--- /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::getValidParameters(){
+ try {
+ string Array[] = {"label", "groups","metric","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PCACommand::PCACommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pca"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared","relabund","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+PCACommand::PCACommand(string option) {
+ try {
+ abort = false;
+
+ globaldata = GlobalData::getInstance();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"label","groups","metric","outputdir", "inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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 = ""; }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pca"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
+ m->mothurOut("You must read a list and a group, shared or relabund file before you can use the pca command."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if (globaldata->getSharedFile() != "") { mode = "shared"; inputFile = globaldata->getSharedFile(); }
+ if (globaldata->getRelAbundFile() != "") { mode = "relabund"; inputFile = globaldata->getRelAbundFile(); }
+
+ //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 = ""; 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); }
+ globaldata->Groups = Groups;
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void PCACommand::help(){
+ try {
+ m->mothurOut("The pca command can only be run after a successful read.otu command."); m->mothurOutEndLine();
+ m->mothurOut("The pca command parameters are label, groups and metric. No parameters are required."); m->mothurOutEndLine();
+ m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multpile labels may be separated by dashes.\n");
+ m->mothurOut("The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n");
+ m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine();
+ m->mothurOut("Example pca(groups=yourGroups).\n");
+ m->mothurOut("Example pca(groups=A-B-C).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "help");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PCACommand::~PCACommand(){}
+//**********************************************************************************************************************
+int PCACommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ 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 == "shared") {
+ 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++) { remove(outputNames[i].c_str()); } 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++) { remove(outputNames[i].c_str()); } 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++) { remove(outputNames[i].c_str()); } 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();
+
+ 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);
+
+ double offset = 0.0000;
+ vector<double> d;
+ vector<double> e;
+ vector<vector<double> > G = matrix;
+ vector<vector<double> > copy_G;
+
+ for(int count=0;count<2;count++){
+ linearCalc.tred2(G, d, e); if (m->control_pressed) { return 0; }
+ linearCalc.qtli(d, e, G); if (m->control_pressed) { return 0; }
+ offset = d[d.size()-1];
+ if(offset > 0.0) break;
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ string outputFileName = fbase + lookupFloat[0]->getLabel();
+ output(outputFileName, globaldata->Groups, G, d);
+
+ if (metric) {
+
+ for (int i = 1; i < 4; i++) {
+
+ vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ double corr = linearCalc.calcPearson(EuclidDists, matrix); //G is the pcoa file, D is the users distance matrix
+
+ m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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 rank = name_list.size();
+ double dsum = 0.0000;
+ for(int i=0;i<rank;i++){
+ dsum += d[i];
+ for(int j=0;j<rank;j++){
+ if(d[j] >= 0) { G[i][j] *= pow(d[j],0.5); }
+ else { G[i][j] = 0.00000; }
+ }
+ }
+
+ ofstream pcaData((fnameRoot+".pca").c_str(), ios::trunc);
+ pcaData.setf(ios::fixed, ios::floatfield);
+ pcaData.setf(ios::showpoint);
+ outputNames.push_back(fnameRoot+".pca");
+ outputTypes["pca"].push_back(fnameRoot+".pca");
+
+ 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<rank;i++){
+ pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
+ }
+
+ pcaData << "group";
+ for(int i=0;i<rank;i++){
+ pcaData << '\t' << "axis" << i+1;
+ }
+ pcaData << endl;
+
+ for(int i=0;i<rank;i++){
+ pcaData << name_list[i] << '\t';
+ for(int j=0;j<rank;j++){
+ pcaData << G[i][j] << '\t';
+ }
+ pcaData << endl;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "output");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+
+
projects / mothur.git / blobdiff