--- /dev/null
+/*
+ * mantelcommand.cpp
+ * mothur
+ *
+ * Created by westcott on 2/9/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mantelcommand.h"
+#include "readphylipvector.h"
+
+
+//**********************************************************************************************************************
+vector<string> 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<string> 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<string> 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<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::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<string> 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<double> > matrix1;
+ vector<string> names1 = readMatrix.read(matrix1);
+
+ if (m->control_pressed) { return 0; }
+
+ //read phylip2
+ ReadPhylipVector readMatrix2(phylipfile2);
+ vector< vector<double> > matrix2;
+ vector<string> 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<double> > 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);
+ }
+}
+
+//**********************************************************************************************************************
+
+
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