5 * Created by westcott on 2/9/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "mantelcommand.h"
11 #include "readphylipvector.h"
13 //**********************************************************************************************************************
14 vector<string> MantelCommand::getValidParameters(){
16 string Array[] = {"phylip1","phylip2","method","iters","outputdir","inputdir"};
17 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
21 m->errorOut(e, "MantelCommand", "getValidParameters");
25 //**********************************************************************************************************************
26 vector<string> MantelCommand::getRequiredParameters(){
28 string Array[] = {"phylip1", "phylip2"};
29 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
33 m->errorOut(e, "MantelCommand", "getRequiredParameters");
37 //**********************************************************************************************************************
38 MantelCommand::MantelCommand(){
40 abort = true; calledHelp = true;
41 vector<string> tempOutNames;
42 outputTypes["mantel"] = tempOutNames;
45 m->errorOut(e, "MantelCommand", "MantelCommand");
50 //**********************************************************************************************************************
51 vector<string> MantelCommand::getRequiredFiles(){
53 vector<string> myArray;
57 m->errorOut(e, "MantelCommand", "getRequiredFiles");
61 //**********************************************************************************************************************
62 MantelCommand::MantelCommand(string option) {
64 abort = false; calledHelp = false;
66 //allow user to run help
67 if(option == "help") { help(); abort = true; calledHelp = true; }
70 //valid paramters for this command
71 string Array[] = {"phylip1","phylip2","method","iters","outputdir","inputdir"};
72 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
74 OptionParser parser(option);
75 map<string, string> parameters = parser.getParameters();
77 ValidParameters validParameter;
78 map<string, string>::iterator it;
80 //check to make sure all parameters are valid for command
81 for (it = parameters.begin(); it != parameters.end(); it++) {
82 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
85 vector<string> tempOutNames;
86 outputTypes["mantel"] = tempOutNames;
88 //if the user changes the input directory command factory will send this info to us in the output parameter
89 string inputDir = validParameter.validFile(parameters, "inputdir", false);
90 if (inputDir == "not found"){ inputDir = ""; }
93 it = parameters.find("phylip1");
94 //user has given a template file
95 if(it != parameters.end()){
96 path = m->hasPath(it->second);
97 //if the user has not given a path then, add inputdir. else leave path alone.
98 if (path == "") { parameters["phylip1"] = inputDir + it->second; }
101 it = parameters.find("phylip2");
102 //user has given a template file
103 if(it != parameters.end()){
104 path = m->hasPath(it->second);
105 //if the user has not given a path then, add inputdir. else leave path alone.
106 if (path == "") { parameters["phylip2"] = inputDir + it->second; }
111 //check for required parameters
112 phylipfile1 = validParameter.validFile(parameters, "phylip1", true);
113 if (phylipfile1 == "not open") { phylipfile1 = ""; abort = true; }
114 else if (phylipfile1 == "not found") { phylipfile1 = ""; m->mothurOut("phylip1 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; }
116 phylipfile2 = validParameter.validFile(parameters, "phylip2", true);
117 if (phylipfile2 == "not open") { phylipfile2 = ""; abort = true; }
118 else if (phylipfile2 == "not found") { phylipfile2 = ""; m->mothurOut("phylip2 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; }
120 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(phylipfile1); }
122 method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
124 string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
125 convert(temp, iters);
127 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; }
130 catch(exception& e) {
131 m->errorOut(e, "MantelCommand", "MantelCommand");
135 //**********************************************************************************************************************
137 void MantelCommand::help(){
139 m->mothurOut("The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n");
140 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");
141 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");
142 m->mothurOut("The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n");
143 m->mothurOut("The mantel command outputs a .mantel file.\n");
144 m->mothurOut("Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n");
146 catch(exception& e) {
147 m->errorOut(e, "MantelCommand", "help");
152 //**********************************************************************************************************************
154 MantelCommand::~MantelCommand(){}
156 //**********************************************************************************************************************
158 int MantelCommand::execute(){
161 if (abort == true) { if (calledHelp) { return 0; } return 2; }
163 /***************************************************/
164 // reading distance files //
165 /***************************************************/
168 ReadPhylipVector readMatrix(phylipfile1);
169 vector< vector<double> > matrix1;
170 vector<string> names1 = readMatrix.read(matrix1);
172 if (m->control_pressed) { return 0; }
175 ReadPhylipVector readMatrix2(phylipfile2);
176 vector<seqDist> temp; //seqDist - int, int, float
177 vector<string> names2 = readMatrix2.read(temp);
179 if (m->control_pressed) { return 0; }
181 //fill matrix2 making sure to make sure the distances are in the same order as matrix1
182 vector< vector<double> > matrix2;
183 if (names1 == names2) { //then everything is in same order and same size
186 matrix2.resize(names2.size());
187 for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
190 for (int i = 0; i < temp.size(); i++) {
191 matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
192 matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
195 }else if (names1.size() != names2.size()) { //wrong size no need to order, abort
196 m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
197 m->control_pressed = true;
198 }else { //sizes are the same, but either the names are different or they are in different order
200 //map location of name in names1 to location of name in names2
201 map<string, int> names1Map;
202 map<string, int>::iterator it;
203 for (int i = 0; i < names1.size(); i++) { names1Map[names1[i]] = i; }
205 map<string, int> names2Map;
206 bool nameError = false;
207 for (int i = 0; i < names2.size(); i++) {
209 //if you find one name error stop looking
211 it = names1Map.find(names2[i]);
212 if (it == names1Map.end()) { nameError = true; }
215 //are names different
216 names2Map[names2[i]] = i;
220 matrix2.resize(names2.size());
221 for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
224 //are we comparing apples to apples?
226 m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
228 for (int i = 0; i < temp.size(); i++) {
229 matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
230 matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
233 }else { //no name error just different orders, so reorder
235 for (int i = 0; i < temp.size(); i++) {
237 //what's the location of this distance comparison in matrix1
238 string matrix2NameI = names2[temp[i].seq1];
239 string matrix2NameJ = names2[temp[i].seq2];
240 int locationI = names1Map[matrix2NameI];
241 int locationJ = names1Map[matrix2NameJ];
243 matrix2[locationI][locationJ] = temp[i].dist;
244 matrix2[locationJ][locationI] = temp[i].dist;
253 if (m->control_pressed) { return 0; }
255 /***************************************************/
256 // calculating mantel and signifigance //
257 /***************************************************/
259 //calc mantel coefficient
260 LinearAlgebra linear;
262 if (method == "pearson") { mantel = linear.calcPearson(matrix1, matrix2); }
263 else if (method == "spearman") { mantel = linear.calcSpearman(matrix1, matrix2); }
264 else if (method == "kendall") { mantel = linear.calcKendall(matrix1, matrix2); }
269 for (int i = 0; i < iters; i++) {
271 if (m->control_pressed) { return 0; }
274 vector< vector<double> > matrix2Copy = matrix2;
275 random_shuffle(matrix2Copy.begin(), matrix2Copy.end());
278 double randomMantel = 0.0;
279 if (method == "pearson") { randomMantel = linear.calcPearson(matrix1, matrix2Copy); }
280 else if (method == "spearman") { randomMantel = linear.calcSpearman(matrix1, matrix2Copy); }
281 else if (method == "kendall") { randomMantel = linear.calcKendall(matrix1, matrix2Copy); }
283 if (randomMantel >= mantel) { count++; }
286 double pValue = count / (float) iters;
288 if (m->control_pressed) { return 0; }
290 string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + "mantel";
291 outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
294 m->openOutputFile(outputFile, out);
296 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
297 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
299 out << "Mantel\tpValue" << endl;
300 out << mantel << '\t' << pValue << endl;
304 cout << "\nmantel = " << mantel << "\tpValue = " << pValue << endl;
305 m->mothurOutJustToLog("\nmantel = " + toString(mantel) + "\tpValue = " + toString(pValue) + "\n");
307 m->mothurOutEndLine();
308 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
309 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
310 m->mothurOutEndLine();
314 catch(exception& e) {
315 m->errorOut(e, "MantelCommand", "execute");
320 //**********************************************************************************************************************