5 * Created by westcott on 1/11/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "nmdscommand.h"
11 #include "readphylipvector.h"
13 //**********************************************************************************************************************
14 vector<string> NMDSCommand::getValidParameters(){
16 string Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir","inputdir"};
17 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
21 m->errorOut(e, "NMDSCommand", "getValidParameters");
25 //**********************************************************************************************************************
26 NMDSCommand::NMDSCommand(){
29 //initialize outputTypes
30 vector<string> tempOutNames;
31 outputTypes["nmds"] = tempOutNames;
32 outputTypes["stress"] = tempOutNames;
35 m->errorOut(e, "NMDSCommand", "NMDSCommand");
39 //**********************************************************************************************************************
40 vector<string> NMDSCommand::getRequiredParameters(){
42 string Array[] = {"phylip"};
43 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
47 m->errorOut(e, "NMDSCommand", "getRequiredParameters");
51 //**********************************************************************************************************************
52 vector<string> NMDSCommand::getRequiredFiles(){
54 vector<string> myArray;
58 m->errorOut(e, "NMDSCommand", "getRequiredFiles");
62 //**********************************************************************************************************************
64 NMDSCommand::NMDSCommand(string option) {
68 //allow user to run help
69 if(option == "help") { help(); abort = true; }
72 //valid paramters for this command
73 string Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir", "inputdir"};
74 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
76 OptionParser parser(option);
77 map<string, string> parameters = parser. getParameters();
79 ValidParameters validParameter;
80 map<string, string>::iterator it;
82 //check to make sure all parameters are valid for command
83 for (it = parameters.begin(); it != parameters.end(); it++) {
84 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
86 //if the user changes the input directory command factory will send this info to us in the output parameter
87 string inputDir = validParameter.validFile(parameters, "inputdir", false);
88 if (inputDir == "not found"){ inputDir = ""; }
91 it = parameters.find("phylip");
92 //user has given a template file
93 if(it != parameters.end()){
94 path = m->hasPath(it->second);
95 //if the user has not given a path then, add inputdir. else leave path alone.
96 if (path == "") { parameters["phylip"] = inputDir + it->second; }
99 it = parameters.find("axes");
100 //user has given a template file
101 if(it != parameters.end()){
102 path = m->hasPath(it->second);
103 //if the user has not given a path then, add inputdir. else leave path alone.
104 if (path == "") { parameters["axes"] = inputDir + it->second; }
108 //initialize outputTypes
109 vector<string> tempOutNames;
110 outputTypes["nmds"] = tempOutNames;
111 outputTypes["stress"] = tempOutNames;
113 //required parameters
114 phylipfile = validParameter.validFile(parameters, "phylip", true);
115 if (phylipfile == "not open") { phylipfile = ""; abort = true; }
116 else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("You must provide a distance file before running the nmds command."); m->mothurOutEndLine(); abort = true; }
118 axesfile = validParameter.validFile(parameters, "axes", true);
119 if (axesfile == "not open") { axesfile = ""; abort = true; }
120 else if (axesfile == "not found") { axesfile = ""; }
122 //if the user changes the output directory command factory will send this info to us in the output parameter
123 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
125 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
128 string temp = validParameter.validFile(parameters, "mindim", false); if (temp == "not found") { temp = "1"; }
129 convert(temp, mindim);
131 temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") { temp = "500"; }
132 convert(temp, maxIters);
134 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10"; }
135 convert(temp, iters);
137 temp = validParameter.validFile(parameters, "maxdim", false); if (temp == "not found") { temp = "2"; }
138 convert(temp, maxdim);
140 temp = validParameter.validFile(parameters, "epsilon", false); if (temp == "not found") { temp = "0.000000000001"; }
141 convert(temp, epsilon);
143 if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
144 if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
148 catch(exception& e) {
149 m->errorOut(e, "NMDSCommand", "NMDSCommand");
153 //**********************************************************************************************************************
154 void NMDSCommand::help(){
156 m->mothurOut("The nmds command is modelled after the nmds code written in R by Sarah Goslee, using Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling."); m->mothurOutEndLine();
157 m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon."); m->mothurOutEndLine();
158 m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
159 m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
160 m->mothurOut("The maxdim parameter allows you to select how maximum dimensions to use. Default=2"); m->mothurOutEndLine();
161 m->mothurOut("The mindim parameter allows you to select how minimum dimensions to use. Default=1"); m->mothurOutEndLine();
162 m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine();
163 m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine();
164 m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine();
165 m->mothurOut("Example nmds(phylip=yourDistanceFile).\n");
166 m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
168 catch(exception& e) {
169 m->errorOut(e, "NMDSCommand", "help");
173 //**********************************************************************************************************************
174 NMDSCommand::~NMDSCommand(){}
175 //**********************************************************************************************************************
176 int NMDSCommand::execute(){
179 if (abort == true) { return 0; }
181 cout.setf(ios::fixed, ios::floatfield);
182 cout.setf(ios::showpoint);
184 vector<string> names;
185 vector< vector< double> > matrix;
187 //read in phylip file
188 ReadPhylipVector readFile(phylipfile);
189 names = readFile.read(matrix);
190 if (m->control_pressed) { return 0; }
193 vector< vector<double> > axes;
194 if (axesfile != "") { axes = readAxes(names); }
196 for (int i = mindim; i <= maxdim; i++) {
197 m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
199 string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "dim" + toString(i) + ".nmds";
200 string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "dim" + toString(i) + ".stress.nmds";
201 outputNames.push_back(outputFileName); outputTypes["nmds"].push_back(outputFileName);
202 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
205 m->openOutputFile(outputFileName, out);
206 m->openOutputFile(stressFileName, out2);
208 out2.setf(ios::fixed, ios::floatfield);
209 out2.setf(ios::showpoint);
210 out.setf(ios::fixed, ios::floatfield);
211 out.setf(ios::showpoint);
213 out2 << "Iter\tStress\tCorr" << endl;
215 for (int j = 0; j < iters; j++) {
216 m->mothurOut(toString(j+1)); m->mothurOutEndLine();
218 //get configuration - either randomly generate or resize to this dimension
219 vector< vector<double> > thisConfig;
220 if (axesfile == "") { thisConfig = generateStartingConfiguration(names.size(), i); }
221 else { thisConfig = getConfiguration(axes, i); }
222 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
224 //calc nmds for this dimension
226 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
227 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
229 //calc euclid distances for new config
230 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
231 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
233 //calc correlation between original distances and euclidean distances from this config
234 double corr = linearCalc.calcPearson(matrix, newEuclid);
236 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
239 out << "Config" << (j+1) << '\t';
240 for (int k = 0; k < i; k++) { out << "X" << (k+1) << '\t'; }
242 out2 << (j+1) << '\t' << stress << '\t' << corr << endl;
244 output(endConfig, names, out);
246 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { remove(outputNames[k].c_str()); } return 0; }
250 out.close(); out2.close();
253 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
255 m->mothurOutEndLine();
256 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
257 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
258 m->mothurOutEndLine();
262 catch(exception& e) {
263 m->errorOut(e, "NMDSCommand", "execute");
267 //**********************************************************************************************************************
268 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
271 vector< vector<double> > newConfig = config;
273 //calc euclid distances
274 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
275 if (m->control_pressed) { return newConfig; }
277 double stress2 = calculateStress(matrix, euclid);
278 stress1 = stress2 + 1.0 + epsilon;
281 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
286 if (m->control_pressed) { return newConfig; }
288 vector< vector<double> > b; b.resize(euclid.size());
289 for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
291 vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
292 for (int i = 0; i < euclid.size(); i++) {
293 for (int j = 0; j < euclid[i].size(); j++) {
294 //eliminate divide by zero error
295 if (euclid[i][j] != 0) {
296 b[i][j] = matrix[i][j] / euclid[i][j];
297 columnSums[j] += b[i][j];
303 //put in diagonal sums
304 for (int i = 0; i < euclid.size(); i++) { b[i][i] = columnSums[i]; }
306 int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
307 double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
310 newConfig = linearCalc.matrix_mult(newConfig, b);
311 for (int i = 0; i < newConfig.size(); i++) {
312 for (int j = 0; j < newConfig[i].size(); j++) {
313 newConfig[i][j] *= (1.0 / n);
317 euclid = linearCalc.calculateEuclidianDistance(newConfig);
319 stress2 = calculateStress(matrix, euclid);
324 catch(exception& e) {
325 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
330 //**********************************************************************************************************************
331 //generate random config
332 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
334 vector< vector<double> > axes; axes.resize(dimension);
335 for (int i = 0; i < axes.size(); i++) { axes[i].resize(numNames); }
337 //generate random number between -1 and 1, precision 6
338 for (int i = 0; i < axes.size(); i++) {
339 for (int j = 0; j < axes[i].size(); j++) {
341 if (m->control_pressed) { return axes; }
343 //generate random int between 0 and 99999
344 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
346 //generate random sign
347 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
349 //if mysign is even then sign = positive, else sign = negative
350 if ((mysign % 2) == 0) { mysign = 1.0; }
351 else { mysign = -1.0; }
353 axes[i][j] = mysign * myrand / (float) 100000;
359 catch(exception& e) {
360 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
364 //**********************************************************************************************************************
365 //normalize configuration
366 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
368 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
371 for (int i = 0; i < axes.size(); i++) {
372 for (int j = 0; j < axes[i].size(); j++) { averageAxes[i] += axes[i][j]; }
374 averageAxes[i] /= (float) numNames;
378 double sumDenom = 0.0;
379 for (int i = 0; i < axes.size(); i++) {
380 for (int j = 0; j < axes[i].size(); j++) {
381 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
385 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
387 for (int i = 0; i < axes.size(); i++) {
388 for (int j = 0; j < axes[i].size(); j++) {
389 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
395 catch(exception& e) {
396 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
400 //**********************************************************************************************************************
402 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
404 vector< vector<double> > newAxes; newAxes.resize(dimension);
406 for (int i = 0; i < dimension; i++) {
407 newAxes[i] = axes[i];
412 catch(exception& e) {
413 m->errorOut(e, "NMDSCommand", "getConfiguration");
417 //**********************************************************************************************************************
418 //find raw stress, and normalize using
419 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
421 double normStress = 0.0;
423 double rawStress = 0.0;
426 for (int i = 0; i < matrix.size(); i++) {
427 for (int j = 0; j < matrix[i].size(); j++) {
428 if (m->control_pressed) { return normStress; }
430 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
431 denom += (config[i][j] * config[i][j]);
436 if ((rawStress != 0.0) && (denom != 0.0)) {
437 normStress = sqrt((rawStress / denom));
442 catch(exception& e) {
443 m->errorOut(e, "NMDSCommand", "calculateStress");
448 //**********************************************************************************************************************
449 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
452 for (int i = 0; i < names.size(); i++) {
454 out << names[i] << '\t';
456 for (int j = 0; j < config.size(); j++) {
457 out << config[j][i] << '\t';
467 catch(exception& e) {
468 m->errorOut(e, "NMDSCommand", "output");
472 /*****************************************************************/
473 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
476 m->openInputFile(axesfile, in);
478 string headerLine = m->getline(in); m->gobble(in);
480 //count the number of axis you are reading
484 int pos = headerLine.find("axis");
485 if (pos != string::npos) {
487 headerLine = headerLine.substr(pos+4);
488 }else { done = true; }
491 if (maxdim > count) {
492 m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
494 if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
497 vector< vector<double> > axes; axes.resize(maxdim);
498 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
500 map <string, vector<double> > orderedAxes;
501 map <string, vector<double> >::iterator it;
505 if (m->control_pressed) { in.close(); return axes; }
508 in >> group; m->gobble(in);
511 if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
513 vector<double> thisGroupsAxes;
514 for (int i = 0; i < count; i++) {
518 //only save the axis we want
519 if (i < maxdim) { thisGroupsAxes.push_back(temp); }
522 if (!ignore) { orderedAxes[group] = thisGroupsAxes; }
529 if (names.size() != orderedAxes.size()) { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
531 //put axes info in same order as distance file, just in case
532 for (int i = 0; i < names.size(); i++) {
533 it = orderedAxes.find(names[i]);
535 if (it != orderedAxes.end()) {
536 vector<double> thisGroupsAxes = it->second;
538 for (int j = 0; j < thisGroupsAxes.size(); j++) {
539 axes[j][i] = thisGroupsAxes[j];
542 }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
547 catch(exception& e) {
548 m->errorOut(e, "NMDSCommand", "readAxes");
552 /**********************************************************************************************************************/