--- /dev/null
+/*
+ * pcacommand.cpp
+ * mothur
+ *
+ * Created by westcott on 1/7/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "pcacommand.h"
+#include "inputdata.h"
+
+//**********************************************************************************************************************
+vector<string> PCACommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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, "PCACommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PCACommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The pca command parameters are shared, relabund, label, groups and metric. shared or relabund is required unless you have a valid current file.";
+ helpString += "The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n";
+ helpString += "The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n";
+ helpString += "The metric parameter allows you to indicate if would like the pearson correlation coefficient calculated. Default=True";
+ helpString += "Example pca(groups=yourGroups).\n";
+ helpString += "Example pca(groups=A-B-C).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PCACommand::PCACommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["pca"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+PCACommand::PCACommand(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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pca"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+
+ //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("shared");
+ //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["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("relabund");
+ //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["relabund"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { mode = "sharedfile"; inputFile = sharedfile; m->setSharedFile(sharedfile); }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { relabundfile = ""; abort = true; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ else { mode = "relabund"; inputFile = relabundfile; m->setRelAbundFile(relabundfile); }
+
+
+ if ((sharedfile == "") && (relabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then list, then rabund, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputFile = sharedfile; mode = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ relabundfile = m->getRelAbundFile();
+ if (relabundfile != "") { inputFile = relabundfile; mode = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a relabund or shared file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+
+ //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(inputFile); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "metric", false); if (temp == "not found"){ temp = "T"; }
+ metric = m->isTrue(temp);
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; if(labels.size() == 0) { m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } }
+ else { m->splitAtDash(label, labels); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else { m->splitAtDash(groups, Groups); }
+ m->setGroups(Groups);
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int PCACommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ cout.setf(ios::fixed, ios::floatfield);
+ cout.setf(ios::showpoint);
+ cerr.setf(ios::fixed, ios::floatfield);
+ cerr.setf(ios::showpoint);
+
+ //get first line of shared file
+ vector< vector<double> > matrix;
+ InputData* input;
+ if (mode == "sharedfile") {
+ input = new InputData(inputFile, "sharedfile");
+ }else if (mode == "relabund") {
+ input = new InputData(inputFile, "relabund");
+ }else { m->mothurOut("[ERROR]: filetype not recognized."); m->mothurOutEndLine(); return 0; }
+
+ vector<SharedRAbundFloatVector*> lookupFloat = input->getSharedRAbundFloatVectors();
+ string lastLabel = lookupFloat[0]->getLabel();
+
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //if the user gave no labels, then use the first one read
+ if (labels.size() == 0) {
+ label = lastLabel;
+
+ process(lookupFloat);
+ }
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
+
+ if(labels.count(lookupFloat[0]->getLabel()) == 1){
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ process(lookupFloat);
+ }
+
+ if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookupFloat[0]->getLabel();
+
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear();
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ process(lookupFloat);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookupFloat[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookupFloat[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear();
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ }
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } lookupFloat.clear();
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ process(lookupFloat);
+
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } lookupFloat.clear();
+ }
+
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } lookupFloat.clear();
+ delete input;
+
+ 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, "PCACommand", "execute");
+ exit(1);
+ }
+}
+
+/**********************************************************************************************************************
+vector< vector<double> > PCACommand::createMatrix(vector<SharedRAbundFloatVector*> lookupFloat){
+ try {
+ vector< vector<double> > matrix; matrix.resize(lookupFloat.size());
+
+ //fill matrix with shared files relative abundances
+ for (int i = 0; i < lookupFloat.size(); i++) {
+ for (int j = 0; j < lookupFloat[i]->getNumBins(); j++) {
+ matrix[i].push_back(lookupFloat[i]->getAbundance(j));
+ }
+ }
+
+ vector< vector<double> > transposeMatrix; transposeMatrix.resize(matrix[0].size());
+ for (int i = 0; i < transposeMatrix.size(); i++) {
+ for (int j = 0; j < matrix.size(); j++) {
+ transposeMatrix[i].push_back(matrix[j][i]);
+ }
+ }
+
+ matrix = linearCalc.matrix_mult(matrix, transposeMatrix);
+
+ return matrix;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "createMatrix");
+ exit(1);
+ }
+}*/
+//**********************************************************************************************************************
+
+int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
+ try {
+ m->mothurOut("\nProcessing " + lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+
+ int numOTUs = lookupFloat[0]->getNumBins();
+ int numSamples = lookupFloat.size();
+
+ vector< vector<double> > matrix(numSamples);
+ vector<double> colMeans(numOTUs);
+
+ //fill matrix with shared relative abundances, re-center
+ for (int i = 0; i < lookupFloat.size(); i++) {
+ matrix[i].resize(numOTUs, 0);
+
+ for (int j = 0; j < numOTUs; j++) {
+ matrix[i][j] = lookupFloat[i]->getAbundance(j);
+ colMeans[j] += matrix[i][j];
+ }
+ }
+
+
+ for(int j=0;j<numOTUs;j++){
+ colMeans[j] = colMeans[j] / (double)numSamples;
+ }
+
+ vector<vector<double> > centered = matrix;
+ for(int i=0;i<numSamples;i++){
+ for(int j=0;j<numOTUs;j++){
+ centered[i][j] = centered[i][j] - colMeans[j];
+ }
+ }
+
+
+ vector< vector<double> > transpose(numOTUs);
+ for (int i = 0; i < numOTUs; i++) {
+ transpose[i].resize(numSamples, 0);
+
+ for (int j = 0; j < numSamples; j++) {
+ transpose[i][j] = centered[j][i];
+ }
+ }
+
+ vector<vector<double> > crossProduct = linearCalc.matrix_mult(transpose, centered);
+
+ vector<double> d;
+ vector<double> e;
+
+ linearCalc.tred2(crossProduct, d, e); if (m->control_pressed) { return 0; }
+ linearCalc.qtli(d, e, crossProduct); if (m->control_pressed) { return 0; }
+
+ vector<vector<double> > X = linearCalc.matrix_mult(centered, crossProduct);
+
+ if (m->control_pressed) { return 0; }
+
+ string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ string outputFileName = fbase + lookupFloat[0]->getLabel();
+ output(outputFileName, m->getGroups(), X, d);
+
+ if (metric) {
+
+ vector<vector<double> > observedEuclideanDistance = linearCalc.getObservedEuclideanDistance(centered);
+
+ for (int i = 1; i < 4; i++) {
+
+ vector< vector<double> > PCAEuclidDists = linearCalc.calculateEuclidianDistance(X, i); //G is the pca file
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ double corr = linearCalc.calcPearson(PCAEuclidDists, observedEuclideanDistance);
+
+ m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "process");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+
+void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
+ try {
+
+ int numEigenValues = d.size();
+ double dsum = 0.0000;
+ for(int i=0;i<numEigenValues;i++){
+ dsum += d[i];
+ }
+
+ ofstream pcaData((fnameRoot+".pca.axes").c_str(), ios::trunc);
+ pcaData.setf(ios::fixed, ios::floatfield);
+ pcaData.setf(ios::showpoint);
+ outputNames.push_back(fnameRoot+".pca.axes");
+ outputTypes["pca"].push_back(fnameRoot+".pca.axes");
+
+ ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
+ pcaLoadings.setf(ios::fixed, ios::floatfield);
+ pcaLoadings.setf(ios::showpoint);
+ outputNames.push_back(fnameRoot+".pca.loadings");
+ outputTypes["loadings"].push_back(fnameRoot+".pca.loadings");
+
+ pcaLoadings << "axis\tloading\n";
+ for(int i=0;i<numEigenValues;i++){
+ pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
+ }
+
+ pcaData << "group";
+ for(int i=0;i<numEigenValues;i++){
+ pcaData << '\t' << "axis" << i+1;
+ }
+ pcaData << endl;
+
+ for(int i=0;i<name_list.size();i++){
+ pcaData << name_list[i] << '\t';
+ for(int j=0;j<numEigenValues;j++){
+ pcaData << G[i][j] << '\t';
+ }
+ pcaData << endl;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "output");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+
+
projects / mothur.git / blobdiff