X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cooccurrencecommand.cpp;h=00de4d6ee612439732207872eba327b8a03f699e;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=f1f849af255004e901777f32fb72aa7bd5e7a129;hpb=4993ef2939f9705644a81085bbfae444af062116;p=mothur.git diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp index f1f849a..00de4d6 100644 --- a/cooccurrencecommand.cpp +++ b/cooccurrencecommand.cpp @@ -51,6 +51,26 @@ string CooccurrenceCommand::getHelpString(){ } } //********************************************************************************************************************** +string CooccurrenceCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "summary") { outputFileName = "cooccurence.summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "CooccurrenceCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** CooccurrenceCommand::CooccurrenceCommand(){ try { abort = true; calledHelp = true; @@ -176,11 +196,11 @@ int CooccurrenceCommand::execute(){ set userLabels = labels; ofstream out; - string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("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"; + out << "metric\tlabel\tScore\tzScore\tstandardDeviation\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))) { @@ -272,20 +292,23 @@ int CooccurrenceCommand::execute(){ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp, ofstream& out){ try { int numOTUS = thisLookUp[0]->getNumBins(); - vector< vector > initmatrix; initmatrix.resize(thisLookUp.size()); + + 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); } - for (int i = 0; i < thisLookUp.size(); i++) { initmatrix[i].resize((thisLookUp[i]->getNumBins()), 0); } vector columntotal; columntotal.resize(thisLookUp.size(), 0); vector rowtotal; rowtotal.resize(numOTUS, 0); - for (int i = 0; i < thisLookUp.size(); i++) { - for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) { + 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) { - initmatrix[i][j] = 1; co_matrix[j][i] = 1; rowtotal[j]++; columntotal[i]++; @@ -299,8 +322,6 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp int ncols = thisLookUp.size();//groups double initscore = 0.0; - vector columntotal; columntotal.resize(ncols, 0); - vector rowtotal; rowtotal.resize(nrows, 0); vector stats; double probabilityMatrix[ncols * nrows]; vector > nullmatrix(nrows, vector(ncols, 0)); @@ -322,15 +343,16 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp } } } - else if (matrix == "sim2") { - for(int i=0;i& thisLookUp } } } - else if (matrix == "sim9") { } + else if (matrix == "sim9" || matrix == "sim2") { } else { m->mothurOut("[ERROR]: No model selected! \n"); m->control_pressed = true; } - - if (metric == "cscore") { initscore = trial.calc_c_score(initmatrix, rowtotal, ncols, nrows); } - else if (metric == "checker") { initscore = trial.calc_checker(initmatrix, rowtotal, ncols, nrows); } + //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, initmatrix); } + 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(); @@ -409,79 +431,14 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp double current; double randnum; int count; - - //burn-in - for(int i=0;i<10000;i++){ - nullmatrix.clear(); - //zero-fill the null matrix - nullmatrix.assign(nrows, vector(ncols, 0)); - - if(matrix == "sim1" || matrix == "sim6" || matrix == "sim8" || matrix == "sim7") { - count = 0; - while(count < n) { - nextnum: - previous = 0.0; - randnum = rand() / double(RAND_MAX); - for(int i=0;i previous) { - nullmatrix[i][j] = 1; - count++; - if (count > n) break; - else - goto nextnum; - } - previous = current; - } - } - } - } - - else if(matrix == "sim2" || matrix == "sim4") { - for(int i=0;i 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 previous && nullmatrix[i][j] != 1) { - nullmatrix[i][j] = 1; - count++; - previous = 0.0; - break; - } - previous = current; - } - } - } - } - + + //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 i=0;i(ncols, 0)); @@ -489,6 +446,7 @@ int CooccurrenceCommand::getCooccurrence(vector& 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); @@ -508,11 +466,21 @@ int CooccurrenceCommand::getCooccurrence(vector& thisLookUp } } - else if(matrix == "sim2" || matrix == "sim4") { + else if (matrix == "sim2") { + for(int i=0;icontrol_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 (initmatrix, rowtotal, columntotal, ncols, nrows); + trial.swap_checkerboards (co_matrix, ncols, nrows); + nullmatrix = co_matrix; } else { m->mothurOut("[ERROR]: No null model selected!\n\n"); m->control_pressed = true; @@ -586,12 +556,20 @@ 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(); + out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore << '\t' << sd << endl; return 0; }