--- /dev/null
+/*
+ * nmdscommand.cpp
+ * mothur
+ *
+ * Created by westcott on 1/11/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "nmdscommand.h"
+#include "readphylipvector.h"
+
+//**********************************************************************************************************************
+vector<string> NMDSCommand::setParameters(){
+ try {
+ CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paxes);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
+ CommandParameter pmaxdim("maxdim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxdim);
+ CommandParameter pmindim("mindim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmindim);
+ CommandParameter piters("iters", "Number", "", "10", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter pmaxiters("maxiters", "Number", "", "500", "", "", "",false,false); parameters.push_back(pmaxiters);
+ CommandParameter pepsilon("epsilon", "Number", "", "0.000000000001", "", "", "",false,false); parameters.push_back(pepsilon);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string NMDSCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "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.\n";
+ helpString += "The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon.\n";
+ helpString += "The phylip parameter allows you to enter your distance file.\n";
+ helpString += "The axes parameter allows you to enter a file containing a starting configuration.\n";
+ helpString += "The maxdim parameter allows you to select the maximum dimensions to use. Default=2\n";
+ helpString += "The mindim parameter allows you to select the minimum dimensions to use. Default=2\n";
+ helpString += "The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500\n";
+ helpString += "The iters parameter allows you to select the number of random configuration to try. Default=10\n";
+ helpString += "The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12.\n";
+ helpString += "Example nmds(phylip=yourDistanceFile).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+NMDSCommand::NMDSCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["nmds"] = tempOutNames;
+ outputTypes["stress"] = tempOutNames;
+ outputTypes["iters"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "NMDSCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+NMDSCommand::NMDSCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser. getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("axes");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["axes"] = inputDir + it->second; }
+ }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["nmds"] = tempOutNames;
+ outputTypes["iters"] = tempOutNames;
+ outputTypes["stress"] = tempOutNames;
+
+ //required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+ else if (phylipfile == "not found") {
+ //if there is a current phylip file, use it
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setPhylipFile(phylipfile); }
+
+ axesfile = validParameter.validFile(parameters, "axes", true);
+ if (axesfile == "not open") { axesfile = ""; abort = true; }
+ else if (axesfile == "not found") { axesfile = ""; }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "mindim", false); if (temp == "not found") { temp = "2"; }
+ m->mothurConvert(temp, mindim);
+
+ temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") { temp = "500"; }
+ m->mothurConvert(temp, maxIters);
+
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10"; }
+ m->mothurConvert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "maxdim", false); if (temp == "not found") { temp = "2"; }
+ m->mothurConvert(temp, maxdim);
+
+ temp = validParameter.validFile(parameters, "epsilon", false); if (temp == "not found") { temp = "0.000000000001"; }
+ m->mothurConvert(temp, epsilon);
+
+ if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
+ if (maxdim < mindim) { maxdim = mindim; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "NMDSCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int NMDSCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ cout.setf(ios::fixed, ios::floatfield);
+ cout.setf(ios::showpoint);
+
+ vector<string> names;
+ vector< vector< double> > matrix;
+
+ //read in phylip file
+ ReadPhylipVector readFile(phylipfile);
+ names = readFile.read(matrix);
+ if (m->control_pressed) { return 0; }
+
+ //read axes
+ vector< vector<double> > axes;
+ if (axesfile != "") { axes = readAxes(names); }
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
+ string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
+ outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
+ outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
+
+ ofstream out, out2;
+ m->openOutputFile(outputFileName, out);
+ m->openOutputFile(stressFileName, out2);
+
+ out2.setf(ios::fixed, ios::floatfield);
+ out2.setf(ios::showpoint);
+ out.setf(ios::fixed, ios::floatfield);
+ out.setf(ios::showpoint);
+
+ out2 << "Dimension\tIter\tStress\tRsq" << endl;
+
+ double bestStress = 10000000;
+ double bestR2 = 10000000;
+ vector< vector<double> > bestConfig;
+ int bestDim = 0;
+
+ for (int i = mindim; i <= maxdim; i++) {
+ m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
+
+ for (int j = 0; j < iters; j++) {
+ m->mothurOut(toString(j+1)); m->mothurOutEndLine();
+
+ //get configuration - either randomly generate or resize to this dimension
+ vector< vector<double> > thisConfig;
+ if (axesfile == "") { thisConfig = generateStartingConfiguration(names.size(), i); }
+ else { thisConfig = getConfiguration(axes, i); }
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
+
+ //calc nmds for this dimension
+ double stress;
+ vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
+
+ //calc euclid distances for new config
+ vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
+
+ //calc correlation between original distances and euclidean distances from this config
+ double rsquared = linearCalc.calcPearson(newEuclid, matrix);
+ rsquared *= rsquared;
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
+
+ //output results
+ out << "Config" << (j+1) << '\t';
+ for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
+ out << endl;
+ out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << rsquared << endl;
+
+ output(endConfig, names, out);
+
+ //save best
+ if (stress < bestStress) {
+ bestDim = i;
+ bestStress = stress;
+ bestR2 = rsquared;
+ bestConfig = endConfig;
+ }
+
+ if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) { m->mothurRemove(outputNames[k]); } return 0; }
+ }
+ }
+
+ out.close(); out2.close();
+
+ //output best config
+ string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
+ outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
+
+ m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
+ m->mothurOut("Lowest stress :\t" + toString(bestStress) + "\n");
+ m->mothurOut("R-squared for configuration:\t" + toString(bestR2) + "\n");
+
+ ofstream outBest;
+ m->openOutputFile(BestFileName, outBest);
+ outBest.setf(ios::fixed, ios::floatfield);
+ outBest.setf(ios::showpoint);
+
+ outBest << '\t';
+ for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
+ outBest << endl;
+
+ output(bestConfig, names, outBest);
+
+ outBest.close();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
+ try {
+
+ vector< vector<double> > newConfig = config;
+
+ //calc euclid distances
+ vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
+ if (m->control_pressed) { return newConfig; }
+
+ double stress2 = calculateStress(matrix, euclid);
+ stress1 = stress2 + 1.0 + epsilon;
+
+ int count = 0;
+ while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
+ count++;
+
+ stress1 = stress2;
+
+ if (m->control_pressed) { return newConfig; }
+
+ vector< vector<double> > b; b.resize(euclid.size());
+ for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
+
+ vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
+ for (int i = 0; i < euclid.size(); i++) {
+ for (int j = 0; j < euclid[i].size(); j++) {
+ //eliminate divide by zero error
+ if (euclid[i][j] != 0) {
+ b[i][j] = matrix[i][j] / euclid[i][j];
+ columnSums[j] += b[i][j];
+ b[i][j] *= -1.0;
+ }
+ }
+ }
+
+ //put in diagonal sums
+ for (int i = 0; i < euclid.size(); i++) { b[i][i] = columnSums[i]; }
+
+ int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
+ double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
+
+ //matrix mult
+ newConfig = linearCalc.matrix_mult(newConfig, b);
+ for (int i = 0; i < newConfig.size(); i++) {
+ for (int j = 0; j < newConfig[i].size(); j++) {
+ newConfig[i][j] *= (1.0 / n);
+ }
+ }
+
+ euclid = linearCalc.calculateEuclidianDistance(newConfig);
+
+ stress2 = calculateStress(matrix, euclid);
+ }
+
+ return newConfig;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+//generate random config
+vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
+ try {
+ vector< vector<double> > axes; axes.resize(dimension);
+ for (int i = 0; i < axes.size(); i++) { axes[i].resize(numNames); }
+
+ //generate random number between -1 and 1, precision 6
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) {
+
+ if (m->control_pressed) { return axes; }
+
+ //generate random int between 0 and 99999
+ int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
+
+ //generate random sign
+ int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
+
+ //if mysign is even then sign = positive, else sign = negative
+ if ((mysign % 2) == 0) { mysign = 1.0; }
+ else { mysign = -1.0; }
+
+ axes[i][j] = mysign * myrand / (float) 100000;
+ }
+ }
+
+ return axes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//normalize configuration
+int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
+ try {
+ vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
+
+ //find average
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) { averageAxes[i] += axes[i][j]; }
+
+ averageAxes[i] /= (float) numNames;
+ }
+
+ //normalize axes
+ double sumDenom = 0.0;
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) {
+ sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
+ }
+ }
+
+ double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
+
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) {
+ axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//get configuration
+vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
+ try {
+ vector< vector<double> > newAxes; newAxes.resize(dimension);
+
+ for (int i = 0; i < dimension; i++) {
+ newAxes[i] = axes[i];
+ }
+
+ return newAxes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "getConfiguration");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//find raw stress, and normalize using
+double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
+ try {
+ double normStress = 0.0;
+ double denom = 0.0;
+ double rawStress = 0.0;
+
+ //find raw stress
+ for (int i = 0; i < matrix.size(); i++) {
+ for (int j = 0; j < matrix[i].size(); j++) {
+ if (m->control_pressed) { return normStress; }
+
+ rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
+ denom += (config[i][j] * config[i][j]);
+ }
+ }
+
+ //normalize stress
+ if ((rawStress != 0.0) && (denom != 0.0)) {
+ normStress = sqrt((rawStress / denom));
+ }
+
+ return normStress;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "calculateStress");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
+ try {
+
+ for (int i = 0; i < names.size(); i++) {
+
+ out << names[i] << '\t';
+
+ for (int j = 0; j < config.size(); j++) {
+ out << config[j][i] << '\t';
+ }
+
+ out << endl;
+ }
+
+ out << endl << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "output");
+ exit(1);
+ }
+}
+/*****************************************************************/
+vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
+ try {
+ ifstream in;
+ m->openInputFile(axesfile, in);
+
+ string headerLine = m->getline(in); m->gobble(in);
+
+ //count the number of axis you are reading
+ bool done = false;
+ int count = 0;
+ while (!done) {
+ int pos = headerLine.find("axis");
+ if (pos != string::npos) {
+ count++;
+ headerLine = headerLine.substr(pos+4);
+ }else { done = true; }
+ }
+
+ if (maxdim > count) {
+ m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
+ maxdim = count;
+ if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
+ }
+
+ vector< vector<double> > axes; axes.resize(maxdim);
+ for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
+
+ map <string, vector<double> > orderedAxes;
+ map <string, vector<double> >::iterator it;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return axes; }
+
+ string group = "";
+ in >> group; m->gobble(in);
+
+ bool ignore = false;
+ if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
+
+ vector<double> thisGroupsAxes;
+ for (int i = 0; i < count; i++) {
+ float temp = 0.0;
+ in >> temp;
+
+ //only save the axis we want
+ if (i < maxdim) { thisGroupsAxes.push_back(temp); }
+ }
+
+ if (!ignore) { orderedAxes[group] = thisGroupsAxes; }
+
+ m->gobble(in);
+ }
+ in.close();
+
+ //sanity check
+ 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; }
+
+ //put axes info in same order as distance file, just in case
+ for (int i = 0; i < names.size(); i++) {
+ it = orderedAxes.find(names[i]);
+
+ if (it != orderedAxes.end()) {
+ vector<double> thisGroupsAxes = it->second;
+
+ for (int j = 0; j < thisGroupsAxes.size(); j++) {
+ axes[j][i] = thisGroupsAxes[j];
+ }
+
+ }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
+ }
+
+ return axes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "readAxes");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+
+
+
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