//**********************************************************************************************************************
-Venn::Venn(string o) : outputDir(o) {
+Venn::Venn(string o, bool n) : outputDir(o), nseqs(n) {
try {
globaldata = GlobalData::getInstance();
m = MothurOut::getInstance();
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.645 * height)) + "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
}
+ if (nseqs) {
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.70 * height)) + "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
+ }
+
outsvg << "</g>\n</svg>\n";
outsvg.close();
}
singleCalc = new Chao1();
}else if (vCalcs[i]->getName() == "sharedace") {
singleCalc = new Ace(10);
- }else if (vCalcs[i]->getName() == "nseqs") {
- singleCalc = new NSeqs();
}
vector<double> data = singleCalc->getValues(sabund);
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.60 * height)) + "\" >The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.645 * height)) + "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
}
-
+
+ if (nseqs) {
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.70 * height)) + "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
+ }
+
outsvg << "</g>\n</svg>\n";
outsvg.close();
delete singleCalc;
if (m->control_pressed) { outsvg.close(); return outputNames; }
//get estimates for sharedAB
- vector<double> results = vCalcs[i]->getValues(subset);
+ vector<double> shared = vCalcs[i]->getValues(subset);
//in essence you want to run it like a single
if (vCalcs[i]->getName() == "sharedsobs") {
singleCalc = new Sobs();
}else if (vCalcs[i]->getName() == "sharedchao") {
singleCalc = new Chao1();
- }else if (vCalcs[i]->getName() == "nseqs") {
- singleCalc = new NSeqs();
}//else if (vCalcs[i]->getName() == "sharedace") {
//singleCalc = new Ace(10);
//}
+ int sharedVal, numSeqsA, numSeqsB;
+ if (nseqs) {
+ NSeqs* nseqsCalc = new NSeqs();
+ vector<double> data = nseqsCalc->getValues(lookup);
+
+ sharedVal = data[0] + data[1];
+ numSeqsA = sabundA->getNumSeqs();
+ numSeqsB = sabundB->getNumSeqs();
+
+ delete nseqsCalc;
+ }
+
+
//get estimates for numA
- vector<double> resultsA = singleCalc->getValues(sabundA);
+ vector<double> numA = singleCalc->getValues(sabundA);
//get estimates for numB
- vector<double> resultsB = singleCalc->getValues(sabundB);
-
- double numA, numB, shared;
- if (vCalcs[i]->getName() == "nseqs") {
- shared = results[0] + results[1]; //add both groups sequences
- numA = resultsA[0] - results[0]; //what's in A - the number of species in A that are in shared otus
- numB = resultsB[0] - results[1]; //what's in B - the number of species in B that are in shared otus
- }else{
- shared = results[0];
- numA = resultsA[0] - shared;
- numB = resultsB[0] - shared;
- }
+ vector<double> numB = singleCalc->getValues(sabundB);
//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(height) + " \" >\n";
outsvg << "<g>\n";
-
+
//draw circles
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.36 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.62 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numB) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numA[0] - shared[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numB[0] - shared[0]) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(shared) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.66 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(resultsA[0]);
- if (resultsA.size() == 3) {
- outsvg << " the lci is " + toString(resultsA[1]) + " and the hci is " + toString(resultsA[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(shared[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.66 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ if (numA.size() == 3) {
+ outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.69 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(resultsB[0]);
- if (resultsB.size() == 3) {
- outsvg << " the lci is " + toString(resultsB[1]) + " and the hci is " + toString(resultsB[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
-
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.72 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared / (float)(numA + numB + shared))*100) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.78 * height)) + "\">The total richness for all groups is " + toString((float)(numA + numB + shared)) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.69 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ if (numB.size() == 3) {
+ outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.72 * height)) + "\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal); }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.78 * height)) + "\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0]))+ "</text>\n";;
+
//close file
outsvg << "</g>\n</svg>\n";
}else if (lookup.size() == 3) {
height = 1600;
+ int windowSize = height;
+
//get sabund vector pointers so you can use the single calculators
//one for each group
if (m->control_pressed) { outsvg.close(); return outputNames; }
+ int sharedVal, sharedABVal, sharedACVal, sharedBCVal, numSeqsA, numSeqsB, numSeqsC;
+
+ if (nseqs) {
+ NSeqs* nseqsCalc = new NSeqs();
+ vector<double> sharedData = nseqsCalc->getValues(lookup);
+
+ vector<SharedRAbundVector*> mysubset; mysubset.push_back(lookup[0]); mysubset.push_back(lookup[1]);
+ vector<double> sharedAB = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[2]);
+ vector<double> sharedAC = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[2]);
+ vector<double> sharedBC = nseqsCalc->getValues(mysubset);
+
+ sharedVal = sharedData[0] + sharedData[1] + sharedData[2];
+ sharedABVal = sharedAB[0] + sharedAB[1];
+ sharedACVal = sharedAC[0] + sharedAC[1];
+ sharedBCVal = sharedBC[0] + sharedBC[1];
+ numSeqsA = sabundA->getNumSeqs();
+ numSeqsB = sabundB->getNumSeqs();
+ numSeqsC = sabundC->getNumSeqs();
+
+ delete nseqsCalc;
+ }
+
+
if (vCalcs[i]->getName() == "sharedace") {
singleCalc = new Ace(10);
vector<double> sharedCwithAB;
//find possible sharedABC values
- double sharedABC1 = 0.0; double sharedABC2 = 0.0; double sharedABC3 = 0.0; double sharedABC = 0.0;
- vector<double> = resultsNseqs;
+ float sharedABC1 = 0.0; float sharedABC2 = 0.0; float sharedABC3 = 0.0; float sharedABC = 0.0;
if (vCalcs[i]->getMultiple() == false) {
//merge BC and estimate with shared with A
else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
}else{
vector<double> data = vCalcs[i]->getValues(lookup);
- resultsNseqs = data;
sharedABC = data[0];
sharedAwithBC.push_back(sharedAB[0] + sharedAC[0] - sharedABC);
sharedBwithAC.push_back(sharedAB[0] + sharedBC[0] - sharedABC);
sharedCwithAB.push_back(sharedAC[0] + sharedBC[0] - sharedABC);
}
- double numA, numB, numC, numAB, numAC, numBC, numABC;
- if (vCalcs[i]->getName() == "nseqs") {
- numABC = resultsNseqs[0] + resultsNseqs[1] + resultsNseqs[2];
- numBC = sharedBC[0] + sharedBC[1] - (resultsNseqs[1] + resultsNseqs[2]);
-
- }else{
- numABC = sharedABC;
- numBC = sharedBC[0] - sharedABC;
- numAB = sharedAB[0] - sharedABC;
- numAC = sharedAC[0] - sharedABC;
- numA = numA[0]-sharedAwithBC[0];
- numB = numB[0]-sharedBwithAC[0];
- numC = numC[0]-sharedCwithAB[0];
- }
-
//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(height) + " \" >\n";
+ 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";
outsvg << "<g>\n";
//draw circles
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.44 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.44 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.33 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.65 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.5 * width)) + "\" cy=\"" + toString(int(0.5 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
//place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.52 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.58 * width) - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.34 * height)) + "\">" + toString(sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.52 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.58 * width) - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.34 * height)) + "\">" + toString(sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
if (numA.size() == 3) {
- outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
+ outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
if (numB.size() == 3) {
- outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
+ outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
if (numC.size() == 3) {
- outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
+ outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.80 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total shared richness is " + toString(sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.80 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total shared richness is " + toString(sharedABC);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal); }
+ outsvg << "</text>\n";
delete singleCalc;
vector<double> sharedabc = vCalcs[i]->getValues(subset);
//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(height) + " \" >\n";
+ 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";
outsvg << "<g>\n";
//draw circles
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.33 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.65 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.5 * width)) + "\" cy=\"" + toString(int(0.5 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
//place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.51 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.59 * width) - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.35 * height)) + "\">" + toString(sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.51 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.59 * width) - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.35 * height)) + "\">" + toString(sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCVal); }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
if (numA.size() == 3) {
- outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
+ outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
if (numB.size() == 3) {
- outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
-
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
+ outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
if (numC.size() == 3) {
- outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
- }else { outsvg << "</text>\n"; }
-
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedab[0] - sharedac[0] - sharedbc[0] + sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The total shared richness is " + toString(sharedabc[0]) + "</text>\n";
+ outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedab[0] - sharedac[0] - sharedbc[0] + sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The total shared richness is " + toString(sharedabc[0]);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal); }
+ outsvg << "</text>\n";
}
-
//close file
outsvg << "</g>\n</svg>\n";
}else if (lookup.size() == 4) {
height = 1600;
+
+ int windowSize = height;
//calc the shared otu
float sharedABCD = 0;
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao") && (vCalcs[i]->getName() != "nseqs")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups. It will be disregarded. "); m->mothurOutEndLine(); }
+ if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups. It will be disregarded. "); m->mothurOutEndLine(); }
else{
string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
outputNames.push_back(filenamesvg);
singleCalc = new Sobs();
}else if (vCalcs[i]->getName() == "sharedchao") {
singleCalc = new Chao1();
- }else if (vCalcs[i]->getName() == "nseqs") {
- singleCalc = new NSeqs();
}
-
//get estimates for numA
data = singleCalc->getValues(sabundA);
data = vCalcs[i]->getValues(lookup);
sharedABCD = data[0];
//cout << "num abcd = " << sharedABCD << endl << endl;
-
-
+ int sharedVal, sharedABCVal, sharedABDVal, sharedACDVal, sharedBCDVal, sharedABVal, sharedACVal, sharedADVal, sharedBCVal, sharedBDVal, sharedCDVal, numSeqsA, numSeqsB, numSeqsC, numSeqsD;
+
+ if (nseqs) {
+ NSeqs* nseqsCalc = new NSeqs();
+ vector<double> sharedData = nseqsCalc->getValues(lookup);
+
+ vector<SharedRAbundVector*> mysubset; mysubset.push_back(lookup[0]); mysubset.push_back(lookup[1]);
+ vector<double> sharedAB = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[2]);
+ vector<double> sharedAC = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[3]);
+ vector<double> sharedAD = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[2]);
+ vector<double> sharedBC = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[3]);
+ vector<double> sharedBD = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[2]); mysubset.push_back(lookup[3]);
+ vector<double> sharedCD = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[2]);
+ vector<double> sharedABC = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[3]);
+ vector<double> sharedABD = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[2]); mysubset.push_back(lookup[3]);
+ vector<double> sharedACD = nseqsCalc->getValues(mysubset);
+
+ mysubset.clear(); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[2]); mysubset.push_back(lookup[3]);
+ vector<double> sharedBCD = nseqsCalc->getValues(mysubset);
+
+ sharedVal = sharedData[0] + sharedData[1] + sharedData[2] + sharedData[3];
+ sharedABCVal = sharedABC[0] + sharedABC[1] + sharedABC[2];
+ sharedABDVal = sharedABD[0] + sharedABD[1] + sharedABD[2];
+ sharedACDVal = sharedACD[0] + sharedACD[1] + sharedACD[2];
+ sharedBCDVal = sharedBCD[0] + sharedBCD[1] + sharedBCD[2];
+ sharedABVal = sharedAB[0] + sharedAB[1];
+ sharedACVal = sharedAC[0] + sharedAC[1];
+ sharedADVal = sharedAD[0] + sharedAD[1];
+ sharedBCVal = sharedBC[0] + sharedBC[1];
+ sharedBDVal = sharedBD[0] + sharedBD[1];
+ sharedCDVal = sharedCD[0] + sharedCD[1];
+ numSeqsA = sabundA->getNumSeqs();
+ numSeqsB = sabundB->getNumSeqs();
+ numSeqsC = sabundC->getNumSeqs();
+ numSeqsD = sabundD->getNumSeqs();
+
+ delete nseqsCalc;
+ }
+
//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(height) + " \" >\n";
+ 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";
outsvg << "<g>\n";
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(windowSize) + "\"/>";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\" >Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.625 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.65 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.675 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.7 * height)) + "\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.625 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.65 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.675 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.7 * height)) + "\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsD); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedADVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBDVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedCDVal); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABCVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABDVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACDVal); }
+ outsvg << "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD);
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCDVal); }
+ outsvg << "</text>\n";
//make adjustments
sharedABC = sharedABC - sharedABCD;
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.63 * width) - ((int)toString(sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.3 * height)) + "\">" + toString(sharedABC) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABCD).length() / 2)) + "\" y=\"" + toString(int(0.4 * height)) + "\">" + toString(sharedABCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total richness of all the groups is " + toString((float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD));
+ if (nseqs) { outsvg << ", and the number of squences in the otus shared by all groups is " + toString(sharedVal); }
+ outsvg << "</text>\n";
-
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total richness of all the groups is " + toString((float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD)) + "</text>\n";
-
-
outsvg << "</g>\n</svg>\n";
outsvg.close();
delete singleCalc;
projects / mothur.git / blobdiff