+++ /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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