--- /dev/null
+/*
+ * amovacommand.cpp
+ * mothur
+ *
+ * Created by westcott on 2/7/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "amovacommand.h"
+#include "readphylipvector.h"
+#include "groupmap.h"
+
+
+//**********************************************************************************************************************
+vector<string> AmovaCommand::setParameters(){
+ try {
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
+ 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, "AmovaCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string AmovaCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.";
+ helpString += "The amova command outputs a .amova file.";
+ helpString += "The amova command parameters are phylip, iters, and alpha. The phylip and design parameters are required, unless you have valid current files.";
+ helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required.";
+ helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.";
+ helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000.";
+ helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).";
+ helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+AmovaCommand::AmovaCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["amova"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "AmovaCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+AmovaCommand::AmovaCommand(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;
+
+ //check to make sure all parameters are valid for command
+ map<string,string>::iterator it;
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["amova"] = tempOutNames;
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //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("design");
+ //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["design"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("phylip");
+ //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["phylip"] = inputDir + it->second; }
+ }
+ }
+
+ phylipFileName = validParameter.validFile(parameters, "phylip", true);
+ if (phylipFileName == "not open") { phylipFileName = ""; abort = true; }
+ else if (phylipFileName == "not found") {
+ //if there is a current phylip file, use it
+ phylipFileName = m->getPhylipFile();
+ if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setPhylipFile(phylipFileName); }
+
+ //check for required parameters
+ designFileName = validParameter.validFile(parameters, "design", true);
+ if (designFileName == "not open") { designFileName = ""; abort = true; }
+ else if (designFileName == "not found") {
+ //if there is a current design file, use it
+ designFileName = m->getDesignFile();
+ if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setDesignFile(designFileName); }
+
+ string temp = validParameter.validFile(parameters, "iters", false);
+ if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "alpha", false);
+ if (temp == "not found") { temp = "0.05"; }
+ m->mothurConvert(temp, experimentwiseAlpha);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "AmovaCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int AmovaCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //read design file
+ designMap = new GroupMap(designFileName);
+ designMap->readDesignMap();
+
+ if (outputDir == "") { outputDir = m->hasPath(phylipFileName); }
+
+ //read in distance matrix and square it
+ ReadPhylipVector readMatrix(phylipFileName);
+ vector<string> sampleNames = readMatrix.read(distanceMatrix);
+
+ for(int i=0;i<distanceMatrix.size();i++){
+ for(int j=0;j<i;j++){
+ distanceMatrix[i][j] *= distanceMatrix[i][j];
+ }
+ }
+
+ //link designMap to rows/columns in distance matrix
+ map<string, vector<int> > origGroupSampleMap;
+ for(int i=0;i<sampleNames.size();i++){
+ string group = designMap->getGroup(sampleNames[i]);
+
+ if (group == "not found") {
+ m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
+ }else { origGroupSampleMap[group].push_back(i); }
+
+ }
+ int numGroups = origGroupSampleMap.size();
+
+ if (m->control_pressed) { delete designMap; return 0; }
+
+ //create a new filename
+ ofstream AMOVAFile;
+ string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + "amova";
+ m->openOutputFile(AMOVAFileName, AMOVAFile);
+ outputNames.push_back(AMOVAFileName); outputTypes["amova"].push_back(AMOVAFileName);
+
+ double fullANOVAPValue = runAMOVA(AMOVAFile, origGroupSampleMap, experimentwiseAlpha);
+ if(fullANOVAPValue <= experimentwiseAlpha && numGroups > 2){
+
+ int numCombos = numGroups * (numGroups-1) / 2;
+ double pairwiseAlpha = experimentwiseAlpha / (double) numCombos;
+
+ map<string, vector<int> >::iterator itA;
+ map<string, vector<int> >::iterator itB;
+
+ for(itA=origGroupSampleMap.begin();itA!=origGroupSampleMap.end();itA++){
+ itB = itA;itB++;
+ for(itB;itB!=origGroupSampleMap.end();itB++){
+
+ map<string, vector<int> > pairwiseGroupSampleMap;
+ pairwiseGroupSampleMap[itA->first] = itA->second;
+ pairwiseGroupSampleMap[itB->first] = itB->second;
+
+ runAMOVA(AMOVAFile, pairwiseGroupSampleMap, pairwiseAlpha);
+ }
+ }
+ m->mothurOut("Experiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
+ m->mothurOut("Pair-wise error rate (Bonferroni): " + toString(pairwiseAlpha) + '\n');
+ }
+ else{
+ m->mothurOut("Experiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
+ }
+ m->mothurOut("If you have borderline P-values, you should try increasing the number of iterations\n");
+ AMOVAFile.close();
+
+ delete designMap;
+
+ 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, "AmovaCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+double AmovaCommand::runAMOVA(ofstream& AMOVAFile, map<string, vector<int> > groupSampleMap, double alpha) {
+ try {
+ map<string, vector<int> >::iterator it;
+
+ int numGroups = groupSampleMap.size();
+ int totalNumSamples = 0;
+
+ for(it = groupSampleMap.begin();it!=groupSampleMap.end();it++){
+ totalNumSamples += it->second.size();
+ }
+
+ double ssTotalOrig = calcSSTotal(groupSampleMap);
+ double ssWithinOrig = calcSSWithin(groupSampleMap);
+ double ssAmongOrig = ssTotalOrig - ssWithinOrig;
+
+ double counter = 0;
+ for(int i=0;i<iters;i++){
+ map<string, vector<int> > randomizedGroup = getRandomizedGroups(groupSampleMap);
+ double ssWithinRand = calcSSWithin(randomizedGroup);
+ if(ssWithinRand < ssWithinOrig){ counter++; }
+ }
+
+ double pValue = (double)counter / (double) iters;
+ string pString = "";
+ if(pValue < 1/(double)iters){ pString = '<' + toString(1/(double)iters); }
+ else { pString = toString(pValue); }
+
+
+ //print anova table
+ it = groupSampleMap.begin();
+ AMOVAFile << it->first;
+ m->mothurOut(it->first);
+ it++;
+ for(it;it!=groupSampleMap.end();it++){
+ AMOVAFile << '-' << it->first;
+ m->mothurOut('-' + it->first);
+ }
+
+ AMOVAFile << "\tAmong\tWithin\tTotal" << endl;
+ m->mothurOut("\tAmong\tWithin\tTotal\n");
+
+ AMOVAFile << "SS\t" << ssAmongOrig << '\t' << ssWithinOrig << '\t' << ssTotalOrig << endl;
+ m->mothurOut("SS\t" + toString(ssAmongOrig) + '\t' + toString(ssWithinOrig) + '\t' + toString(ssTotalOrig) + '\n');
+
+ int dfAmong = numGroups - 1; double MSAmong = ssAmongOrig / (double) dfAmong;
+ int dfWithin = totalNumSamples - numGroups; double MSWithin = ssWithinOrig / (double) dfWithin;
+ int dfTotal = totalNumSamples - 1; double Fs = MSAmong / MSWithin;
+
+ AMOVAFile << "df\t" << dfAmong << '\t' << dfWithin << '\t' << dfTotal << endl;
+ m->mothurOut("df\t" + toString(dfAmong) + '\t' + toString(dfWithin) + '\t' + toString(dfTotal) + '\n');
+
+ AMOVAFile << "MS\t" << MSAmong << '\t' << MSWithin << endl << endl;
+ m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n\n");
+
+ AMOVAFile << "Fs:\t" << Fs << endl;
+ m->mothurOut("Fs:\t" + toString(Fs) + '\n');
+
+ AMOVAFile << "p-value: " << pString;
+ m->mothurOut("p-value: " + pString);
+
+ if(pValue < alpha){
+ AMOVAFile << "*";
+ m->mothurOut("*");
+ }
+ AMOVAFile << endl << endl;
+ m->mothurOutEndLine();m->mothurOutEndLine();
+
+ return pValue;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "runAMOVA");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+map<string, vector<int> > AmovaCommand::getRandomizedGroups(map<string, vector<int> > origMapping){
+ try{
+ vector<int> sampleIndices;
+ vector<int> samplesPerGroup;
+
+ map<string, vector<int> >::iterator it;
+ for(it=origMapping.begin();it!=origMapping.end();it++){
+ vector<int> indices = it->second;
+ samplesPerGroup.push_back(indices.size());
+ sampleIndices.insert(sampleIndices.end(), indices.begin(), indices.end());
+ }
+
+ random_shuffle(sampleIndices.begin(), sampleIndices.end());
+
+ int index = 0;
+ map<string, vector<int> > randomizedGroups = origMapping;
+ for(it=randomizedGroups.begin();it!=randomizedGroups.end();it++){
+ for(int i=0;i<it->second.size();i++){
+ it->second[i] = sampleIndices[index++];
+ }
+ }
+
+ return randomizedGroups;
+ }
+ catch (exception& e) {
+ m->errorOut(e, "AmovaCommand", "getRandomizedGroups");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+double AmovaCommand::calcSSTotal(map<string, vector<int> >& groupSampleMap) {
+ try {
+
+ vector<int> indices;
+ map<string, vector<int> >::iterator it;
+ for(it=groupSampleMap.begin();it!=groupSampleMap.end();it++){
+ indices.insert(indices.end(), it->second.begin(), it->second.end());
+ }
+ sort(indices.begin(), indices.end());
+
+ int numIndices =indices.size();
+ double ssTotal = 0.0;
+
+ for(int i=1;i<numIndices;i++){
+ int row = indices[i];
+
+ for(int j=0;j<i;j++){
+ ssTotal += distanceMatrix[row][indices[j]];
+ }
+ }
+ ssTotal /= numIndices;
+
+ return ssTotal;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "calcSSTotal");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+double AmovaCommand::calcSSWithin(map<string, vector<int> >& groupSampleMap) {
+ try {
+
+ double ssWithin = 0.0;
+
+ map<string, vector<int> >::iterator it;
+ for(it=groupSampleMap.begin();it!=groupSampleMap.end();it++){
+
+ double withinGroup = 0;
+
+ vector<int> samples = it->second;
+
+ for(int i=0;i<samples.size();i++){
+ int row = samples[i];
+
+ for(int j=0;j<samples.size();j++){
+ int col = samples[j];
+
+ if(col < row){
+ withinGroup += distanceMatrix[row][col];
+ }
+
+ }
+ }
+
+ ssWithin += withinGroup / samples.size();
+ }
+
+ return ssWithin;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "calcSSWithin");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
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