X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=pcacommand.cpp;fp=pcacommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=27e448bdfa1060a91c701c25fe301907e3529ec7;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/pcacommand.cpp b/pcacommand.cpp deleted file mode 100644 index 27e448b..0000000 --- a/pcacommand.cpp +++ /dev/null @@ -1,444 +0,0 @@ -/* - * 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); - } -} -/*********************************************************************************************************************************/ - -