X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pcacommand.cpp;h=7103adb8a150a3e6f9871989ba94bd45d2b6a542;hp=2e8f132eefa8a491f1b5e23a2d9650da22ee1c84;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18 diff --git a/pcacommand.cpp b/pcacommand.cpp index 2e8f132..7103adb 100644 --- a/pcacommand.cpp +++ b/pcacommand.cpp @@ -11,50 +11,71 @@ #include "inputdata.h" //********************************************************************************************************************** -vector PCACommand::getValidParameters(){ +vector PCACommand::setParameters(){ try { - string Array[] = {"label", "groups","metric","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + 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); } return myArray; } catch(exception& e) { - m->errorOut(e, "PCACommand", "getValidParameters"); + m->errorOut(e, "PCACommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -PCACommand::PCACommand(){ +string PCACommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["pca"] = tempOutNames; - outputTypes["loadings"] = tempOutNames; + 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", "PCACommand"); + m->errorOut(e, "PCACommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector PCACommand::getRequiredParameters(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "getRequiredParameters"); - 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); + } } + //********************************************************************************************************************** -vector PCACommand::getRequiredFiles(){ +PCACommand::PCACommand(){ try { - string Array[] = {"shared","relabund","or"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["pca"] = tempOutNames; + outputTypes["loadings"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "PCACommand", "getRequiredFiles"); + m->errorOut(e, "PCACommand", "PCACommand"); exit(1); } } @@ -64,15 +85,12 @@ PCACommand::PCACommand(string option) { try { abort = false; calledHelp = false; - globaldata = GlobalData::getInstance(); - //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"label","groups","metric","outputdir", "inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser. getParameters(); @@ -84,22 +102,62 @@ PCACommand::PCACommand(string option) { 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 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 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; } + } } - if (globaldata->getSharedFile() != "") { mode = "shared"; inputFile = globaldata->getSharedFile(); } - if (globaldata->getRelAbundFile() != "") { mode = "relabund"; inputFile = globaldata->getRelAbundFile(); } + //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 = ""; @@ -110,13 +168,13 @@ PCACommand::PCACommand(string option) { metric = m->isTrue(temp); label = validParameter.validFile(parameters, "label", false); - if (label == "not found") { label = ""; labels = globaldata->labels; if(labels.size() == 0) { m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } } + 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); } - globaldata->Groups = Groups; + m->setGroups(Groups); } @@ -127,25 +185,6 @@ PCACommand::PCACommand(string option) { } } //********************************************************************************************************************** -void PCACommand::help(){ - try { - m->mothurOut("The pca command can only be run after a successful read.otu command of a shared or relabund file."); 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. Multiple 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 { @@ -159,7 +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"); @@ -181,7 +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()); @@ -214,7 +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; @@ -242,7 +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(); @@ -256,7 +295,8 @@ int PCACommand::execute(){ exit(1); } } -//********************************************************************************************************************** + +/********************************************************************************************************************** vector< vector > PCACommand::createMatrix(vector lookupFloat){ try { vector< vector > matrix; matrix.resize(lookupFloat.size()); @@ -283,62 +323,82 @@ vector< vector > PCACommand::createMatrix(vectorerrorOut(e, "PCACommand", "createMatrix"); exit(1); } -} +}*/ //********************************************************************************************************************** + int PCACommand::process(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()); + 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)); + matrix[i].resize(numOTUs, 0); + + for (int j = 0; j < numOTUs; j++) { + matrix[i][j] = lookupFloat[i]->getAbundance(j); + colMeans[j] += matrix[i][j]; } } - 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]); + + 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.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, globaldata->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 pcoa file - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + vector< vector > PCAEuclidDists = linearCalc.calculateEuclidianDistance(X, i); //G is the pca file - 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++) { 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; } } } @@ -351,44 +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