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/*
* 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","mantel",false,true,true); parameters.push_back(pphylip1);
CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none","mantel",false,true,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);
}
}
//**********************************************************************************************************************
string MantelCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "mantel") { pattern = "[filename],mantel"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MantelCommand", "getOutputPattern");
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; }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile1));
string outputFile = getOutputFileName("mantel",variables);
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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