#include "ace.h"
#include "sobs.h"
#include "chao1.h"
+#include "nseqs.h"
#include "sharedchao1.h"
#include "sharedsobscollectsummary.h"
//**********************************************************************************************************************
-Venn::Venn(){
+Venn::Venn(string o, bool n, string f, int fs, bool so) : outputDir(o), nseqs(n), inputfile(f), fontSize(fs), sharedOtus(so) {
try {
- globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
+ m = MothurOut::getInstance();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Venn class function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Venn", "Venn");
exit(1);
}
}
//**********************************************************************************************************************
-void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
+vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
try {
-
+
+ vector<string> outputNames;
+
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
- openOutputFile(filenamesvg, outsvg);
+ string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "." + sabund->getLabel() + "." + vCalcs[i]->getName() + ".svg";
+ outputNames.push_back(filenamesvg);
+ m->openOutputFile(filenamesvg, outsvg);
+
+ if (m->control_pressed) { outsvg.close(); return outputNames; }
vector<double> data = vCalcs[i]->getValues(sabund);
+ int width = 1500;
+ int height = 1500;
+
//svg image
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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(height) + " \" >\n";
outsvg << "<g>\n";
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
+ outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" + toString(int(0.50 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString((width / 2) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(data[0]) + "</text>\n";
if (data.size() == 3) {
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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();
}
+
+ return outputNames;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Venn", "getPic");
exit(1);
}
}
//**********************************************************************************************************************
-void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
+vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
try {
-
+
vector<SharedRAbundVector*> subset;
+ vector<string> outputNames;
+
+ int width = 1500;
+ int height = 1500;
/******************* 1 Group **************************/
if (lookup.size() == 1) {
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
- openOutputFile(filenamesvg, outsvg);
-
+ string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + ".svg";
+ outputNames.push_back(filenamesvg);
+ m->openOutputFile(filenamesvg, outsvg);
+
+ if (m->control_pressed) { outsvg.close(); return outputNames; }
+
//in essence you want to run it like a single
if (vCalcs[i]->getName() == "sharedsobs") {
singleCalc = new Sobs();
vector<double> data = singleCalc->getValues(sabund);
//svg image
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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(height) + " \">\n";
outsvg << "<g>\n";
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" + toString(int(0.50 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.50 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.50 * width) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(data[0]) + "</text>\n";
if (data.size() == 3) {
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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;
}
-
/******************* 2 Groups **************************/
}else if (lookup.size() == 2) {
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
- openOutputFile(filenamesvg, outsvg);
+ string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + ".svg";
+
+ outputNames.push_back(filenamesvg);
+ m->openOutputFile(filenamesvg, outsvg);
+
+ 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) {
+ NSeqs* nseqsCalc = new NSeqs();
+ vector<double> data = nseqsCalc->getValues(lookup);
+ cout << data[0] << '\t' << data[1] << endl;
+ sharedVal = data[0] + data[1];
+ numSeqsA = sabundA->getNumSeqs();
+ numSeqsB = sabundB->getNumSeqs();
+ uniqSeqsToA = numSeqsA-data[0];
+ uniqSeqsToB = numSeqsB-data[1];
+
+ delete nseqsCalc;
+ }
+
+
//get estimates for numA
vector<double> numA = singleCalc->getValues(sabundA);
vector<double> numB = singleCalc->getValues(sabundB);
//image window
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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(height) + " \" >\n";
outsvg << "<g>\n";
//draw circles
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB[0]).length() / 2)) + "\" y=\"195\">" + toString(numB[0] - shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared[0]).length() / 2)) + "\" y=\"195\">" + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"460\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]);
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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]) + "</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) + "; " + toString(uniqSeqsToA) + " sequences are not shared"; }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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]) + "</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) + "; " + toString(uniqSeqsToB) + " sequences are not shared"; }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"500\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"540\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0])) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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) + "; " + toString((sharedVal / (float)(numSeqsA + numSeqsB))*100) + "% of these sequences are shared"; }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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";
outsvg.close();
- delete sabundA;
- delete sabundB;
delete singleCalc;
}
-
/******************* 3 Groups **************************/
}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
SAbundVector sA, sB, sC;
sA = lookup[0]->getSAbundVector(); sabundA = &sA;
sB = lookup[1]->getSAbundVector(); sabundB = &sB;
sC = lookup[2]->getSAbundVector(); sabundC = &sC;
-
+
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- //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() == "sharedace") {
- singleCalc = new Ace(10);
- }
-
- //get estimates for numA
- vector<double> numA = singleCalc->getValues(sabundA);
-
- //get estimates for numB
- vector<double> numB = singleCalc->getValues(sabundB);
-
- //get estimates for numC
- vector<double> numC = singleCalc->getValues(sabundC);
+ string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + ".svg";
+ outputNames.push_back(filenamesvg);
+ m->openOutputFile(filenamesvg, outsvg);
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
- openOutputFile(filenamesvg, outsvg);
-
- //get estimates for sharedAB, sharedAC and sharedBC
- subset.clear();
- subset.push_back(lookup[0]); subset.push_back(lookup[1]);
- vector<double> sharedAB = vCalcs[i]->getValues(subset);
+ if (m->control_pressed) { outsvg.close(); return outputNames; }
- subset.clear();
- subset.push_back(lookup[0]); subset.push_back(lookup[2]);
- vector<double> sharedAC = vCalcs[i]->getValues(subset);
+ int sharedVal, sharedABVal, sharedACVal, sharedBCVal, numSeqsA, numSeqsB, numSeqsC, uniqSeqsToA, uniqSeqsToB, uniqSeqsToC;
- subset.clear();
- subset.push_back(lookup[1]); subset.push_back(lookup[2]);
- vector<double> sharedBC = vCalcs[i]->getValues(subset);
-
- vector<double> sharedAwithBC;
- vector<double> sharedBwithAC;
- vector<double> sharedCwithAB;
+ 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();
+ uniqSeqsToA = numSeqsA-sharedData[0];
+ uniqSeqsToB = numSeqsC-sharedData[1];
+ uniqSeqsToC = numSeqsB-sharedData[1];
+
+ delete nseqsCalc;
+ }
+
- //find possible sharedABC values
- float sharedABC1, sharedABC2, sharedABC3, sharedABC;
-
- if (vCalcs[i]->getName() != "sharedchao") {
- //merge BC and estimate with shared with A
- SharedRAbundVector* merge = new SharedRAbundVector();
- for (int j = 0; j < lookup[1]->size(); j++) {
- merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
- }
+ if (vCalcs[i]->getName() == "sharedace") {
+ singleCalc = new Ace(10);
+
+ //get estimates for numA
+ vector<double> numA = singleCalc->getValues(sabundA);
+
+ //get estimates for numB
+ vector<double> numB = singleCalc->getValues(sabundB);
+
+ //get estimates for numC
+ vector<double> numC = singleCalc->getValues(sabundC);
+
+
+ //get estimates for sharedAB, sharedAC and sharedBC
subset.clear();
- subset.push_back(lookup[0]); subset.push_back(merge);
- sharedAwithBC = vCalcs[i]->getValues(subset);
+ subset.push_back(lookup[0]); subset.push_back(lookup[1]);
+ vector<double> sharedAB = vCalcs[i]->getValues(subset);
+
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[2]);
+ vector<double> sharedAC = vCalcs[i]->getValues(subset);
+
+ subset.clear();
+ subset.push_back(lookup[1]); subset.push_back(lookup[2]);
+ vector<double> sharedBC = vCalcs[i]->getValues(subset);
+
+ vector<double> sharedAwithBC;
+ vector<double> sharedBwithAC;
+ vector<double> sharedCwithAB;
+
+ //find possible sharedABC values
+ 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
+ SharedRAbundVector* merge = new SharedRAbundVector();
+ for (int j = 0; j < lookup[1]->size(); j++) {
+ merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
+ }
+
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(merge);
+ sharedAwithBC = vCalcs[i]->getValues(subset);
+
+ delete merge;
+ //merge AC and estimate with shared with B
+ merge = new SharedRAbundVector();
+ for (int j = 0; j < lookup[0]->size(); j++) {
+ merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
+ }
+
+ subset.clear();
+ subset.push_back(merge); subset.push_back(lookup[1]);
+ sharedBwithAC = vCalcs[i]->getValues(subset);
+
+ delete merge;
+ //merge AB and estimate with shared with C
+ merge = new SharedRAbundVector();
+ for (int j = 0; j < lookup[0]->size(); j++) {
+ merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), "");
+ }
+
+ subset.clear();
+ subset.push_back(lookup[2]); subset.push_back(merge);
+ sharedCwithAB = vCalcs[i]->getValues(subset);
+ delete merge;
+
+ sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
+ sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
+ sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
+
+ //if any of the possible m's are - throw them out
+ if (sharedABC1 < 0.00001) { sharedABC1 = 0; }
+ if (sharedABC2 < 0.00001) { sharedABC2 = 0; }
+ if (sharedABC3 < 0.00001) { sharedABC3 = 0; }
- delete merge;
- //merge AC and estimate with shared with B
- merge = new SharedRAbundVector();
- for (int j = 0; j < lookup[0]->size(); j++) {
- merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
+ //sharedABC is the minimum of the 3 possibilities
+ if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
+ else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
+ else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
+ }else{
+ vector<double> data = vCalcs[i]->getValues(lookup);
+ 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);
}
-
- subset.clear();
- subset.push_back(merge); subset.push_back(lookup[1]);
- sharedBwithAC = 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(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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA) + "; " + toString(uniqSeqsToA) + " sequences are not shared"; }
+ outsvg << "</text>\n";
- delete merge;
- //merge AB and estimate with shared with C
- merge = new SharedRAbundVector();
- for (int j = 0; j < lookup[0]->size(); j++) {
- merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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]);
}
-
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB) + "; " + toString(uniqSeqsToB) + " sequences are not shared"; }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC) + "; " + toString(uniqSeqsToC) + " sequences are not shared"; }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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;
+
+ }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.push_back(lookup[0]);
+ vector<double> numA = vCalcs[i]->getValues(subset);
+
+ //get estimates for numB
subset.clear();
- subset.push_back(lookup[2]); subset.push_back(merge);
- sharedCwithAB = vCalcs[i]->getValues(subset);
- delete merge;
-
- sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
- sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
- sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
-
- //if any of the possible m's are - throw them out
- if (sharedABC1 < 0.0) { sharedABC1 = 0; }
- if (sharedABC2 < 0.0) { sharedABC2 = 0; }
- if (sharedABC3 < 0.0) { sharedABC3 = 0; }
-
- //sharedABC is the minimum of the 3 possibilities
- if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
- else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
- else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
- }else{
- vector<double> data = vCalcs[i]->getValues(lookup);
- 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);
- }
-
- //image window
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
- outsvg << "<g>\n";
+ subset.push_back(lookup[1]);
+ vector<double> numB = vCalcs[i]->getValues(subset);
+
+ //get estimates for numC
+ subset.clear();
+ subset.push_back(lookup[2]);
+ vector<double> numC = vCalcs[i]->getValues(subset);
- //draw circles
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
-//cout << "numA = " << numA[0] << " numB = " << numB[0] << " numC = " << numC[0] << endl;
-//cout << "sharedAB = " << sharedAB[0] << " sharedAC = " << sharedAC[0] << " sharedBC = " << sharedBC[0] << endl;
-//cout << "sharedAwithBC = " << sharedAwithBC[0] << " sharedBwithAC = " << sharedBwithAC[0] << " sharedCwithAB = " << sharedCwithAB[0] << endl;
- //place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"170\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\" y=\"170\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\" y=\"170\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\" y=\"430\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\" y=\"280\">" + toString(sharedABC) + "</text>\n";
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[1]);
+ 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, 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, 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, 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";
+ 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(sharedAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and " + globaldata->Groups[2] + " is " + toString(sharedAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of sepecies shared between groups " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString(sharedBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and combined groups " + globaldata->Groups[1] + globaldata->Groups[2] + " is " + toString(sharedAwithBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"740\">The number of sepecies shared between groups " + globaldata->Groups[1] + " and combined groups " + globaldata->Groups[0] + globaldata->Groups[2] + " is " + toString(sharedBwithAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"760\">The number of sepecies shared between groups " + globaldata->Groups[2] + " and combined groups " + globaldata->Groups[0] + globaldata->Groups[1] + " is " + toString(sharedCwithAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + globaldata->Groups[0] + " 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 << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + globaldata->Groups[1] + " 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\" x=\"175\" y=\"620\">The number of species in group " + globaldata->Groups[2] + " 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=\"" + toString(fontSize) + "\" 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]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); }
+ outsvg << "</text>\n";
+
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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]);
+ }
+ if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); }
+ outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"640\">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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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";
outsvg.close();
- delete singleCalc;
+
+
}
/******************* 4 Groups **************************/
}else if (lookup.size() == 4) {
+
+ height = 1600;
+
+ int windowSize = height;
+
//calc the shared otu
float sharedABCD = 0;
float numA = 0; float numB = 0; float numC = 0; float numD = 0;
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { cout << vCalcs[i]->getName() << " is not a valid calculator with four groups. It will be disregarded. " << endl; }
+ 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 = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
- openOutputFile(filenamesvg, outsvg);
+ string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
+ outputNames.push_back(filenamesvg);
+ m->openOutputFile(filenamesvg, outsvg);
-
+ if (m->control_pressed) { outsvg.close(); return outputNames; }
+
//in essence you want to run it like a single
if (vCalcs[i]->getName() == "sharedsobs") {
singleCalc = new Sobs();
//get estimates for numA
data = singleCalc->getValues(sabundA);
numA = data[0];
+ //cout << "num a = " << numA << endl;
//get estimates for numB
data = singleCalc->getValues(sabundB);
numB = data[0];
-
+ //cout << "num b = " << numB << endl;
//get estimates for numC
data = singleCalc->getValues(sabundC);
numC = data[0];
-
+ //cout << "num c = " << numC << endl;
//get estimates for numD
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;
+
+ 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 width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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(windowSize) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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;
+ //cout << "num abc = " << sharedABC << endl;
+ sharedABD = sharedABD - sharedABCD;
+ //cout << "num abd = " << sharedABD << endl;
+ sharedACD = sharedACD - sharedABCD;
+ //cout << "num acd = " << sharedACD << endl;
+ sharedBCD = sharedBCD - sharedABCD;
+ //cout << "num bcd = " << sharedBCD << endl;
+
+ sharedAB = sharedAB - sharedABC - sharedABCD - sharedABD; //cout << "num ab = " << sharedAB << endl;
+ sharedAC = sharedAC - sharedABC - sharedABCD - sharedACD; //cout << "num ac = " << sharedAC << endl;
+ sharedAD = sharedAD - sharedABD - sharedABCD - sharedACD; //cout << "num ad = " << sharedAD << endl;
+ sharedBC = sharedBC - sharedABC - sharedABCD - sharedBCD; //cout << "num bc = " << sharedBC << endl;
+ sharedBD = sharedBD - sharedABD - sharedABCD - sharedBCD; // cout << "num bd = " << sharedBD << endl;
+ sharedCD = sharedCD - sharedACD - sharedABCD - sharedBCD; //cout << "num cd = " << sharedCD << endl;
+
+ numA = numA - sharedAB - sharedAC - sharedAD - sharedABCD - sharedABC - sharedACD - sharedABD;
+ //cout << "num a = " << numA << endl;
+ numB = numB - sharedAB - sharedBC - sharedBD - sharedABCD - sharedABC - sharedABD - sharedBCD;
+ //cout << "num b = " << numB << endl;
+ numC = numC - sharedAC - sharedBC - sharedCD - sharedABCD - sharedABC - sharedACD - sharedBCD;
+ //cout << "num c = " << numC << endl;
+ numD = numD - sharedAD - sharedBD - sharedCD - sharedABCD - sharedBCD - sharedACD - sharedABD;
+ //cout << "num d = " << numD << endl;
+
//draw circles
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
- outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
- outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
- outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 270 315) \" cx=\"270\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
+ outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 " + toString(int(0.51 * width)) + " " + toString(int(0.27 * height)) + ") \" cx=\"" + toString(int(0.51 * width)) + "\" cy=\"" + toString(int(0.27 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
+ outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 " + toString(int(0.51 * width)) + " " + toString(int(0.27 * height)) + ") \" cx=\"" + toString(int(0.51 * width)) + "\" cy=\"" + toString(int(0.27 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
+ outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 " + toString(int(0.63 * width)) + " " + toString(int(0.36 * height)) + ") \" cx=\"" + toString(int(0.63 * width)) + "\" cy=\"" + toString(int(0.36 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
+ outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 " + toString(int(0.36 * width)) + " " + toString(int(0.36 * height)) + ") \" cx=\"" + toString(int(0.36 * width)) + "\" cy=\"" + toString(int(0.36 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
//A = red, B = green, C = blue, D = yellow
//place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)toString(numA).length() / 2)) + "\" y=\"110\">" + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedAB).length() / 2)) + "\" y=\"160\">" + toString(sharedAB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)toString(numB).length() / 2)) + "\" y=\"110\">" + toString(numB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(sharedAC).length() / 2)) + "\" y=\"190\">" + toString(sharedAC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(550 - ((int)toString(numC).length() / 2)) + "\" y=\"230\">" + toString(numC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(550 - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"210\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(215 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"190\">" + toString(sharedBC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(150 - ((int)toString(numD).length() / 2)) + "\" y=\"230\">" + toString(numD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(150 - ((int)lookup[3]->getGroup().length() / 2)) + "\" y=\"210\">" + lookup[3]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(240 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedAD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(470 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedBD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedCD).length() / 2)) + "\" y=\"430\">" + toString(sharedCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(275 - ((int)toString(sharedABD).length() / 2)) + "\" y=\"240\">" + toString(sharedABD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(400 - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"360\">" + toString(sharedBCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(305 - ((int)toString(sharedACD).length() / 2)) + "\" y=\"360\">" + toString(sharedACD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(440 - ((int)toString(sharedABC).length() / 2)) + "\" y=\"240\">" + toString(sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedABCD).length() / 2)) + "\" y=\"320\">" + toString(sharedABCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"250\" y=\"490\">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 << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"510\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[2] + " is " + toString(((sharedAC + sharedACD + sharedABC + sharedABCD) / (float)(numA + numC + sharedAB + sharedAC + sharedAD + sharedBC + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"530\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[3] + " is " + toString(((sharedAD + sharedACD + sharedABD + sharedABCD) / (float)(numA + numD + sharedAB + sharedAC + sharedAD + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"550\">Percentage of species that are shared in groups " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString(((sharedBC + sharedABC + sharedBCD + sharedABCD) / (float)(numB + numC + sharedAB + sharedAC + sharedCD + sharedBD + sharedBC + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"570\">Percentage of species that are shared in groups " + globaldata->Groups[1] + " and " + globaldata->Groups[3] + " is " + toString(((sharedBD + sharedABD + sharedBCD + sharedABCD) / (float)(numB + numD + sharedAB + sharedAD + sharedCD + sharedBD + sharedBC + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"590\">Percentage of species that are shared in groups " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString(((sharedCD + sharedBCD + sharedACD + sharedABCD) / (float)(numC + numD + sharedAC + sharedAD + sharedCD + sharedBD + sharedBC + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"610\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString(((sharedABC + sharedABCD) / (float)(numA + numB + numC + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"630\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + " and " + globaldata->Groups[3] + " is " + toString(((sharedABD + sharedABCD) / (float)(numA + numB + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"650\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString(((sharedACD + sharedABCD) / (float)(numA + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"670\">Percentage of species that are shared in groups " + globaldata->Groups[1] + ", " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString(((sharedBCD + sharedABCD) / (float)(numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
- //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"690\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + ", " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString((sharedABCD / (float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
-
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.66 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" + toString(int(0.14 * height)) + "\">" + toString(numA) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.66 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.11 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB).length() / 2)) + "\" y=\"" + toString(int(0.2 * height)) + "\">" + toString(sharedAB) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.36 * width) - ((int)toString(numB).length() / 2)) + "\" y=\"" + toString(int(0.14 * height)) + "\">" + toString(numB) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.36 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.11 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)toString(sharedAC).length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + toString(sharedAC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.785 * width) - ((int)toString(numC).length() / 2)) + "\" y=\"" + toString(int(0.29 * height)) + "\">" + toString(numC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.785 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.26 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.31 * width) - ((int)toString(sharedBD).length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + toString(sharedBD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.22 * width) - ((int)toString(numD).length() / 2)) + "\" y=\"" + toString(int(0.29 * height)) + "\">" + toString(numD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.22 * width) - ((int)lookup[3]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.26 * height)) + "\">" + lookup[3]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.34 * width) - ((int)toString(sharedAD).length() / 2)) + "\" y=\"" + toString(int(0.41 * height)) + "\">" + toString(sharedAD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.675 * width) - ((int)toString(sharedBC).length() / 2)) + "\" y=\"" + toString(int(0.41 * height)) + "\">" + toString(sharedBC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedCD).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(sharedCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.39 * width) - ((int)toString(sharedABD).length() / 2)) + "\" y=\"" + toString(int(0.3 * height)) + "\">" + toString(sharedABD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.57 * width) - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"" + toString(int(0.45 * height)) + "\">" + toString(sharedBCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.435 * width) - ((int)toString(sharedACD).length() / 2)) + "\" y=\"" + toString(int(0.45 * height)) + "\">" + toString(sharedACD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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=\"" + toString(fontSize) + "\" 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 << "</g>\n</svg>\n";
outsvg.close();
delete singleCalc;
}
}
-
}
+ return outputNames;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Venn", "getPic");
exit(1);
}
}
projects / mothur.git / blobdiff