*/
#include "venn.h"
+#include "ace.h"
+#include "sobs.h"
+#include "chao1.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";
}
}
//**********************************************************************************************************************
-void Venn::getPic(OrderVector* order) {
+void Venn::getPic(OrderVector* order, vector<Calculator*> vCalcs) {
try {
+ SAbundVector s;
+ s = order->getSAbundVector(); sabund = &s;
- rabund = order->getRAbundVector();
-
- string filenamesvg = globaldata->inputFileName + ".venn." + order->getLabel() + ".svg";
-
- openOutputFile(filenamesvg, outsvg);
-
+ for(int i=0;i<vCalcs.size();i++){
+ string filenamesvg = globaldata->inputFileName + ".venn." + order->getLabel() + vCalcs[i]->getName() + ".svg";
+ openOutputFile(filenamesvg, outsvg);
+
+ vector<double> data = vCalcs[i]->getValues(sabund);
- //svg image
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
- outsvg << "<g>\n";
+ //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 " + order->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"100\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(rabund.getNumBins()).length() / 2)) + "\" y=\"195\">" + toString(rabund.getNumBins()) + "</text>\n";
- outsvg << "</g>\n</svg>\n";
-
- outsvg.close();
+ 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 << "<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";
+
+ 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 << "</g>\n</svg>\n";
+ outsvg.close();
+ }
}
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";
}
}
//**********************************************************************************************************************
-void Venn::getPic(SharedOrderVector* sharedorder) {
+void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
try {
//fills vector of sharedsabunds - lookup
getSharedVectors(sharedorder);
-
- 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";
-
+ /******************* 1 Group **************************/
if (lookup.size() == 1) {
- int numA = 0;
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- //are they only in one
- if (lookup[0]->getAbundance(i) != 0) { numA++; }
+
+ SAbundVector s;
+ s = lookup[0]->getSAbundVector(); 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";
+ 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);
+ }
+
+ vector<double> data = vCalcs[i]->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 << "<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";
+
+ 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 << "</g>\n</svg>\n";
+ outsvg.close();
}
-
- 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 << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(numA).length() / 2)) + "\" y=\"195\">" + toString(numA) + "</text>\n";
+ /******************* 2 Groups **************************/
+
}else if (lookup.size() == 2) {
- //calc the shared otu
- int shared = 0;
- int numA = 0;
- int numB = 0;
+ //get sabund vector pointers so you can use the single calculators
+ //one for each group
+ SAbundVector sA, sB;
+ SAbundVector* sabundA; SAbundVector* sabundB;
+ sA = lookup[0]->getSAbundVector(); sabundA = &sA;
+ sB = lookup[1]->getSAbundVector(); sabundB = &sB;
- //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)) { numA++; }
- if ((lookup[1]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0)) { numB++; }
- //are they shared
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0)) { shared++; }
+ //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
+ vector<double> shared = vCalcs[i]->getValues(lookup[0], lookup[1]);
+
+ //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);
+ }
+
+ //get estimates for numA
+ vector<double> numA = vCalcs[i]->getValues(sabundA);
+
+ //get estimates for numB
+ vector<double> numB = vCalcs[i]->getValues(sabundB);
+
+
+ //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 " + sharedorder->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(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";
+
+ //close file
+ outsvg << "</g>\n</svg>\n";
+ outsvg.close();
+
}
- //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 << "<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).length() / 2)) + "\" y=\"195\">" + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB).length() / 2)) + "\" y=\"195\">" + toString(numB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared).length() / 2)) + "\" y=\"195\">" + toString(shared) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"580\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString((shared / (float)(numA + numB + shared))) + "</text>\n";
-
+ /******************* 3 Groups **************************/
+
}else if (lookup.size() == 3) {
- //calc the shared otu
- int sharedABC = 0;
- int numA = 0; int numB = 0; int numC = 0;
- int sharedAB = 0; int sharedAC = 0; int sharedBC = 0;
+ //get sabund vector pointers so you can use the single calculators
+ //one for each group
+ SAbundVector sA, sB, sC;
+ SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
+ sA = lookup[0]->getSAbundVector(); sabundA = &sA;
+ sB = lookup[1]->getSAbundVector(); sabundB = &sB;
+ sC = lookup[2]->getSAbundVector(); sabundC = &sC;
- //float scalerB;
+ //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]);
- //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)) { numA++; }
- if ((lookup[1]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0)) { numB++; }
- if ((lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { numC++; }
- //are they shared by 2
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0)) { sharedAB++; }
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0)) { sharedAC++; }
- if ((lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBC++; }
+ //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, "");
+ }
- //are they shared by all
- if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0)) { sharedABC++; }
- }
-
- //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 << "<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\"/>";
+ vector<double> sharedAwithBC = vCalcs[i]->getValues(lookup[0], merge);
- //place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA).length() / 2)) + "\" y=\"170\">" + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB).length() / 2)) + "\" y=\"170\">" + toString(sharedAB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)toString(numB).length() / 2)) + "\" y=\"170\">" + toString(numB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC).length() / 2)) + "\" y=\"305\">" + toString(sharedAC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(numC).length() / 2)) + "\" y=\"430\">" + toString(numC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\" y=\"280\">" + toString(sharedABC) + "</text>\n";
+ 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);
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"580\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(((sharedAB + sharedABC) / (float)(numA + numB + sharedAB + sharedABC))) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"610\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[2] + " is " + toString(((sharedAC + sharedABC) / (float)(numA + numC + sharedAC + sharedABC))) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"640\">Percentage of species that are shared in groups " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString(((sharedBC + sharedABC) / (float)(numB + numC + sharedBC + sharedABC))) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"670\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString((sharedABC / (float)(numA + numB + numC + sharedAB + sharedAC + sharedBC + sharedABC))) + "</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, "");
+ }
+
+ 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);
+ }
+
+ //get estimates for numA
+ vector<double> numA = vCalcs[i]->getValues(sabundA);
+
+ //get estimates for numB
+ vector<double> numB = vCalcs[i]->getValues(sabundB);
+
+ //get estimates for numC
+ vector<double> numC = vCalcs[i]->getValues(sabundC);
+
+ //find possible sharedABC values
+ float sharedABC1, sharedABC2, sharedABC3, sharedABC;
+
+ 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; }
+
+ //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 << "<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(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(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(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";
+
+ //close file
+ outsvg << "</g>\n</svg>\n";
+ outsvg.close();
+ }
+
+ /******************* 4 Groups **************************/
}else if (lookup.size() == 4) {
//calc the shared otu
//A = red, B = green, C = blue, D = yellow
- //float scalerB;
+ 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 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++; }
}
-
+
+ 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";
+
//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=\"" + 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 << "<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();
+
}
- outsvg << "</g>\n</svg>\n";
- outsvg.close();
-
+
}
}
}
-//**********************************************************************************************************************
-
-
projects / mothur.git / blobdiff