X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mantelcommand.cpp;fp=mantelcommand.cpp;h=409eae414779acb412abec7aa295b61e82cd0e16;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/mantelcommand.cpp b/mantelcommand.cpp new file mode 100644 index 0000000..409eae4 --- /dev/null +++ b/mantelcommand.cpp @@ -0,0 +1,241 @@ +/* + * mantelcommand.cpp + * mothur + * + * Created by westcott on 2/9/11. + * Copyright 2011 Schloss Lab. All rights reserved. + * + */ + +#include "mantelcommand.h" +#include "readphylipvector.h" + + +//********************************************************************************************************************** +vector MantelCommand::setParameters(){ + try { + CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip1); + CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip2); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); + CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod); + 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, "MantelCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string MantelCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman.\n"; + helpString += "The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n"; + helpString += "The mantel command parameters are phylip1, phylip2, iters and method. The phylip1 and phylip2 parameters are required. Matrices must be the same size and contain the same names.\n"; + helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n"; + helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n"; + helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n"; + helpString += "The mantel command outputs a .mantel file.\n"; + helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +MantelCommand::MantelCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["mantel"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "MantelCommand"); + exit(1); + } +} +//********************************************************************************************************************** +MantelCommand::MantelCommand(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; } + } + + vector tempOutNames; + outputTypes["mantel"] = 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("phylip1"); + //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["phylip1"] = inputDir + it->second; } + } + + it = parameters.find("phylip2"); + //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["phylip2"] = inputDir + it->second; } + } + } + + + //check for required parameters + phylipfile1 = validParameter.validFile(parameters, "phylip1", true); + if (phylipfile1 == "not open") { phylipfile1 = ""; abort = true; } + else if (phylipfile1 == "not found") { phylipfile1 = ""; m->mothurOut("phylip1 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; } + + phylipfile2 = validParameter.validFile(parameters, "phylip2", true); + if (phylipfile2 == "not open") { phylipfile2 = ""; abort = true; } + else if (phylipfile2 == "not found") { phylipfile2 = ""; m->mothurOut("phylip2 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; } + + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(phylipfile1); } + + method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; } + + string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + m->mothurConvert(temp, iters); + + if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; } + } + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "MantelCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int MantelCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + /***************************************************/ + // reading distance files // + /***************************************************/ + + //read phylip1 + ReadPhylipVector readMatrix(phylipfile1); + vector< vector > matrix1; + vector names1 = readMatrix.read(matrix1); + + if (m->control_pressed) { return 0; } + + //read phylip2 + ReadPhylipVector readMatrix2(phylipfile2); + vector< vector > matrix2; + vector names2 = readMatrix2.read(matrix2); + + if (m->control_pressed) { return 0; } + + //make sure matrix2 and matrix1 are in the same order + if (names1 == names2) { //then everything is in same order and same size + }else if (names1.size() != names2.size()) { //wrong size no need to order, abort + m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine(); + m->control_pressed = true; + }else { //sizes are the same, but either the names are different or they are in different order + m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine(); + } + + if (m->control_pressed) { return 0; } + + /***************************************************/ + // calculating mantel and signifigance // + /***************************************************/ + + //calc mantel coefficient + LinearAlgebra linear; + double mantel = 0.0; + if (method == "pearson") { mantel = linear.calcPearson(matrix1, matrix2); } + else if (method == "spearman") { mantel = linear.calcSpearman(matrix1, matrix2); } + else if (method == "kendall") { mantel = linear.calcKendall(matrix1, matrix2); } + + + //calc signifigance + int count = 0; + for (int i = 0; i < iters; i++) { + + if (m->control_pressed) { return 0; } + + //randomize matrix2 + vector< vector > matrix2Copy = matrix2; + random_shuffle(matrix2Copy.begin(), matrix2Copy.end()); + + //calc random mantel + double randomMantel = 0.0; + if (method == "pearson") { randomMantel = linear.calcPearson(matrix1, matrix2Copy); } + else if (method == "spearman") { randomMantel = linear.calcSpearman(matrix1, matrix2Copy); } + else if (method == "kendall") { randomMantel = linear.calcKendall(matrix1, matrix2Copy); } + + if (randomMantel >= mantel) { count++; } + } + + double pValue = count / (float) iters; + + if (m->control_pressed) { return 0; } + + string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + "mantel"; + outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile); + ofstream out; + + m->openOutputFile(outputFile, out); + + out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint); + + out << "Mantel\tpValue" << endl; + out << mantel << '\t' << pValue << endl; + + out.close(); + + cout << "\nmantel = " << mantel << "\tpValue = " << pValue << endl; + m->mothurOutJustToLog("\nmantel = " + toString(mantel) + "\tpValue = " + toString(pValue) + "\n"); + + 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, "MantelCommand", "execute"); + exit(1); + } +} + +//********************************************************************************************************************** + +