Clustering by single-linkage point ordering.
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OPTICS : single-linkage point ordering -------------------------------------- OPTICS is an algorithm to detect the single-linkage structure in data collections. The algorithm detects, for each point, the number of neighbours within a pre-defined radius 'epsilon' and, if the number is larger than the predefined threshold 'minPoints', proceeds with the closest neighbour point, otherwise with the next point in the list of unprocessed points. OPTICS does not provide a clustering structure per se, but the point ordering together with the closest-neighbour information can be used to extract a cluster structure. The algorithm is useful for large data sets with overlapping areas of varying point density. The code has been tested to work for >300000 data points. The algorithm requires only two input para- meters: a neighbourhood radius (epsilon) and a minimum number of neighbour points (MinPts). If we set epsilon to the largest distance in the dataset then each point is reachable and this parameter has no influence on the results. Briefly, the algorithm starts at a random data point, cal- culates the distance to all points within the neighbourhood radius (epsilon) and, if at least a minimal number of points (MinPts) is encountered, it records the nearest neighbour distance (Reachability Distance) and the smallest radius that encircles MinPts objects (Core Distance). If less than MinPts points fall within epsilon, the point is considered as noise. The algorithm repeats the same procedure for the nearest neighbour point and proceeds iteratively until all data points have been visited, thereby generating an ordered list. Setting epsilon to the largest distance implies that none of the fragments is labelled 'noise' and each is included in one cluster at least. This choice allows to scan afterwards for clusters at any density. The ordered list of Reachability Distances (RDs) can be drawn as a comprehensive nearest neighbour distance plot (called Reachability Plot). The output files are as follows: - file 'output.dat' contains the ordered list of input data; given are their location 'dataID' in the input data file, core distance 'CD' and reachability distance 'RD'. - file 'cluster.dat' contains the cluster structure of the data; given are the cluster identifier 'id', the id of the 'parent' cluster, 'start' and 'end' in the ordered list and 'size' of the cluster, its smallest core distance 'minCD' and the identifier 'minCDid' of that point. - file 'center.dat' contains the cluster centres; given are the centre's location 'index', identifier in the ordered list 'order', cluster identifier 'clusterID', core distance 'CD', reachability distance 'RD' and coordinates 'x' 'y' 'z'. References ---------- Users publishing results obtained with the program should acknowledge its use by citation: - Pandini, A, Fornili, A, Kleinjung, J Structural alphabets derived from attractors in conformational space. BMC Bioinformatics 11:97 (20 February), 2010. Other references: - Ankerst M, Breunig MM, Kriegel HP, Sander J: OPTICS: Ordering Points To Identify the Clustering Structure. SIGMOD Proceedings ACM SIGMOD International Conference on Management of Data, June 1-3, 1999, Philadelphia, Pennsylvania, USA ACM PressDelis A, Faloutsos C, Ghandeharizadeh S 1999, 49-60. - Daszykowski M, Walczak B, Massart DL: Looking for natural patterns in analytical data. 2. Tracing local density with OPTICS. Journal of chemical information and computer sciences 2002, 42(3):500-507. Install / Uninstall ------------------- Please read the general 'INSTALL' instructions. There are several versions of the program that are invoked upon compilation with 'configure --enable-data-<version>': - optics_ang for input data in angle coordinates compile using the command './configure --enable-data-ang' - optics_str for input data in string format compile using the command './configure --enable-data-str' - optics_vec for input data in vector (of arbitrary length) format compile using the command './configure --enable-data-vec' - optics_xyz for input data in xyz (Cartesian) coordinates compile using the command './configure --enable-data-xyz' - optics_dist for input data as distance matrix compile using the command './configure --enable-data-dist' The 'optics_ang' program requires the 'pcre' pattern matching library. See http://www.pcre.org/ for installation options. The 'optics_vec' program has several distance metrics, one of which is enabled by a '#define' instruction at the top of the program. Run 'configure --help' for more information. For documentation execute 'doxygen doxygen.cfg' in the 'src' directory. Documentation files are created in 'doc/html' and 'doc/latex'. The latex documentation is completed by executing 'make pdf' in the 'doc/latex' directory, which creates 'refman.ps' and 'refman.pdf'. Usage ----- optics: perform OPTICS single-linkage point ordering (C) 2008-2015 by Jens Kleinjung and Alessandro Pandini This program is free software. optics [--datafile ...] [OPTIONS ...] --datafile <filename> (mode: mandatory, type: char, default: input.dat) --outputfile <filename> (mode: optional, type: char, default: output.dat) --clusterfile <filename> (mode: optional, type: char, default: cluster.dat) --centerfile <filename> (mode: optional, type: char, default: center.dat) --uniquefile <filename> (mode: optional, type: char, default: unique.dat) --eps <epsilon cutoff> (mode: optional, type: float, default: 2.91) --minpts <min number of neighbours> (mode: optional, type: int, default: 1) --w <window size for string version> (mode: optional, type: int, default: 1) --silent (mode: optional, no argument, default: off) --cite (mode: optional , type: no_arg, default: off) --version (mode: optional , type: no_arg, default: off) --help Use the configure options described in 'README Install/Uninstall' to compile a specific verion. Input formats ------------- - optics_ang - optics_str - optics_vec The input format is array of vectors of arbitrary length composed of space separated floats. - optics_xyz - optics_dist - optics_dist The input format is a triangular matrix of distance values in float format. See for example the 'tests/dist.dat' file. The matrix contains the distances of the [i,j] point pairs [0,1] [0,2] [0,3] [0,4] [0,5] [1,2] [1,3] [1,4] [1,5] [2,3] [2,4] [2,5] [3,4] [3,5] [4,5] with values 5 3 2 8 1 7 4 7 2 4 2 4 7 3 2 White space and line breaks are irrelevant for the input format, only the order of values in the above sense must be correct. Return values ------------- 0 : Clean termination. 1 : Error. ------------------------------------------------------------------------------- Copyright (C) 2008-2016 Jens Kleinjung Copyright (C) 2008-2016 Alessandro Pandini The development was kindly supported by grants from the European Science Foundation "Frontiers of Functional Genomics" and "Marie-Curie Intra-European Fellowships for Career development" (Call identifier: PEOPLE-2007-2-1-IEF). Further support was given by the MRC National Institute for Medical Research. Availability ------------ The program is made available under the GNU Public License for academic scientific purposes, under the condition that proper acknowledgement is made to the authors of the program in publications resulting from the use of the program. License ------- This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
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