+++ /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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