X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mantelcommand.cpp;fp=mantelcommand.cpp;h=0f6d0d7277fbaf7271f2e428b3d11cd0abd303f3;hb=5553e33be3a45eee6bed2ac9a5c4ca0aa0e8d5e4;hp=0000000000000000000000000000000000000000;hpb=10891fa4322cd356285cd8058f3b399bc766c5ea;p=mothur.git diff --git a/mantelcommand.cpp b/mantelcommand.cpp new file mode 100644 index 0000000..0f6d0d7 --- /dev/null +++ b/mantelcommand.cpp @@ -0,0 +1,322 @@ +/* + * 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::getValidParameters(){ + try { + string Array[] = {"phylip1","phylip2","method","iters","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector MantelCommand::getRequiredParameters(){ + try { + string Array[] = {"phylip1", "phylip2"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +MantelCommand::MantelCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["mantel"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "MantelCommand"); + exit(1); + } +} + +//********************************************************************************************************************** +vector MantelCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "getRequiredFiles"); + 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 { + //valid paramters for this command + string Array[] = {"phylip1","phylip2","method","iters","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; } + } + + 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"; } + convert(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); + } +} +//********************************************************************************************************************** + +void MantelCommand::help(){ + try { + m->mothurOut("The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n"); + m->mothurOut("The mantel command parameters are phylip1, phylip2 and method. The phylip1 and phylip2 parameters are required. Matrices must be the same size and contain the same names.\n"); + m->mothurOut("The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n"); + m->mothurOut("The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n"); + m->mothurOut("The mantel command outputs a .mantel file.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n"); + } + catch(exception& e) { + m->errorOut(e, "MantelCommand", "help"); + exit(1); + } +} + +//********************************************************************************************************************** + +MantelCommand::~MantelCommand(){} + +//********************************************************************************************************************** + +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 temp; //seqDist - int, int, float + vector names2 = readMatrix2.read(temp); + + if (m->control_pressed) { return 0; } + + //fill matrix2 making sure to make sure the distances are in the same order as matrix1 + vector< vector > matrix2; + if (names1 == names2) { //then everything is in same order and same size + + //initialize space + matrix2.resize(names2.size()); + for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); } + + //fill matrix2 + for (int i = 0; i < temp.size(); i++) { + matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist; + matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist; + } + + }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 + + //map location of name in names1 to location of name in names2 + map names1Map; + map::iterator it; + for (int i = 0; i < names1.size(); i++) { names1Map[names1[i]] = i; } + + map names2Map; + bool nameError = false; + for (int i = 0; i < names2.size(); i++) { + + //if you find one name error stop looking + if (!nameError) { + it = names1Map.find(names2[i]); + if (it == names1Map.end()) { nameError = true; } + } + + //are names different + names2Map[names2[i]] = i; + } + + //initialize space + matrix2.resize(names2.size()); + for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); } + + //fill matrix2 + //are we comparing apples to apples? + if (nameError) { + m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine(); + + for (int i = 0; i < temp.size(); i++) { + matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist; + matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist; + } + + }else { //no name error just different orders, so reorder + + for (int i = 0; i < temp.size(); i++) { + + //what's the location of this distance comparison in matrix1 + string matrix2NameI = names2[temp[i].seq1]; + string matrix2NameJ = names2[temp[i].seq2]; + int locationI = names1Map[matrix2NameI]; + int locationJ = names1Map[matrix2NameJ]; + + matrix2[locationI][locationJ] = temp[i].dist; + matrix2[locationJ][locationI] = temp[i].dist; + } + } + + } + + //frees up space + temp.clear(); + + 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); + } +} + +//********************************************************************************************************************** + +