
|
+
The initial value of tau, representing the neighborhood function.
|
4168
|
+
|
4169
|
+
niter (input) int
|
4170
|
+
The number of iterations to be performed.
|
4171
|
+
|
4172
|
+
dist (input) char
|
4173
|
+
Defines which distance measure is used, as given by the table:
|
4174
|
+
dist=='e': Euclidean distance
|
4175
|
+
dist=='b': City-block distance
|
4176
|
+
dist=='c': correlation
|
4177
|
+
dist=='a': absolute value of the correlation
|
4178
|
+
dist=='u': uncentered correlation
|
4179
|
+
dist=='x': absolute uncentered correlation
|
4180
|
+
dist=='s': Spearman's rank correlation
|
4181
|
+
dist=='k': Kendall's tau
|
4182
|
+
For other values of dist, the default (Euclidean distance) is used.
|
4183
|
+
|
4184
|
+
celldata (output) double[nxgrid][nygrid][ncolumns] if transpose==0;
|
4185
|
+
double[nxgrid][nygrid][nrows] if tranpose==1
|
4186
|
+
The gene expression data for each node (cell) in the 2D grid. This can be
|
4187
|
+
interpreted as the centroid for the cluster corresponding to that cell. If
|
4188
|
+
celldata is NULL, then the centroids are not returned. If celldata is not
|
4189
|
+
NULL, enough space should be allocated to store the centroid data before callingsomcluster.
|
4190
|
+
|
4191
|
+
clusterid (output), int[nrows][2] if transpose==0;
|
4192
|
+
int[ncolumns][2] if transpose==1
|
4193
|
+
For each item (gene or microarray) that is clustered, the coordinates of the
|
4194
|
+
cell in the 2D grid to which the item was assigned. If clusterid is NULL, the
|
4195
|
+
cluster assignments are not returned. If clusterid is not NULL, enough memory
|
4196
|
+
should be allocated to store the clustering information before calling
|
4197
|
+
somcluster.
|
4198
|
+
|
4199
|
+
========================================================================
|
4200
|
+
*/
|
4201
|
+
{ const int nobjects = (transpose==0) ? nrows : ncolumns;
|
4202
|
+
const int ndata = (transpose==0) ? ncolumns : nrows;
|
4203
|
+
int i,j;
|
4204
|
+
const int lcelldata = (celldata==NULL) ? 0 : 1;
|
4205
|
+
|
4206
|
+
if (nobjects < 2) return;
|
4207
|
+
|
4208
|
+
if (lcelldata==0)
|
4209
|
+
{ celldata = malloc(nxgrid*nygrid*ndata*sizeof(double**));
|
4210
|
+
for (i = 0; i < nxgrid; i++)
|
4211
|
+
{ celldata[i] = malloc(nygrid*ndata*sizeof(double*));
|
4212
|
+
for (j = 0; j < nygrid; j++)
|
4213
|
+
celldata[i][j] = malloc(ndata*sizeof(double));
|
4214
|
+
}
|
4215
|
+
}
|
4216
|
+
|
4217
|
+
somworker (nrows, ncolumns, data, mask, weight, transpose, nxgrid, nygrid,
|
4218
|
+
inittau, celldata, niter, dist);
|
4219
|
+
if (clusterid)
|
4220
|
+
somassign (nrows, ncolumns, data, mask, weight, transpose,
|
4221
|
+
nxgrid, nygrid, celldata, dist, clusterid);
|
4222
|
+
if(lcelldata==0)
|
4223
|
+
{ for (i = 0; i < nxgrid; i++)
|
4224
|
+
for (j = 0; j < nygrid; j++)
|
4225
|
+
free(celldata[i][j]);
|
4226
|
+
for (i = 0; i < nxgrid; i++)
|
4227
|
+
free(celldata[i]);
|
4228
|
+
free(celldata);
|
4229
|
+
}
|
4230
|
+
return;
|
4231
|
+
}
|
4232
|
+
|
4233
|
+
/* ******************************************************************** */
|
4234
|
+
|
4235
|
+
double clusterdistance (int nrows, int ncolumns, double** data,
|
4236
|
+
int** mask, double weight[], int n1, int n2, int index1[], int index2[],
|
4237
|
+
char dist, char method, int transpose)
|
4238
|
+
|
4239
|
+
/*
|
4240
|
+
Purpose
|
4241
|
+
=======
|
4242
|
+
|
4243
|
+
The clusterdistance routine calculates the distance between two clusters
|
4244
|
+
containing genes or microarrays using the measured gene expression vectors. The
|
4245
|
+
distance between clusters, given the genes/microarrays in each cluster, can be
|
4246
|
+
defined in several ways. Several distance measures can be used.
|
4247
|
+
|
4248
|
+
The routine returns the distance in double precision.
|
4249
|
+
If the parameter transpose is set to a nonzero value, the clusters are
|
4250
|
+
interpreted as clusters of microarrays, otherwise as clusters of gene.
|
4251
|
+
|
4252
|
+
Arguments
|
4253
|
+
=========
|
4254
|
+
|
4255
|
+
nrows (input) int
|
4256
|
+
The number of rows (i.e., the number of genes) in the gene expression data
|
4257
|
+
matrix.
|
4258
|
+
|
4259
|
+
ncolumns (input) int
|
4260
|
+
The number of columns (i.e., the number of microarrays) in the gene expression
|
4261
|
+
data matrix.
|
4262
|
+
|
4263
|
+
data (input) double[nrows][ncolumns]
|
4264
|
+
The array containing the data of the vectors.
|
4265
|
+
|
4266
|
+
mask (input) int[nrows][ncolumns]
|
4267
|
+
This array shows which data values are missing. If mask[i][j]==0, then
|
4268
|
+
data[i][j] is missing.
|
4269
|
+
|
4270
|
+
weight (input) double[ncolumns] if transpose==0;
|
4271
|
+
double[nrows] if transpose==1
|
4272
|
+
The weights that are used to calculate the distance.
|
4273
|
+
|
4274
|
+
n1 (input) int
|
4275
|
+
The number of elements in the first cluster.
|
4276
|
+
|
4277
|
+
n2 (input) int
|
4278
|
+
The number of elements in the second cluster.
|
4279
|
+
|
4280
|
+
index1 (input) int[n1]
|
4281
|
+
Identifies which genes/microarrays belong to the first cluster.
|
4282
|
+
|
4283
|
+
index2 (input) int[n2]
|
4284
|
+
Identifies which genes/microarrays belong to the second cluster.
|
4285
|
+
|
4286
|
+
dist (input) char
|
4287
|
+
Defines which distance measure is used, as given by the table:
|
4288
|
+
dist=='e': Euclidean distance
|
4289
|
+
dist=='b': City-block distance
|
4290
|
+
dist=='c': correlation
|
4291
|
+
dist=='a': absolute value of the correlation
|
4292
|
+
dist=='u': uncentered correlation
|
4293
|
+
dist=='x': absolute uncentered correlation
|
4294
|
+
dist=='s': Spearman's rank correlation
|
4295
|
+
dist=='k': Kendall's tau
|
4296
|
+
For other values of dist, the default (Euclidean distance) is used.
|
4297
|
+
|
4298
|
+
method (input) char
|
4299
|
+
Defines how the distance between two clusters is defined, given which genes
|
4300
|
+
belong to which cluster:
|
4301
|
+
method=='a': the distance between the arithmetic means of the two clusters
|
4302
|
+
method=='m': the distance between the medians of the two clusters
|
4303
|
+
method=='s': the smallest pairwise distance between members of the two clusters
|
4304
|
+
method=='x': the largest pairwise distance between members of the two clusters
|
4305
|
+
method=='v': average of the pairwise distances between members of the clusters
|
4306
|
+
|
4307
|
+
transpose (input) int
|
4308
|
+
If transpose is equal to zero, the distances between the rows is
|
4309
|
+
calculated. Otherwise, the distances between the columns is calculated.
|
4310
|
+
The former is needed when genes are being clustered; the latter is used
|
4311
|
+
when microarrays are being clustered.
|
4312
|
+
|
4313
|
+
========================================================================
|
4314
|
+
*/
|
4315
|
+
{ /* Set the metric function as indicated by dist */
|
4316
|
+
double (*metric)
|
4317
|
+
(int, double**, double**, int**, int**, const double[], int, int, int) =
|
4318
|
+
setmetric(dist);
|
4319
|
+
|
4320
|
+
/* if one or both clusters are empty, return */
|
4321
|
+
if (n1 < 1 || n2 < 1) return -1.0;
|
4322
|
+
/* Check the indices */
|
4323
|
+
if (transpose==0)
|
4324
|
+
{ int i;
|
4325
|
+
for (i = 0; i < n1; i++)
|
4326
|
+
{ int index = index1[i];
|
4327
|
+
if (index < 0 || index >= nrows) return -1.0;
|
4328
|
+
}
|
4329
|
+
for (i = 0; i < n2; i++)
|
4330
|
+
{ int index = index2[i];
|
4331
|
+
if (index < 0 || index >= nrows) return -1.0;
|
4332
|
+
}
|
4333
|
+
}
|
4334
|
+
else
|
4335
|
+
{ int i;
|
4336
|
+
for (i = 0; i < n1; i++)
|
4337
|
+
{ int index = index1[i];
|
4338
|
+
if (index < 0 || index >= ncolumns) return -1.0;
|
4339
|
+
}
|
4340
|
+
for (i = 0; i < n2; i++)
|
4341
|
+
{ int index = index2[i];
|
4342
|
+
if (index < 0 || index >= ncolumns) return -1.0;
|
4343
|
+
}
|
4344
|
+
}
|
4345
|
+
|
4346
|
+
switch (method)
|
4347
|
+
{ case 'a':
|
4348
|
+
{ /* Find the center */
|
4349
|
+
int i,j,k;
|
4350
|
+
if (transpose==0)
|
4351
|
+
{ double distance;
|
4352
|
+
double* cdata[2];
|
4353
|
+
int* cmask[2];
|
4354
|
+
int* count[2];
|
4355
|
+
count[0] = calloc(ncolumns,sizeof(int));
|
4356
|
+
count[1] = calloc(ncolumns,sizeof(int));
|
4357
|
+
cdata[0] = calloc(ncolumns,sizeof(double));
|
4358
|
+
cdata[1] = calloc(ncolumns,sizeof(double));
|
4359
|
+
cmask[0] = malloc(ncolumns*sizeof(int));
|
4360
|
+
cmask[1] = malloc(ncolumns*sizeof(int));
|
4361
|
+
for (i = 0; i < n1; i++)
|
4362
|
+
{ k = index1[i];
|
4363
|
+
for (j = 0; j < ncolumns; j++)
|
4364
|
+
if (mask[k][j] != 0)
|
4365
|
+
{ cdata[0][j] = cdata[0][j] + data[k][j];
|
4366
|
+
count[0][j] = count[0][j] + 1;
|
4367
|
+
}
|
4368
|
+
}
|
4369
|
+
for (i = 0; i < n2; i++)
|
4370
|
+
{ k = index2[i];
|
4371
|
+
for (j = 0; j < ncolumns; j++)
|
4372
|
+
if (mask[k][j] != 0)
|
4373
|
+
{ cdata[1][j] = cdata[1][j] + data[k][j];
|
4374
|
+
count[1][j] = count[1][j] + 1;
|
4375
|
+
}
|
4376
|
+
}
|
4377
|
+
for (i = 0; i < 2; i++)
|
4378
|
+
for (j = 0; j < ncolumns; j++)
|
4379
|
+
{ if (count[i][j]>0)
|
4380
|
+
{ cdata[i][j] = cdata[i][j] / count[i][j];
|
4381
|
+
cmask[i][j] = 1;
|
4382
|
+
}
|
4383
|
+
else
|
4384
|
+
cmask[i][j] = 0;
|
4385
|
+
}
|
4386
|
+
distance =
|
4387
|
+
metric (ncolumns,cdata,cdata,cmask,cmask,weight,0,1,0);
|
4388
|
+
for (i = 0; i < 2; i++)
|
4389
|
+
{ free (cdata[i]);
|
4390
|
+
free (cmask[i]);
|
4391
|
+
free (count[i]);
|
4392
|
+
}
|
4393
|
+
return distance;
|
4394
|
+
}
|
4395
|
+
else
|
4396
|
+
{ double distance;
|
4397
|
+
int** count = malloc(nrows*sizeof(int*));
|
4398
|
+
double** cdata = malloc(nrows*sizeof(double*));
|
4399
|
+
int** cmask = malloc(nrows*sizeof(int*));
|
4400
|
+
for (i = 0; i < nrows; i++)
|
4401
|
+
{ count[i] = calloc(2,sizeof(int));
|
4402
|
+
cdata[i] = calloc(2,sizeof(double));
|
4403
|
+
cmask[i] = malloc(2*sizeof(int));
|
4404
|
+
}
|
4405
|
+
for (i = 0; i < n1; i++)
|
4406
|
+
{ k = index1[i];
|
4407
|
+
for (j = 0; j < nrows; j++)
|
4408
|
+
{ if (mask[j][k] != 0)
|
4409
|
+
{ cdata[j][0] = cdata[j][0] + data[j][k];
|
4410
|
+
count[j][0] = count[j][0] + 1;
|
4411
|
+
}
|
4412
|
+
}
|
4413
|
+
}
|
4414
|
+
for (i = 0; i < n2; i++)
|
4415
|
+
{ k = index2[i];
|
4416
|
+
for (j = 0; j < nrows; j++)
|
4417
|
+
{ if (mask[j][k] != 0)
|
4418
|
+
{ cdata[j][1] = cdata[j][1] + data[j][k];
|
4419
|
+
count[j][1] = count[j][1] + 1;
|
4420
|
+
}
|
4421
|
+
}
|
4422
|
+
}
|
4423
|
+
for (i = 0; i < nrows; i++)
|
4424
|
+
for (j = 0; j < 2; j++)
|
4425
|
+
if (count[i][j]>0)
|
4426
|
+
{ cdata[i][j] = cdata[i][j] / count[i][j];
|
4427
|
+
cmask[i][j] = 1;
|
4428
|
+
}
|
4429
|
+
else
|
4430
|
+
cmask[i][j] = 0;
|
4431
|
+
distance = metric (nrows,cdata,cdata,cmask,cmask,weight,0,1,1);
|
4432
|
+
for (i = 0; i < nrows; i++)
|
4433
|
+
{ free (count[i]);
|
4434
|
+
free (cdata[i]);
|
4435
|
+
free (cmask[i]);
|
4436
|
+
}
|
4437
|
+
free (count);
|
4438
|
+
free (cdata);
|
4439
|
+
free (cmask);
|
4440
|
+
return distance;
|
4441
|
+
}
|
4442
|
+
}
|
4443
|
+
case 'm':
|
4444
|
+
{ int i, j, k;
|
4445
|
+
if (transpose==0)
|
4446
|
+
{ double distance;
|
4447
|
+
double* temp = malloc(nrows*sizeof(double));
|
4448
|
+
double* cdata[2];
|
4449
|
+
int* cmask[2];
|
4450
|
+
for (i = 0; i < 2; i++)
|
4451
|
+
{ cdata[i] = malloc(ncolumns*sizeof(double));
|
4452
|
+
cmask[i] = malloc(ncolumns*sizeof(int));
|
4453
|
+
}
|
4454
|
+
for (j = 0; j < ncolumns; j++)
|
4455
|
+
{ int count = 0;
|
4456
|
+
for (k = 0; k < n1; k++)
|
4457
|
+
{ i = index1[k];
|
4458
|
+
if (mask[i][j])
|
4459
|
+
{ temp[count] = data[i][j];
|
4460
|
+
count++;
|
4461
|
+
}
|
4462
|
+
}
|
4463
|
+
if (count>0)
|
4464
|
+
{ cdata[0][j] = median (count,temp);
|
4465
|
+
cmask[0][j] = 1;
|
4466
|
+
}
|
4467
|
+
else
|
4468
|
+
{ cdata[0][j] = 0.;
|
4469
|
+
cmask[0][j] = 0;
|
4470
|
+
}
|
4471
|
+
}
|
4472
|
+
for (j = 0; j < ncolumns; j++)
|
4473
|
+
{ int count = 0;
|
4474
|
+
for (k = 0; k < n2; k++)
|
4475
|
+
{ i = index2[k];
|
4476
|
+
if (mask[i][j])
|
4477
|
+
{ temp[count] = data[i][j];
|
4478
|
+
count++;
|
4479
|
+
}
|
4480
|
+
}
|
4481
|
+
if (count>0)
|
4482
|
+
{ cdata[1][j] = median (count,temp);
|
4483
|
+
cmask[1][j] = 1;
|
4484
|
+
}
|
4485
|
+
else
|
4486
|
+
{ cdata[1][j] = 0.;
|
4487
|
+
cmask[1][j] = 0;
|
4488
|
+
}
|
4489
|
+
}
|
4490
|
+
distance = metric (ncolumns,cdata,cdata,cmask,cmask,weight,0,1,0);
|
4491
|
+
for (i = 0; i < 2; i++)
|
4492
|
+
{ free (cdata[i]);
|
4493
|
+
free (cmask[i]);
|
4494
|
+
}
|
4495
|
+
free(temp);
|
4496
|
+
return distance;
|
4497
|
+
}
|
4498
|
+
else
|
4499
|
+
{ double distance;
|
4500
|
+
double* temp = malloc(ncolumns*sizeof(double));
|
4501
|
+
double** cdata = malloc(nrows*sizeof(double*));
|
4502
|
+
int** cmask = malloc(nrows*sizeof(int*));
|
4503
|
+
for (i = 0; i < nrows; i++)
|
4504
|
+
{ cdata[i] = malloc(2*sizeof(double));
|
4505
|
+
cmask[i] = malloc(2*sizeof(int));
|
4506
|
+
}
|
4507
|
+
for (j = 0; j < nrows; j++)
|
4508
|
+
{ int count = 0;
|
4509
|
+
for (k = 0; k < n1; k++)
|
4510
|
+
{ i = index1[k];
|
4511
|
+
if (mask[j][i])
|
4512
|
+
{ temp[count] = data[j][i];
|
4513
|
+
count++;
|
4514
|
+
}
|
4515
|
+
}
|
4516
|
+
if (count>0)
|
4517
|
+
{ cdata[j][0] = median (count,temp);
|
4518
|
+
cmask[j][0] = 1;
|
4519
|
+
}
|
4520
|
+
else
|
4521
|
+
{ cdata[j][0] = 0.;
|
4522
|
+
cmask[j][0] = 0;
|
4523
|
+
}
|
4524
|
+
}
|
4525
|
+
for (j = 0; j < nrows; j++)
|
4526
|
+
{ int count = 0;
|
4527
|
+
for (k = 0; k < n2; k++)
|
4528
|
+
{ i = index2[k];
|
4529
|
+
if (mask[j][i])
|
4530
|
+
{ temp[count] = data[j][i];
|
4531
|
+
count++;
|
4532
|
+
}
|
4533
|
+
}
|
4534
|
+
if (count>0)
|
4535
|
+
{ cdata[j][1] = median (count,temp);
|
4536
|
+
cmask[j][1] = 1;
|
4537
|
+
}
|
4538
|
+
else
|
4539
|
+
{ cdata[j][1] = 0.;
|
4540
|
+
cmask[j][1] = 0;
|
4541
|
+
}
|
4542
|
+
}
|
4543
|
+
distance = metric (nrows,cdata,cdata,cmask,cmask,weight,0,1,1);
|
4544
|
+
for (i = 0; i < nrows; i++)
|
4545
|
+
{ free (cdata[i]);
|
4546
|
+
free (cmask[i]);
|
4547
|
+
}
|
4548
|
+
free(cdata);
|
4549
|
+
free(cmask);
|
4550
|
+
free(temp);
|
4551
|
+
return distance;
|
4552
|
+
}
|
4553
|
+
}
|
4554
|
+
case 's':
|
4555
|
+
{ int i1, i2, j1, j2;
|
4556
|
+
const int n = (transpose==0) ? ncolumns : nrows;
|
4557
|
+
double mindistance = DBL_MAX;
|
4558
|
+
for (i1 = 0; i1 < n1; i1++)
|
4559
|
+
for (i2 = 0; i2 < n2; i2++)
|
4560
|
+
{ double distance;
|
4561
|
+
j1 = index1[i1];
|
4562
|
+
j2 = index2[i2];
|
4563
|
+
distance = metric (n,data,data,mask,mask,weight,j1,j2,transpose);
|
4564
|
+
if (distance < mindistance) mindistance = distance;
|
4565
|
+
}
|
4566
|
+
return mindistance;
|
4567
|
+
}
|
4568
|
+
case 'x':
|
4569
|
+
{ int i1, i2, j1, j2;
|
4570
|
+
const int n = (transpose==0) ? ncolumns : nrows;
|
4571
|
+
double maxdistance = 0;
|
4572
|
+
for (i1 = 0; i1 < n1; i1++)
|
4573
|
+
for (i2 = 0; i2 < n2; i2++)
|
4574
|
+
{ double distance;
|
4575
|
+
j1 = index1[i1];
|
4576
|
+
j2 = index2[i2];
|
4577
|
+
distance = metric (n,data,data,mask,mask,weight,j1,j2,transpose);
|
4578
|
+
if (distance > maxdistance) maxdistance = distance;
|
4579
|
+
}
|
4580
|
+
return maxdistance;
|
4581
|
+
}
|
4582
|
+
case 'v':
|
4583
|
+
{ int i1, i2, j1, j2;
|
4584
|
+
const int n = (transpose==0) ? ncolumns : nrows;
|
4585
|
+
double distance = 0;
|
4586
|
+
for (i1 = 0; i1 < n1; i1++)
|
4587
|
+
for (i2 = 0; i2 < n2; i2++)
|
4588
|
+
{ j1 = index1[i1];
|
4589
|
+
j2 = index2[i2];
|
4590
|
+
distance += metric (n,data,data,mask,mask,weight,j1,j2,transpose);
|
4591
|
+
}
|
4592
|
+
distance /= (n1*n2);
|
4593
|
+
return distance;
|
4594
|
+
}
|
4595
|
+
}
|
4596
|
+
/* Never get here */
|
4597
|
+
return -2.0;
|
4598
|
+
}
|