X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;fp=pcacommand.cpp;h=0842c53163a51da38800598281cde5c30d3e6778;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=0000000000000000000000000000000000000000;hpb=605ab6fa594317a38f0df7bb6797740c735b2348;p=mothur.git diff --git a/pcacommand.cpp b/pcacommand.cpp new file mode 100644 index 0000000..0842c53 --- /dev/null +++ b/pcacommand.cpp @@ -0,0 +1,405 @@ +/* + * 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::getValidParameters(){ + try { + string Array[] = {"label", "groups","metric","outputdir","inputdir"}; + vector 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 tempOutNames; + outputTypes["pca"] = tempOutNames; + outputTypes["loadings"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "PCACommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector PCACommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector PCACommand::getRequiredFiles(){ + try { + string Array[] = {"shared","relabund","or"}; + vector 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 myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + 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; } + } + //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 (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 > 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 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++) { 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::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 > 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(); + + 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); + + 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; + } + + 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 > 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 name_list, vector >& G, vector d) { + try { + int rank = name_list.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").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;ierrorOut(e, "PCACommand", "output"); + exit(1); + } +} +/*********************************************************************************************************************************/ + +