//**********************************************************************************************************************
-Venn::Venn(string o, bool n, string f, int fs) : outputDir(o), nseqs(n), inputfile(f), fontSize(fs) {
+Venn::Venn(string o, bool n, string f, int fs, bool so) : outputDir(o), nseqs(n), inputfile(f), fontSize(fs), sharedOtus(so) {
try {
m = MothurOut::getInstance();
}
if (m->control_pressed) { outsvg.close(); return outputNames; }
//get estimates for sharedAB
- vector<double> shared = vCalcs[i]->getValues(subset);
+ vector<string> labels;
+ vector<double> shared = vCalcs[i]->getValues(subset, labels);
//in essence you want to run it like a single
if (vCalcs[i]->getName() == "sharedsobs") {
singleCalc = new Sobs();
+ if (sharedOtus && (labels.size() != 0)) {
+ string filenameShared = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + ".sharedotus";
+
+ outputNames.push_back(filenameShared);
+ ofstream outShared;
+ m->openOutputFile(filenameShared, outShared);
+ outShared << "Groups\tNumShared\tOTULabels\n";
+ outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() << '\t' << labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ outShared.close();
+ }
}else if (vCalcs[i]->getName() == "sharedchao") {
singleCalc = new Chao1();
- }//else if (vCalcs[i]->getName() == "sharedace") {
- //singleCalc = new Ace(10);
- //}
+ }
int sharedVal, numSeqsA, numSeqsB, uniqSeqsToA, uniqSeqsToB;
if (nseqs) {
}else { //sharedchao and sharedsobs are multigroup
+ ofstream outShared;
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs")) {
+ string filenameShared = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + ".sharedotus";
+
+ outputNames.push_back(filenameShared);
+
+ m->openOutputFile(filenameShared, outShared);
+ outShared << "Groups\tNumShared\tOTULabels\n";
+ }
vector<SharedRAbundVector*> subset;
//get estimates for numA
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[1]);
- vector<double> sharedab = vCalcs[i]->getValues(subset);
+ vector<string> labels;
+ vector<double> sharedab = vCalcs[i]->getValues(subset, labels);
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() << '\t' << labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[2]);
- vector<double> sharedac = vCalcs[i]->getValues(subset);
+ vector<double> sharedac = vCalcs[i]->getValues(subset, labels);
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
subset.clear();
subset.push_back(lookup[1]); subset.push_back(lookup[2]);
- vector<double> sharedbc = vCalcs[i]->getValues(subset);
+ vector<double> sharedbc = vCalcs[i]->getValues(subset, labels);
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[1]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
+
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
- vector<double> sharedabc = vCalcs[i]->getValues(subset);
+ vector<double> sharedabc = vCalcs[i]->getValues(subset, labels);
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ outShared.close();
+ }
//image window
outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(width) + " " + toString(windowSize) + " \" >\n";
data = singleCalc->getValues(sabundD);
numD = data[0];
//cout << "num d = " << numD << endl;
+
+ ofstream outShared;
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs")) {
+ string filenameShared = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + ".sharedotus";
+
+ outputNames.push_back(filenameShared);
+
+ m->openOutputFile(filenameShared, outShared);
+ outShared << "Groups\tNumShared\tOTULabels\n";
+ }
//get estimates for pairs
subset.clear();
+ vector<string> labels;
subset.push_back(lookup[0]); subset.push_back(lookup[1]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedAB = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num ab = " << sharedAB << endl;
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[2]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedAC = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num ac = " << sharedAC << endl;
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[3]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedAD = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[3]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num ad = " << sharedAD << endl;
subset.clear();
subset.push_back(lookup[1]); subset.push_back(lookup[2]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedBC = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[1]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num bc = " << sharedBC << endl;
subset.clear();
subset.push_back(lookup[1]); subset.push_back(lookup[3]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedBD = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[1]->getGroup() + "-" + lookup[3]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num bd = " << sharedBD << endl;
subset.clear();
subset.push_back(lookup[2]); subset.push_back(lookup[3]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedCD = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[2]->getGroup() + "-" + lookup[3]->getGroup() << '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num cd = " << sharedCD << endl;
//get estimates for combos of 3
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedABC = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup()+ "-" + lookup[2]->getGroup()<< '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num abc = " << sharedABC << endl;
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedACD = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[2]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ }
//cout << "num acd = " << sharedACD << endl;
subset.clear();
subset.push_back(lookup[1]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset,labels);
sharedBCD = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[1]->getGroup() + "-" + lookup[2]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ outShared << labels[labels.size()-1];
+ outShared << endl;
+ }
//cout << "num bcd = " << sharedBCD << endl;
subset.clear();
subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[3]);
- data = vCalcs[i]->getValues(subset);
+ data = vCalcs[i]->getValues(subset, labels);
sharedABD = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ outShared << labels[labels.size()-1];
+ outShared << endl;
+ }
//cout << "num abd = " << sharedABD << endl;
//get estimate for all four
- data = vCalcs[i]->getValues(lookup);
+ data = vCalcs[i]->getValues(lookup, labels);
sharedABCD = data[0];
+ if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") && (labels.size() != 0)) {
+ outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
+ for (int k = 0; k < labels.size()-1; k++) {
+ outShared << labels[k] << ",";
+ }
+ if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
+ outShared << endl;
+ outShared.close();
+ }
//cout << "num abcd = " << sharedABCD << endl << endl;
int sharedVal, sharedABCVal, sharedABDVal, sharedACDVal, sharedBCDVal, sharedABVal, sharedACVal, sharedADVal, sharedBCVal, sharedBDVal, sharedCDVal, numSeqsA, numSeqsB, numSeqsC, numSeqsD;
projects / mothur.git / blobdiff