X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pcacommand.cpp;h=7103adb8a150a3e6f9871989ba94bd45d2b6a542;hp=8b0a51e3a658574d033076412d3c0e2074c150eb;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17 diff --git a/pcacommand.cpp b/pcacommand.cpp index 8b0a51e..7103adb 100644 --- a/pcacommand.cpp +++ b/pcacommand.cpp @@ -13,13 +13,13 @@ //********************************************************************************************************************** vector 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); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); 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 myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -37,7 +37,7 @@ string PCACommand::getHelpString(){ 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 indicate you if would like the pearson correlation coefficient calculated. Default=True"; + 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"; @@ -48,6 +48,23 @@ string PCACommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string PCACommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "pca") { pattern = "[filename],[distance],pca.axes"; } + else if (type == "loadings") { pattern = "[filename],[distance],pca.loadings"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "getOutputPattern"); + exit(1); + } +} + //********************************************************************************************************************** PCACommand::PCACommand(){ try { @@ -70,6 +87,7 @@ PCACommand::PCACommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -116,12 +134,12 @@ PCACommand::PCACommand(string option) { sharedfile = validParameter.validFile(parameters, "shared", true); if (sharedfile == "not open") { sharedfile = ""; abort = true; } else if (sharedfile == "not found") { sharedfile = ""; } - else { mode = "sharedfile"; inputFile = 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; } + else { mode = "relabund"; inputFile = relabundfile; m->setRelAbundFile(relabundfile); } if ((sharedfile == "") && (relabundfile == "")) { @@ -156,7 +174,7 @@ PCACommand::PCACommand(string option) { groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { m->splitAtDash(groups, Groups); } - m->Groups = Groups; + m->setGroups(Groups); } @@ -180,7 +198,7 @@ int PCACommand::execute(){ //get first line of shared file vector< vector > matrix; InputData* input; - if (mode == "shared") { + if (mode == "sharedfile") { input = new InputData(inputFile, "sharedfile"); }else if (mode == "relabund") { input = new InputData(inputFile, "relabund"); @@ -202,7 +220,7 @@ int PCACommand::execute(){ //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 (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()); @@ -235,7 +253,7 @@ int PCACommand::execute(){ } - 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 (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::iterator it; @@ -263,7 +281,7 @@ int PCACommand::execute(){ 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; } + 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(); @@ -277,6 +295,7 @@ int PCACommand::execute(){ exit(1); } } + /********************************************************************************************************************** vector< vector > PCACommand::createMatrix(vector lookupFloat){ try { @@ -306,82 +325,80 @@ vector< vector > PCACommand::createMatrix(vector& lookupFloat){ try { m->mothurOut("\nProcessing " + lookupFloat[0]->getLabel()); m->mothurOutEndLine(); + + int numOTUs = lookupFloat[0]->getNumBins(); + int numSamples = lookupFloat.size(); - vector< vector > matrix; matrix.resize(lookupFloat.size()); - - ofstream out; - string temp = outputDir + "matrix.transpose.out"; - m->openOutputFile(temp, out); - out << "matrix" << endl; + vector< vector > matrix(numSamples); + vector colMeans(numOTUs); - //fill matrix with shared files relative abundances + //fill matrix with shared relative abundances, re-center 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)); - out << lookupFloat[i]->getAbundance(j) << '\t'; - } - out << endl; - } - out << endl << endl << "transpose" << endl; - vector< vector > 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]); - out << matrix[j][i] << '\t'; + matrix[i].resize(numOTUs, 0); + + for (int j = 0; j < numOTUs; j++) { + matrix[i][j] = lookupFloat[i]->getAbundance(j); + colMeans[j] += matrix[i][j]; } - out << endl; } - matrix = linearCalc.matrix_mult(matrix, transposeMatrix); + + for(int j=0;j > centered = matrix; + for(int i=0;i > 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 > crossProduct = linearCalc.matrix_mult(transpose, centered); - double offset = 0.0000; vector d; vector e; - vector > G = matrix; - //vector > copy_G; - - for(int count=0;count<2;count++){ - linearCalc.recenter(offset, matrix, G); if (m->control_pressed) { return 0; } - 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; - } + + linearCalc.tred2(crossProduct, d, e); if (m->control_pressed) { return 0; } + linearCalc.qtli(d, e, crossProduct); if (m->control_pressed) { return 0; } + + vector > 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->Groups, G, d); + //string outputFileName = fbase + lookupFloat[0]->getLabel(); + output(fbase, lookupFloat[0]->getLabel(), m->getGroups(), X, d); if (metric) { + vector > observedEuclideanDistance = linearCalc.getObservedEuclideanDistance(centered); + for (int i = 1; i < 4; i++) { - vector< vector > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pca 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 pca file, D is the users distance matrix - - m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine(); + vector< vector > 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++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } } } @@ -394,44 +411,48 @@ int PCACommand::process(vector& lookupFloat){ } /*********************************************************************************************************************************/ -void PCACommand::output(string fnameRoot, vector name_list, vector >& G, vector d) { +void PCACommand::output(string fbase, string label, vector name_list, vector >& G, vector d) { try { - int rank = name_list.size(); + + int numEigenValues = d.size(); double dsum = 0.0000; - for(int i=0;i= 0) { G[i][j] *= pow(d[j],0.5); } - else { G[i][j] = 0.00000; } - } } - ofstream pcaData((fnameRoot+".pca.axes").c_str(), ios::trunc); + ofstream pcaData; + map variables; + variables["[filename]"] = fbase; + variables["[distance]"] = label; + string pcaFileName = getOutputFileName("pca",variables); + m->openOutputFile(pcaFileName, pcaData); pcaData.setf(ios::fixed, ios::floatfield); pcaData.setf(ios::showpoint); - outputNames.push_back(fnameRoot+".pca.axes"); - outputTypes["pca"].push_back(fnameRoot+".pca.axes"); + outputNames.push_back(pcaFileName); + outputTypes["pca"].push_back(pcaFileName); - ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc); + ofstream pcaLoadings; + string loadingsFilename = getOutputFileName("loadings",variables); + m->openOutputFile(loadingsFilename, pcaLoadings); pcaLoadings.setf(ios::fixed, ios::floatfield); pcaLoadings.setf(ios::showpoint); - outputNames.push_back(fnameRoot+".pca.loadings"); - outputTypes["loadings"].push_back(fnameRoot+".pca.loadings"); + outputNames.push_back(loadingsFilename); + outputTypes["loadings"].push_back(loadingsFilename); pcaLoadings << "axis\tloading\n"; - for(int i=0;i