--- /dev/null
+/*
+ * anosimcommand.cpp
+ * mothur
+ *
+ * Created by westcott on 2/14/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "anosimcommand.h"
+#include "inputdata.h"
+#include "readphylipvector.h"
+
+//**********************************************************************************************************************
+vector<string> AnosimCommand::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, "AnosimCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string AnosimCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "Referenced: Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\n";
+ helpString += "The anosim command outputs a .anosim file. \n";
+ helpString += "The anosim command parameters are phylip, iters, and alpha. The phylip and design parameters are required, unless you have valid current files.\n";
+ helpString += "The design parameter allows you to assign your samples to groups when you are running anosim. It is required. \n";
+ 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.\n";
+ helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n";
+ helpString += "The anosim command should be in the following format: anosim(phylip=file.dist, design=file.design).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+AnosimCommand::AnosimCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["anosim"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "AnosimCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+AnosimCommand::AnosimCommand(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["anosim"] = 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, "AnosimCommand", "AnosimCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int AnosimCommand::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 ANOSIMFile;
+ string ANOSIMFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + "anosim";
+ m->openOutputFile(ANOSIMFileName, ANOSIMFile);
+ outputNames.push_back(ANOSIMFileName); outputTypes["anosim"].push_back(ANOSIMFileName);
+ m->mothurOut("\ncomparison\tR-value\tP-value\n");
+ ANOSIMFile << "comparison\tR-value\tP-value\n";
+
+
+ double fullANOSIMPValue = runANOSIM(ANOSIMFile, distanceMatrix, origGroupSampleMap, experimentwiseAlpha);
+
+
+ if(fullANOSIMPValue <= experimentwiseAlpha && numGroups > 2){
+
+ int numCombos = numGroups * (numGroups-1) / 2;
+ double pairwiseAlpha = experimentwiseAlpha / (double) numCombos;
+
+ for(map<string, vector<int> >::iterator itA=origGroupSampleMap.begin();itA!=origGroupSampleMap.end();itA++){
+ map<string, vector<int> >::iterator itB = itA;
+ itB++;
+ for(itB;itB!=origGroupSampleMap.end();itB++){
+
+ map<string, vector<int> > subGroupSampleMap;
+
+ subGroupSampleMap[itA->first] = itA->second; string groupA = itA->first;
+ subGroupSampleMap[itB->first] = itB->second; string groupB = itB->first;
+
+ vector<int> subIndices;
+ for(map<string, vector<int> >::iterator it=subGroupSampleMap.begin();it!=subGroupSampleMap.end();it++){
+ subIndices.insert(subIndices.end(), it->second.begin(), it->second.end());
+ }
+ int subNumSamples = subIndices.size();
+
+ sort(subIndices.begin(), subIndices.end());
+
+ vector<vector<double> > subDistMatrix(distanceMatrix.size());
+ for(int i=0;i<distanceMatrix.size();i++){
+ subDistMatrix[i].assign(distanceMatrix.size(), -1);
+ }
+
+ for(int i=0;i<subNumSamples;i++){
+ for(int j=0;j<i;j++){
+ subDistMatrix[subIndices[i]][subIndices[j]] = distanceMatrix[subIndices[i]][subIndices[j]];
+ }
+ }
+
+ runANOSIM(ANOSIMFile, subDistMatrix, subGroupSampleMap, pairwiseAlpha);
+
+ }
+ }
+
+ m->mothurOut("\nExperiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
+ m->mothurOut("Pair-wise error rate (Bonferroni): " + toString(pairwiseAlpha) + '\n');
+ }
+ else{
+ m->mothurOut("\nExperiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
+ }
+ m->mothurOut("If you have borderline P-values, you should try increasing the number of iterations\n");
+ ANOSIMFile.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, "AnosimCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+double AnosimCommand::runANOSIM(ofstream& ANOSIMFile, vector<vector<double> > dMatrix, map<string, vector<int> > groupSampleMap, double alpha) {
+ try {
+
+
+ vector<vector<double> > rankMatrix = convertToRanks(dMatrix);
+ double RValue = calcR(rankMatrix, groupSampleMap);
+
+ int pCount = 0;
+ for(int i=0;i<iters;i++){
+ map<string, vector<int> > randGroupSampleMap = getRandomizedGroups(groupSampleMap);
+ double RValueRand = calcR(rankMatrix, randGroupSampleMap);
+ if(RValue <= RValueRand){ pCount++; }
+ }
+
+ double pValue = (double)pCount / (double) iters;
+ string pString = "";
+ if(pValue < 1/(double)iters){ pString = '<' + toString(1/(double)iters); }
+ else { pString = toString(pValue); }
+
+
+ map<string, vector<int> >::iterator it=groupSampleMap.begin();
+ m->mothurOut(it->first);
+ ANOSIMFile << it->first;
+ it++;
+ for(it;it!=groupSampleMap.end();it++){
+ m->mothurOut('-' + it->first);
+ ANOSIMFile << '-' << it->first;
+
+ }
+ m->mothurOut('\t' + toString(RValue) + '\t' + pString);
+ ANOSIMFile << '\t' << RValue << '\t' << pString;
+
+ if(pValue < alpha){
+ ANOSIMFile << "*";
+ m->mothurOut("*");
+ }
+ ANOSIMFile << endl;
+ m->mothurOutEndLine();
+
+ return pValue;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "calcAnisom");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+double AnosimCommand::calcR(vector<vector<double> > rankMatrix, map<string, vector<int> > groupSampleMap){
+ try {
+
+ int numSamples = 0;
+ for(map<string, vector<int> >::iterator it=groupSampleMap.begin();it!=groupSampleMap.end();it++){
+ numSamples += it->second.size();
+ }
+
+
+ double within = 0.0;
+ int numWithinComps = 0;
+
+ for(map<string, vector<int> >::iterator it=groupSampleMap.begin();it!=groupSampleMap.end();it++){
+ vector<int> indices = it->second;
+ for(int i=0;i<indices.size();i++){
+ for(int j=0;j<i;j++){
+ if(indices[i] > indices[j]) { within += rankMatrix[indices[i]][indices[j]]; }
+ else { within += rankMatrix[indices[j]][indices[i]]; }
+ numWithinComps++;
+ }
+ }
+ }
+
+ within /= (float) numWithinComps;
+
+ double between = 0.0;
+ int numBetweenComps = 0;
+
+ map<string, vector<int> >::iterator itB;
+
+ for(map<string, vector<int> >::iterator itA=groupSampleMap.begin();itA!=groupSampleMap.end();itA++){
+
+ for(int i=0;i<itA->second.size();i++){
+ int A = itA->second[i];
+ map<string, vector<int> >::iterator itB = itA;
+ itB++;
+ for(itB;itB!=groupSampleMap.end();itB++){
+ for(int j=0;j<itB->second.size();j++){
+ int B = itB->second[j];
+ if(A>B) { between += rankMatrix[A][B]; }
+ else { between += rankMatrix[B][A]; }
+ numBetweenComps++;
+ }
+ }
+
+ }
+ }
+
+
+ between /= (float) numBetweenComps;
+
+ double Rvalue = (between - within)/(numSamples * (numSamples-1) / 4.0);
+
+ return Rvalue;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "calcWithinBetween");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+vector<vector<double> > AnosimCommand::convertToRanks(vector<vector<double> > dist) {
+ try {
+ vector<seqDist> cells;
+ vector<vector<double> > ranks = dist;
+
+ for (int i = 0; i < dist.size(); i++) {
+ for (int j = 0; j < i; j++) {
+ if(dist[i][j] != -1){
+ seqDist member(i, j, dist[i][j]);
+ cells.push_back(member);
+ }
+ }
+ }
+
+
+ //sort distances
+ sort(cells.begin(), cells.end(), compareSequenceDistance);
+
+ //find ranks of distances
+ int index = 0;
+ int indexSum = 0;
+ for(int i=0;i<cells.size()-1;i++){
+
+ index = i;
+ indexSum = i + 1;
+ while(dist[cells[index].seq1][cells[index].seq2] == dist[cells[index+1].seq1][cells[index+1].seq2]){
+ index++;
+ indexSum += index + 1;
+ }
+
+ if(index == i){
+ ranks[cells[i].seq1][cells[i].seq2] = i+1;
+ }
+ else{
+ double aveIndex = (double)indexSum / (double)(index - i + 1);
+ for(int j=i;j<=index;j++){
+ ranks[cells[j].seq1][cells[j].seq2] = aveIndex;
+ }
+ i = index;
+ }
+ }
+
+ if(indexSum == cells.size() - 1){
+ ranks[cells[cells.size()-1].seq1][cells[cells.size()-1].seq2] = indexSum + 1;
+ }
+
+ return ranks;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "convertToRanks");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+map<string, vector<int> > AnosimCommand::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, "AnosimCommand", "randomizeGroups");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
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