X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;fp=pcacommand.cpp;h=27e448bdfa1060a91c701c25fe301907e3529ec7;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/pcacommand.cpp b/pcacommand.cpp new file mode 100644 index 0000000..27e448b --- /dev/null +++ b/pcacommand.cpp @@ -0,0 +1,444 @@ +/* + * pcacommand.cpp + * mothur + * + * Created by westcott on 1/7/11. + * Copyright 2011 Schloss Lab. All rights reserved. + * + */ + +#include "pcacommand.h" +#include "inputdata.h" + +//********************************************************************************************************************** +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); + + 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", "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 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 myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser. getParameters(); + + ValidParameters validParameter; + map::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 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 > 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 lookupFloat = input->getSharedRAbundFloatVectors(); + string lastLabel = lookupFloat[0]->getLabel(); + + set processedLabels; + set 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::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 > PCACommand::createMatrix(vector lookupFloat){ + try { + vector< vector > 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 > 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& lookupFloat){ + try { + m->mothurOut("\nProcessing " + lookupFloat[0]->getLabel()); m->mothurOutEndLine(); + + int numOTUs = lookupFloat[0]->getNumBins(); + int numSamples = lookupFloat.size(); + + vector< vector > matrix(numSamples); + vector 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 > 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); + + vector d; + vector e; + + 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->getGroups(), X, d); + + if (metric) { + + vector > observedEuclideanDistance = linearCalc.getObservedEuclideanDistance(centered); + + for (int i = 1; i < 4; i++) { + + 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++) { m->mothurRemove(outputNames[i]); } return 0; } + } + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "process"); + exit(1); + } +} +/*********************************************************************************************************************************/ + +void PCACommand::output(string fnameRoot, vector name_list, vector >& G, vector d) { + try { + + int numEigenValues = d.size(); + double dsum = 0.0000; + for(int i=0;ierrorOut(e, "PCACommand", "output"); + exit(1); + } +} +/*********************************************************************************************************************************/ + +