--- /dev/null
+/*
+ * cooccurrencecommand.cpp
+ * Mothur
+ *
+ * Created by kiverson on 1/2/12.
+ * Copyright 2012 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "cooccurrencecommand.h"
+
+//**********************************************************************************************************************
+vector<string> CooccurrenceCommand::setParameters() {
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter pmetric("metric", "Multiple", "cscore-checker-combo-vratio", "cscore", "", "", "",false,false); parameters.push_back(pmetric);
+ CommandParameter pmatrix("matrixmodel", "Multiple", "sim1-sim2-sim3-sim4-sim5-sim6-sim7-sim8-sim9", "sim2", "", "", "",false,false); parameters.push_back(pmatrix);
+ CommandParameter pruns("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pruns);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+
+ 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, "CooccurrenceCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string CooccurrenceCommand::getHelpString(){
+ try {
+ string helpString = "The cooccurrence command calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance.";
+ helpString += "The cooccurrence command parameters are shared, metric, matrixmodel, iters, label and groups.";
+ helpString += "The matrixmodel parameter options are sim1, sim2, sim3, sim4, sim5, sim6, sim7, sim8 and sim9. Default=sim2";
+ helpString += "The metric parameter options are cscore, checker, combo and vratio. Default=cscore";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
+ helpString += "The cooccurrence command should be in the following format: \n";
+ helpString += "cooccurrence(shared=yourSharedFile) \n";
+ helpString += "Example cooccurrence(shared=final.an.shared).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourShared).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CooccurrenceCommand::CooccurrenceCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "CooccurrenceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CooccurrenceCommand::CooccurrenceCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //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();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+
+ //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("shared");
+ //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["shared"] = inputDir + it->second; }
+ }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
+
+
+ //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 = m->hasPath(sharedfile); }
+
+
+ metric = validParameter.validFile(parameters, "metric", false); if (metric == "not found") { metric = "cscore"; }
+
+ if ((metric != "cscore") && (metric != "checker") && (metric != "combo") && (metric != "vratio")) {
+ m->mothurOut("[ERROR]: " + metric + " is not a valid metric option for the cooccurrence command. Choices are cscore, checker, combo, vratio."); m->mothurOutEndLine(); abort = true;
+ }
+
+ matrix = validParameter.validFile(parameters, "matrixmodel", false); if (matrix == "not found") { matrix = "sim2"; }
+
+ if ((matrix != "sim1") && (matrix != "sim2") && (matrix != "sim3") && (matrix != "sim4") && (matrix != "sim5" ) && (matrix != "sim6" ) && (matrix != "sim7" ) && (matrix != "sim8" ) && (matrix != "sim9" )) {
+ m->mothurOut("[ERROR]: " + matrix + " is not a valid matrix option for the cooccurrence command. Choices are sim1, sim2, sim3, sim4, sim5, sim6, sim7, sim8, sim9."); m->mothurOutEndLine(); abort = true;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+ m->setGroups(Groups);
+
+ string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, runs);
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "CooccurrenceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CooccurrenceCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ ofstream out;
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary";
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ out << "metric\tlabel\tScore\tpValue\n";
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ getCooccurrence(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ getCooccurrence(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookup[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+
+ if (m->control_pressed) { outputTypes.clear(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) { delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ getCooccurrence(lookup, out);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ out.close();
+
+ //reset groups parameter
+ delete input;
+ m->clearGroups();
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
+ try {
+ int numOTUS = thisLookUp[0]->getNumBins();
+ vector< vector<int> > co_matrix; co_matrix.resize(thisLookUp[0]->getNumBins());
+ for (int i = 0; i < thisLookUp[0]->getNumBins(); i++) { co_matrix[i].resize((thisLookUp.size()), 0); }
+ vector<int> columntotal; columntotal.resize(thisLookUp.size(), 0);
+ vector<int> rowtotal; rowtotal.resize(numOTUS, 0);
+
+ for (int i = 0; i < thisLookUp.size(); i++) { //nrows in the shared file
+ for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) { //cols of original shared file
+ if (m->control_pressed) { return 0; }
+ int abund = thisLookUp[i]->getAbundance(j);
+
+ if(abund > 0) {
+ co_matrix[j][i] = 1;
+ rowtotal[j]++;
+ columntotal[i]++;
+ }
+ }
+ }
+
+ //nrows is ncols of inital matrix. All the functions need this value. They assume the transposition has already taken place and nrows and ncols refer to that matrix.
+ //comatrix and initmatrix are still vectors of vectors of ints as in the original script. The abundancevector is only what was read in ie not a co-occurrence matrix!
+ int nrows = numOTUS;//rows of inital matrix
+ int ncols = thisLookUp.size();//groups
+ double initscore = 0.0;
+
+ vector<double> stats;
+ double probabilityMatrix[ncols * nrows];
+ vector<vector<int> > nullmatrix(nrows, vector<int>(ncols, 0));
+
+ TrialSwap2 trial;
+
+ int n = accumulate( columntotal.begin(), columntotal.end(), 0 );
+
+ //============================================================
+
+ //generate a probability matrix. Only do this once.
+ float start = 0.0;
+
+ if (matrix == "sim1") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + 1/double(nrows*ncols);
+ start = start + 1/double(nrows*ncols);
+ }
+ }
+ }
+ //don't need a prob matrix because we just shuffle the rows, may use this in the future
+ else if (matrix == "sim2") { }
+// for(int i=0;i<nrows;i++) {
+// start = 0.0;
+// for(int j=0;j<ncols;j++) {
+// probabilityMatrix[ncols * i + j] = start + 1/double(ncols);
+// start = start + 1/double(ncols);
+// }
+// }
+// }
+
+ else if (matrix == "sim3") {
+ for(int j=0;j<ncols;j++) {
+ start = 0.0;
+ for(int i=0;i<nrows;i++) {
+ probabilityMatrix[ncols * i + j] = start + 1/double(nrows);
+ start = start + 1/double(nrows);
+ }
+ }
+ }
+
+ else if (matrix == "sim4") {
+ for(int i=0;i<nrows;i++) {
+ start = 0.0;
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + columntotal[j]/double(n);
+ start = start + columntotal[j]/double(n);
+ }
+ }
+ }
+
+ else if (matrix == "sim5") {
+ for(int j=0;j<ncols;j++) {
+ start = 0.0;
+ for(int i=0;i<nrows;i++) {
+ probabilityMatrix[ncols * i + j] = start + rowtotal[i]/double(n);
+ start = start + rowtotal[i]/double(n);
+ }
+ }
+ }
+
+ else if (matrix == "sim6") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + columntotal[j]/double(n*nrows);
+ start = start + columntotal[j]/double(n*nrows);
+ }
+ }
+ }
+
+
+ else if (matrix == "sim7") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + rowtotal[i]/double(n*ncols);
+ start = start + rowtotal[i]/double(n*ncols);
+ }
+ }
+ }
+
+ else if (matrix == "sim8") {
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ probabilityMatrix[ncols * i + j] = start + (rowtotal[i]*columntotal[j])/double(n*n);
+ start = start + (rowtotal[i]*columntotal[j])/double(n*n);
+ }
+ }
+ }
+ else if (matrix == "sim9" || matrix == "sim2") { }
+ else {
+ m->mothurOut("[ERROR]: No model selected! \n");
+ m->control_pressed = true;
+ }
+
+
+ //co_matrix is the transposed shared file, initmatrix is the original shared file
+ if (metric == "cscore") { initscore = trial.calc_c_score(co_matrix, rowtotal, ncols, nrows); }
+ else if (metric == "checker") { initscore = trial.calc_checker(co_matrix, rowtotal, ncols, nrows); }
+ else if (metric == "vratio") { initscore = trial.calc_vratio(nrows, ncols, rowtotal, columntotal); }
+ else if (metric == "combo") { initscore = trial.calc_combo(nrows, ncols, co_matrix); }
+ else { m->mothurOut("[ERROR]: No metric selected!\n"); m->control_pressed = true; return 1; }
+
+ m->mothurOut("Initial c score: " + toString(initscore)); m->mothurOutEndLine();
+
+ double previous;
+ double current;
+ double randnum;
+ int count;
+
+ //burn-in for sim9
+ if(matrix == "sim9") {
+ for(int i=0;i<10000;i++) trial.swap_checkerboards (co_matrix, ncols, nrows);
+ }
+
+ //populate null matrix from probability matrix, do this a lot.
+ for(int k=0;k<runs;k++){
+ nullmatrix.clear();
+ //zero-fill the null matrix
+ nullmatrix.assign(nrows, vector<int>(ncols, 0));
+
+ if(matrix == "sim1" || matrix == "sim6" || matrix == "sim8" || matrix == "sim7") {
+ count = 0;
+ while(count < n) {
+ if (m->control_pressed) { return 0; }
+ nextnum2:
+ previous = 0.0;
+ randnum = rand() / double(RAND_MAX);
+ for(int i=0;i<nrows;i++) {
+ for(int j=0;j<ncols;j++) {
+ current = probabilityMatrix[ncols * i + j];
+ if(randnum <= current && randnum > previous) {
+ nullmatrix[i][j] = 1;
+ count++;
+ if (count > n) break;
+ else
+ goto nextnum2;
+ }
+ previous = current;
+ }
+ }
+ }
+ }
+
+ else if (matrix == "sim2") {
+ for(int i=0;i<nrows;i++) {
+ random_shuffle( co_matrix[i].begin(), co_matrix[i].end() );
+ }
+ //do this for the scoring since those all have nullmatrix as a parameter
+ //nullmatrix gets cleared at the begining of each run
+ nullmatrix = co_matrix;
+ }
+
+ else if(matrix == "sim4") {
+ for(int i=0;i<nrows;i++) {
+ count = 0;
+ while(count < rowtotal[i]) {
+ previous = 0.0;
+ if (m->control_pressed) { return 0; }
+ randnum = rand() / double(RAND_MAX);
+ for(int j=0;j<ncols;j++) {
+ current = probabilityMatrix[ncols * i + j];
+ if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
+ nullmatrix[i][j] = 1;
+ count++;
+ previous = 0.0;
+ break;
+ }
+ previous = current;
+ }
+ }
+ }
+ }
+
+ else if(matrix == "sim3" || matrix == "sim5") {
+ //columns
+ for(int j=0;j<ncols;j++) {
+ count = 0;
+ while(count < columntotal[j]) {
+ if (m->control_pressed) { return 0; }
+ randnum = rand() / double(RAND_MAX);
+ for(int i=0;i<nrows;i++) {
+ current = probabilityMatrix[ncols * i + j];
+ if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
+ nullmatrix[i][j] = 1;
+ count++;
+ previous = 0.0;
+ break;
+ }
+ previous = current;
+ }
+ }
+ }
+ }
+
+ //swap_checkerboards takes the original matrix and swaps checkerboards
+ else if(matrix == "sim9") {
+ trial.swap_checkerboards (co_matrix, ncols, nrows);
+ nullmatrix = co_matrix;
+ }
+ else {
+ m->mothurOut("[ERROR]: No null model selected!\n\n"); m->control_pressed = true;
+ return 1;
+ }
+
+ //run metric on null matrix and add score to the stats vector
+ if (metric == "cscore"){
+ stats.push_back(trial.calc_c_score(nullmatrix, rowtotal, ncols, nrows));
+ }
+ else if (metric == "checker") {
+ stats.push_back(trial.calc_checker(nullmatrix, rowtotal, ncols, nrows));
+ }
+ else if (metric == "vratio") {
+ stats.push_back(trial.calc_vratio(nrows, ncols, rowtotal, columntotal));
+ }
+ else if (metric == "combo") {
+ stats.push_back(trial.calc_combo(nrows, ncols, nullmatrix));
+ }
+ else {
+ m->mothurOut("[ERROR]: No metric selected!\n\n"); m->control_pressed = true;
+ return 1;
+ }
+
+ }
+
+
+
+ double total = 0.0;
+ for (int i=0; i<stats.size();i++) { total+=stats[i]; }
+
+ double nullMean = double (total/(double)stats.size());
+
+ m->mothurOutEndLine(); m->mothurOut("average metric score: " + toString(nullMean)); m->mothurOutEndLine();
+
+ double pvalue = 0.0;
+ if (metric == "cscore" || metric == "checker") { pvalue = trial.calc_pvalue_greaterthan (stats, initscore); }
+ else{ pvalue = trial.calc_pvalue_lessthan (stats, initscore); }
+
+ m->mothurOut("pvalue: " + toString(pvalue)); m->mothurOutEndLine();
+ out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << pvalue << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "Cooccurrence");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff