5 * Created by westcott on 2/9/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "mantelcommand.h"
11 #include "readphylipvector.h"
14 //**********************************************************************************************************************
15 vector<string> MantelCommand::setParameters(){
17 CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip1);
18 CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip2);
19 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
20 CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
21 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
22 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
24 vector<string> myArray;
25 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
29 m->errorOut(e, "MantelCommand", "setParameters");
33 //**********************************************************************************************************************
34 string MantelCommand::getHelpString(){
36 string helpString = "";
37 helpString += "Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman.\n";
38 helpString += "The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n";
39 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";
40 helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n";
41 helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n";
42 helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n";
43 helpString += "The mantel command outputs a .mantel file.\n";
44 helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n";
48 m->errorOut(e, "MantelCommand", "getHelpString");
52 //**********************************************************************************************************************
53 string MantelCommand::getOutputFileNameTag(string type, string inputName=""){
55 string outputFileName = "";
56 map<string, vector<string> >::iterator it;
58 //is this a type this command creates
59 it = outputTypes.find(type);
60 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
62 if (type == "mantel") { outputFileName = "mantel"; }
63 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
65 return outputFileName;
68 m->errorOut(e, "MantelCommand", "getOutputFileNameTag");
72 //**********************************************************************************************************************
73 MantelCommand::MantelCommand(){
75 abort = true; calledHelp = true;
77 vector<string> tempOutNames;
78 outputTypes["mantel"] = tempOutNames;
81 m->errorOut(e, "MantelCommand", "MantelCommand");
85 //**********************************************************************************************************************
86 MantelCommand::MantelCommand(string option) {
88 abort = false; calledHelp = false;
90 //allow user to run help
91 if(option == "help") { help(); abort = true; calledHelp = true; }
92 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
95 vector<string> myArray = setParameters();
97 OptionParser parser(option);
98 map<string, string> parameters = parser.getParameters();
100 ValidParameters validParameter;
101 map<string, string>::iterator it;
103 //check to make sure all parameters are valid for command
104 for (it = parameters.begin(); it != parameters.end(); it++) {
105 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
108 vector<string> tempOutNames;
109 outputTypes["mantel"] = tempOutNames;
111 //if the user changes the input directory command factory will send this info to us in the output parameter
112 string inputDir = validParameter.validFile(parameters, "inputdir", false);
113 if (inputDir == "not found"){ inputDir = ""; }
116 it = parameters.find("phylip1");
117 //user has given a template file
118 if(it != parameters.end()){
119 path = m->hasPath(it->second);
120 //if the user has not given a path then, add inputdir. else leave path alone.
121 if (path == "") { parameters["phylip1"] = inputDir + it->second; }
124 it = parameters.find("phylip2");
125 //user has given a template file
126 if(it != parameters.end()){
127 path = m->hasPath(it->second);
128 //if the user has not given a path then, add inputdir. else leave path alone.
129 if (path == "") { parameters["phylip2"] = inputDir + it->second; }
134 //check for required parameters
135 phylipfile1 = validParameter.validFile(parameters, "phylip1", true);
136 if (phylipfile1 == "not open") { phylipfile1 = ""; abort = true; }
137 else if (phylipfile1 == "not found") { phylipfile1 = ""; m->mothurOut("phylip1 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; }
139 phylipfile2 = validParameter.validFile(parameters, "phylip2", true);
140 if (phylipfile2 == "not open") { phylipfile2 = ""; abort = true; }
141 else if (phylipfile2 == "not found") { phylipfile2 = ""; m->mothurOut("phylip2 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; }
143 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(phylipfile1); }
145 method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
147 string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
148 m->mothurConvert(temp, iters);
150 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; }
153 catch(exception& e) {
154 m->errorOut(e, "MantelCommand", "MantelCommand");
158 //**********************************************************************************************************************
160 int MantelCommand::execute(){
163 if (abort == true) { if (calledHelp) { return 0; } return 2; }
165 /***************************************************/
166 // reading distance files //
167 /***************************************************/
170 ReadPhylipVector readMatrix(phylipfile1);
171 vector< vector<double> > matrix1;
172 vector<string> names1 = readMatrix.read(matrix1);
174 if (m->control_pressed) { return 0; }
177 ReadPhylipVector readMatrix2(phylipfile2);
178 vector< vector<double> > matrix2;
179 vector<string> names2 = readMatrix2.read(matrix2);
181 if (m->control_pressed) { return 0; }
183 //make sure matrix2 and matrix1 are in the same order
184 if (names1 == names2) { //then everything is in same order and same size
185 }else if (names1.size() != names2.size()) { //wrong size no need to order, abort
186 m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
187 m->control_pressed = true;
188 }else { //sizes are the same, but either the names are different or they are in different order
189 m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
192 if (m->control_pressed) { return 0; }
194 /***************************************************/
195 // calculating mantel and signifigance //
196 /***************************************************/
198 //calc mantel coefficient
199 LinearAlgebra linear;
201 if (method == "pearson") { mantel = linear.calcPearson(matrix1, matrix2); }
202 else if (method == "spearman") { mantel = linear.calcSpearman(matrix1, matrix2); }
203 else if (method == "kendall") { mantel = linear.calcKendall(matrix1, matrix2); }
208 for (int i = 0; i < iters; i++) {
210 if (m->control_pressed) { return 0; }
213 vector< vector<double> > matrix2Copy = matrix2;
214 random_shuffle(matrix2Copy.begin(), matrix2Copy.end());
217 double randomMantel = 0.0;
218 if (method == "pearson") { randomMantel = linear.calcPearson(matrix1, matrix2Copy); }
219 else if (method == "spearman") { randomMantel = linear.calcSpearman(matrix1, matrix2Copy); }
220 else if (method == "kendall") { randomMantel = linear.calcKendall(matrix1, matrix2Copy); }
222 if (randomMantel >= mantel) { count++; }
225 double pValue = count / (float) iters;
227 if (m->control_pressed) { return 0; }
229 string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + getOutputFileNameTag("mantel");
230 outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
233 m->openOutputFile(outputFile, out);
235 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
236 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
238 out << "Mantel\tpValue" << endl;
239 out << mantel << '\t' << pValue << endl;
243 cout << "\nmantel = " << mantel << "\tpValue = " << pValue << endl;
244 m->mothurOutJustToLog("\nmantel = " + toString(mantel) + "\tpValue = " + toString(pValue) + "\n");
246 m->mothurOutEndLine();
247 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
248 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
249 m->mothurOutEndLine();
253 catch(exception& e) {
254 m->errorOut(e, "MantelCommand", "execute");
259 //**********************************************************************************************************************