+++ /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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