+++ /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);
- }
-}
-/*********************************************************************************************************************************/
-
-
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