X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=cooccurrencecommand.cpp;h=48fba8c9727b4df62b7a37cbb629a55c7c082d74;hp=f0a46aaf9dfc0a729df15549a7d8fecc4c02d52a;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=4545a2f620673a0dc2186fdbe2157e39b037cbd0 diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp index f0a46aa..48fba8c 100644 --- a/cooccurrencecommand.cpp +++ b/cooccurrencecommand.cpp @@ -12,14 +12,14 @@ //********************************************************************************************************************** vector 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); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,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 myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -51,6 +51,21 @@ string CooccurrenceCommand::getHelpString(){ } } //********************************************************************************************************************** +string CooccurrenceCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "summary") { pattern = "[filename],cooccurence.summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "CooccurrenceCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** CooccurrenceCommand::CooccurrenceCommand(){ try { abort = true; calledHelp = true; @@ -176,11 +191,13 @@ int CooccurrenceCommand::execute(){ set userLabels = labels; ofstream out; - string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + string outputFileName = getOutputFileName("summary", variables); 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"; + out << "metric\tlabel\tScore\tzScore\tstandardDeviation\tnp_Pvalue\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))) { @@ -272,6 +289,12 @@ int CooccurrenceCommand::execute(){ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp, ofstream& out){ try { int numOTUS = thisLookUp[0]->getNumBins(); + + if(numOTUS < 2) { + m->mothurOut("Not enough OTUs for co-occurrence analysis, skipping"); m->mothurOutEndLine(); + return 0; + } + vector< vector > 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 columntotal; columntotal.resize(thisLookUp.size(), 0); @@ -295,11 +318,11 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp int nrows = numOTUS;//rows of inital matrix int ncols = thisLookUp.size();//groups double initscore = 0.0; - + vector stats; - double probabilityMatrix[ncols * nrows]; + vector probabilityMatrix; probabilityMatrix.resize(ncols * nrows, 0); vector > nullmatrix(nrows, vector(ncols, 0)); - + TrialSwap2 trial; int n = accumulate( columntotal.begin(), columntotal.end(), 0 ); @@ -318,7 +341,7 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp } } //don't need a prob matrix because we just shuffle the rows, may use this in the future -// else if (matrix == "sim2") { + else if (matrix == "sim2") { } // for(int i=0;i& thisLookUp 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); @@ -453,6 +477,7 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp 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& thisLookUp for(int j=0;jcontrol_pressed) { return 0; } randnum = rand() / double(RAND_MAX); for(int i=0;i& thisLookUp //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; @@ -526,12 +553,21 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp m->mothurOutEndLine(); m->mothurOut("average metric score: " + toString(nullMean)); m->mothurOutEndLine(); + //calc_p_value is not a statistical p-value, it's just the average that are either > or < the initscore. + //All it does is show what is expected in a competitively structured community + //zscore is output so p-value can be looked up in a ztable double pvalue = 0.0; if (metric == "cscore" || metric == "checker") { pvalue = trial.calc_pvalue_greaterthan (stats, initscore); } else{ pvalue = trial.calc_pvalue_lessthan (stats, initscore); } + + double sd = trial.getSD(runs, stats, nullMean); + + double zscore = trial.get_zscore(sd, nullMean, initscore); - m->mothurOut("pvalue: " + toString(pvalue)); m->mothurOutEndLine(); - out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << pvalue << endl; + m->mothurOut("zscore: " + toString(zscore)); m->mothurOutEndLine(); + m->mothurOut("standard deviation: " + toString(sd)); m->mothurOutEndLine(); + m->mothurOut("non-parametric p-value: " + toString(pvalue)); m->mothurOutEndLine(); + out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore << '\t' << sd << '\t' << pvalue << endl; return 0; }