#include "ace.h"
#include "sobs.h"
#include "chao1.h"
+#include "sharedchao1.h"
+#include "sharedsobscollectsummary.h"
//**********************************************************************************************************************
Venn::Venn(){
try {
globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
+
}
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";
+ errorOut(e, "Venn", "Venn");
exit(1);
}
}
//**********************************************************************************************************************
-void Venn::getPic(OrderVector* order, vector<Calculator*> vCalcs) {
+void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
try {
- SAbundVector s;
- s = order->getSAbundVector(); sabund = &s;
-
+
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = globaldata->inputFileName + ".venn." + order->getLabel() + vCalcs[i]->getName() + ".svg";
+ string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);
vector<double> data = vCalcs[i]->getValues(sabund);
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 " + order->getLabel() + "</text>\n";
+ 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";
}
}
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";
+ errorOut(e, "Venn", "getPic");
exit(1);
}
}
//**********************************************************************************************************************
-void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
+void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
try {
- //fills vector of sharedsabunds - lookup
- getSharedVectors(sharedorder);
+ vector<SharedRAbundVector*> subset;
/******************* 1 Group **************************/
if (lookup.size() == 1) {
SAbundVector s;
- s = lookup[0]->getSAbundVector(); sabund = &s;
+ s = lookup[0]->getSAbundVector(); SAbundVector* sabund = &s;
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + vCalcs[i]->getName() + "." + groupComb + ".svg";
+ string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);
//in essence you want to run it like a single
- if (vCalcs[i]->getName() == "SharedSobs") {
- delete vCalcs[i];
- vCalcs[i] = new Sobs();
- }else if (vCalcs[i]->getName() == "SharedChao") {
- delete vCalcs[i];
- vCalcs[i] = new Chao1();
- }else if (vCalcs[i]->getName() == "SharedAce") {
- delete vCalcs[i];
- vCalcs[i] = new Ace(10);
+ 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);
}
- vector<double> data = vCalcs[i]->getValues(sabund);
+ vector<double> data = singleCalc->getValues(sabund);
//svg image
outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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 " + sharedorder->getLabel() + "</text>\n";
+ 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";
if (data.size() == 3) {
outsvg << "</g>\n</svg>\n";
outsvg.close();
+ delete singleCalc;
+
}
-
/******************* 2 Groups **************************/
}else if (lookup.size() == 2) {
//one for each group
SAbundVector sA, sB;
SAbundVector* sabundA; SAbundVector* sabundB;
- sA = lookup[0]->getSAbundVector(); sabundA = &sA;
- sB = lookup[1]->getSAbundVector(); sabundB = &sB;
+ sabundA = new SAbundVector(lookup[0]->getSAbundVector());// sabundA = &sA;
+ sabundB = new SAbundVector(lookup[1]->getSAbundVector());// sabundB = &sB;
+
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[1]);
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + vCalcs[i]->getName() + "." + groupComb + ".svg";
+ string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);
//get estimates for sharedAB
- vector<double> shared = vCalcs[i]->getValues(lookup[0], lookup[1]);
+ vector<double> shared = vCalcs[i]->getValues(subset);
//in essence you want to run it like a single
- if (vCalcs[i]->getName() == "SharedSobs") {
- delete vCalcs[i];
- vCalcs[i] = new Sobs();
- }else if (vCalcs[i]->getName() == "SharedChao") {
- delete vCalcs[i];
- vCalcs[i] = new Chao1();
- }else if (vCalcs[i]->getName() == "SharedAce") {
- delete vCalcs[i];
- vCalcs[i] = new Ace(10);
+ 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 = vCalcs[i]->getValues(sabundA);
-
+ vector<double> numA = singleCalc->getValues(sabundA);
+
//get estimates for numB
- vector<double> numB = vCalcs[i]->getValues(sabundB);
-
+ vector<double> numB = singleCalc->getValues(sabundB);
//image window
outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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 " + sharedorder->getLabel() + "</text>\n";
+ 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]) + "</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]) + "</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=\"460\">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 << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">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\" x=\"175\" y=\"500\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">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]))) + "</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";
//close file
outsvg << "</g>\n</svg>\n";
outsvg.close();
-
+ delete singleCalc;
}
-
/******************* 3 Groups **************************/
}else if (lookup.size() == 3) {
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++){
- string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + vCalcs[i]->getName() + "." + groupComb + ".svg";
- openOutputFile(filenamesvg, outsvg);
-
- //get estimates for sharedAB, sharedAC and sharedBC
- vector<double> sharedAB = vCalcs[i]->getValues(lookup[0], lookup[1]);
- vector<double> sharedAC = vCalcs[i]->getValues(lookup[0], lookup[2]);
- vector<double> sharedBC = vCalcs[i]->getValues(lookup[1], lookup[2]);
- //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, "");
- }
-
- vector<double> sharedAwithBC = vCalcs[i]->getValues(lookup[0], merge);
-
- 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, "");
- }
-
- vector<double> sharedBwithAC = vCalcs[i]->getValues(lookup[1], merge);
-
- 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, "");
- }
-
- vector<double> sharedCwithAB = vCalcs[i]->getValues(lookup[2], merge);
-
-
//in essence you want to run it like a single
- if (vCalcs[i]->getName() == "SharedSobs") {
- delete vCalcs[i];
- vCalcs[i] = new Sobs();
- }else if (vCalcs[i]->getName() == "SharedChao") {
- delete vCalcs[i];
- vCalcs[i] = new Chao1();
- }else if (vCalcs[i]->getName() == "SharedAce") {
- delete vCalcs[i];
- vCalcs[i] = new Ace(10);
+ 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 = vCalcs[i]->getValues(sabundA);
+ vector<double> numA = singleCalc->getValues(sabundA);
//get estimates for numB
- vector<double> numB = vCalcs[i]->getValues(sabundB);
+ vector<double> numB = singleCalc->getValues(sabundB);
//get estimates for numC
- vector<double> numC = vCalcs[i]->getValues(sabundC);
-
+ vector<double> numC = singleCalc->getValues(sabundC);
+
+
+ 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);
+
+ 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, sharedABC2, sharedABC3, sharedABC;
+ 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)), 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)), j, "");
+ }
- sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
- sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
- sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
+ 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)), 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 < 0.0) { sharedABC1 = 0; }
- if (sharedABC2 < 0.0) { sharedABC2 = 0; }
- if (sharedABC3 < 0.0) { sharedABC3 = 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; }
+
+ //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);
+ }
- //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; }
-
//image window
outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
outsvg << "<g>\n";
//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 " + sharedorder->getLabel() + "</text>\n";
+ 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\"/>";
-
+
//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)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)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)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";
- 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]) + "</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]) + "</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]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"640\">The total number of species in all groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of sepecies shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">The number of sepecies 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\" x=\"175\" y=\"740\">The number of sepecies 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\" x=\"175\" y=\"760\">The number of sepecies 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\" x=\"175\" y=\"580\">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 << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">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\" x=\"175\" y=\"620\">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\" 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\" x=\"175\" y=\"780\">The total shared richness is " + toString(sharedABC) + "</text>\n";
//close file
outsvg << "</g>\n</svg>\n";
outsvg.close();
+ delete singleCalc;
+
}
/******************* 4 Groups **************************/
}else if (lookup.size() == 4) {
//calc the shared otu
- int sharedABCD = 0;
- int numA = 0; int numB = 0; int numC = 0; int numD = 0;
- int sharedAB = 0; int sharedAC = 0; int sharedBC = 0; int sharedAD = 0; int sharedBD = 0; int sharedCD = 0;
- int sharedABC = 0; int sharedACD = 0; int sharedBCD = 0; int sharedABD = 0;
+ float sharedABCD = 0;
+ float numA = 0; float numB = 0; float numC = 0; float numD = 0;
+ float sharedAB = 0; float sharedAC = 0; float sharedBC = 0; float sharedAD = 0; float sharedBD = 0; float sharedCD = 0;
+ float sharedABC = 0; float sharedACD = 0; float sharedBCD = 0; float sharedABD = 0;
+ vector<double> data;
+ //get sabund vector pointers so you can use the single calculators
+ //one for each group
+ SAbundVector sA, sB, sC, sD;
+ SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC; SAbundVector* sabundD;
+ sA = lookup[0]->getSAbundVector(); sabundA = &sA;
+ sB = lookup[1]->getSAbundVector(); sabundB = &sB;
+ sC = lookup[2]->getSAbundVector(); sabundC = &sC;
+ sD = lookup[3]->getSAbundVector(); sabundD = &sD;
//A = red, B = green, C = blue, D = yellow
- if ((vCalcs.size() > 1) || (vCalcs[0]->getName() != "SharedSobs")) { cout << "The only calculator able to be used with 4 groups is sharedsobs. I will run that for you. " << endl; }
-
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- //are they only in one
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numA++; }
- if ((lookup[1]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numB++; }
- if ((lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numC++; }
- if ((lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0)) { numD++; }
- //are they shared by 2
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAB++; }
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAC++; }
- if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedBC++; }
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0)) { sharedAD++; }
- if ((lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBD++; }
- if ((lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedCD++; }
- //are they shared by 3
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) == 0)) { sharedABC++; }
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0)) { sharedACD++; }
- if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBCD++; }
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0)) { sharedABD++; }
- //are they shared by all
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0)) { sharedABCD++; }
- }
+ //make a file for each calculator
+ for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + "." + groupComb + ".svg";
- openOutputFile(filenamesvg, outsvg);
-
- //image window
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
- outsvg << "<g>\n";
+ if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups. It will be disregarded. "); mothurOutEndLine(); }
+ else{
+ string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+ openOutputFile(filenamesvg, outsvg);
- //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 " + sharedorder->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 ";
-
- //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(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(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(215 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"190\">" + toString(sharedBC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(150 - ((int)toString(numC).length() / 2)) + "\" y=\"230\">" + toString(numD) + "</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=\"100\" y=\"490\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(((sharedAB + sharedABD + sharedABC + sharedABCD) / (float)(numA + numB + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + 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 << "</g>\n</svg>\n";
- outsvg.close();
+
+ //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();
+ }
+
+ //get estimates for numA
+ data = singleCalc->getValues(sabundA);
+ numA = data[0];
+
+ //get estimates for numB
+ data = singleCalc->getValues(sabundB);
+ numB = data[0];
+
+ //get estimates for numC
+ data = singleCalc->getValues(sabundC);
+ numC = data[0];
+
+ //get estimates for numD
+ data = singleCalc->getValues(sabundD);
+ numD = data[0];
- }
-
-
-
-
- }
- 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";
- exit(1);
- }
-}
-//**********************************************************************************************************************
-void Venn::getSharedVectors(SharedOrderVector* order){
- try {
-
- //delete lookup
- for (int j = 0; j < lookup.size(); j++) {
- delete lookup[j];
- }
+ //get estimates for pairs
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[1]);
+ data = vCalcs[i]->getValues(subset);
+ sharedAB = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[2]);
+ data = vCalcs[i]->getValues(subset);
+ sharedAC = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[3]);
+ data = vCalcs[i]->getValues(subset);
+ sharedAD = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[1]); subset.push_back(lookup[2]);
+ data = vCalcs[i]->getValues(subset);
+ sharedBC = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[1]); subset.push_back(lookup[3]);
+ data = vCalcs[i]->getValues(subset);
+ sharedBD = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[2]); subset.push_back(lookup[3]);
+ data = vCalcs[i]->getValues(subset);
+ sharedCD = data[0];
+
+
+ //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);
+ sharedABC = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
+ data = vCalcs[i]->getValues(subset);
+ sharedACD = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[1]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
+ data = vCalcs[i]->getValues(subset);
+ sharedBCD = data[0];
+
+ subset.clear();
+ subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[3]);
+ data = vCalcs[i]->getValues(subset);
+ sharedABD = data[0];
+
+ //get estimate for all four
+ data = vCalcs[i]->getValues(lookup);
+ sharedABCD = data[0];
- lookup.clear();
-
- groupComb = "";
-
- //create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
- temp->setLabel(order->getLabel());
- temp->setGroup(globaldata->Groups[i]);
- groupComb += globaldata->Groups[i];
- lookup.push_back(temp);
- }
- int numSeqs = order->size();
- //sample all the members
- for(int i=0;i<numSeqs;i++){
- //get first sample
- individual chosen = order->get(i);
- int abundance;
-
- //set info for sharedvector in chosens group
- for (int j = 0; j < lookup.size(); j++) {
- if (chosen.group == lookup[j]->getGroup()) {
- abundance = lookup[j]->getAbundance(chosen.bin);
- lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
- break;
+ //image window
+ outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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 << "<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 ";
+
+ //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 << "</g>\n</svg>\n";
+ outsvg.close();
+ delete singleCalc;
}
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "Venn", "getPic");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Venn class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
+
projects / mothur.git / blobdiff