+++ /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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