5 * Created by Sarah Westcott on 3/30/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
16 //**********************************************************************************************************************
19 globaldata = GlobalData::getInstance();
20 format = globaldata->getFormat();
21 util = new SharedUtil();
24 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
28 cout << "An unknown error has occurred in the Venn class function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
32 //**********************************************************************************************************************
33 void Venn::getPic(OrderVector* order, vector<Calculator*> vCalcs) {
36 s = order->getSAbundVector(); sabund = &s;
38 for(int i=0;i<vCalcs.size();i++){
39 string filenamesvg = globaldata->inputFileName + ".venn." + order->getLabel() + vCalcs[i]->getName() + ".svg";
40 openOutputFile(filenamesvg, outsvg);
42 vector<double> data = vCalcs[i]->getValues(sabund);
45 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
48 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
49 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + order->getLabel() + "</text>\n";
50 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
51 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
53 if (data.size() == 3) {
54 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
55 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
58 outsvg << "</g>\n</svg>\n";
63 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
67 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
71 //**********************************************************************************************************************
72 void Venn::getPic(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
75 //fills vector of sharedsabunds - lookup
76 util->getSharedVectors(globaldata->Groups, lookup, sharedorder); //fills group vectors from order vector.
78 /******************* 1 Group **************************/
79 if (lookup.size() == 1) {
82 s = lookup[0]->getSAbundVector(); sabund = &s;
84 //make a file for each calculator
85 for(int i=0;i<vCalcs.size();i++){
86 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
87 openOutputFile(filenamesvg, outsvg);
89 //in essence you want to run it like a single
90 if (vCalcs[i]->getName() == "sharedsobs") {
92 vCalcs[i] = new Sobs();
93 }else if (vCalcs[i]->getName() == "sharedchao") {
95 vCalcs[i] = new Chao1();
96 }else if (vCalcs[i]->getName() == "sharedace") {
98 vCalcs[i] = new Ace(10);
101 vector<double> data = vCalcs[i]->getValues(sabund);
104 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
107 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
108 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
109 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
110 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "</text>\n";
111 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
113 if (data.size() == 3) {
114 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
115 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
118 outsvg << "</g>\n</svg>\n";
122 /******************* 2 Groups **************************/
124 }else if (lookup.size() == 2) {
125 //get sabund vector pointers so you can use the single calculators
128 SAbundVector* sabundA; SAbundVector* sabundB;
129 sabundA = new SAbundVector(lookup[0]->getSAbundVector());// sabundA = &sA;
130 sabundB = new SAbundVector(lookup[1]->getSAbundVector());// sabundB = &sB;
132 //make a file for each calculator
133 for(int i=0;i<vCalcs.size();i++){
134 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
135 openOutputFile(filenamesvg, outsvg);
137 //get estimates for sharedAB
138 vector<double> shared = vCalcs[i]->getValues(lookup[0], lookup[1]);
140 //in essence you want to run it like a single
141 if (vCalcs[i]->getName() == "sharedsobs") {
143 vCalcs[i] = new Sobs();
144 }else if (vCalcs[i]->getName() == "sharedchao") {
146 vCalcs[i] = new Chao1();
147 }else if (vCalcs[i]->getName() == "sharedace") {
149 vCalcs[i] = new Ace(10);
152 //get estimates for numA
153 vector<double> numA = vCalcs[i]->getValues(sabundA);
155 //get estimates for numB
156 vector<double> numB = vCalcs[i]->getValues(sabundB);
157 cout << numA[0] << '\t' << numB[0] << '\t' << shared[0] << endl;
160 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
164 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
165 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
166 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>";
167 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>";
168 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
169 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB[0]).length() / 2)) + "\" y=\"195\">" + toString(numB[0] - shared[0]) + "</text>\n";
170 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[0]->getGroup() + "</text>\n";
171 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[1]->getGroup() + "</text>\n";
172 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared[0]).length() / 2)) + "\" y=\"195\">" + toString(shared[0]) + "</text>\n";
173 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"460\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]);
174 if (numA.size() == 3) {
175 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
176 }else { outsvg << "</text>\n"; }
178 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]);
179 if (numB.size() == 3) {
180 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
181 }else { outsvg << "</text>\n"; }
183 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";
184 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";
185 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";
188 outsvg << "</g>\n</svg>\n";
194 /******************* 3 Groups **************************/
196 }else if (lookup.size() == 3) {
197 //get sabund vector pointers so you can use the single calculators
199 SAbundVector sA, sB, sC;
200 SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
201 sA = lookup[0]->getSAbundVector(); sabundA = &sA;
202 sB = lookup[1]->getSAbundVector(); sabundB = &sB;
203 sC = lookup[2]->getSAbundVector(); sabundC = &sC;
205 //make a file for each calculator
206 for(int i=0;i<vCalcs.size();i++){
207 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
208 openOutputFile(filenamesvg, outsvg);
210 //get estimates for sharedAB, sharedAC and sharedBC
211 vector<double> sharedAB = vCalcs[i]->getValues(lookup[0], lookup[1]);
212 vector<double> sharedAC = vCalcs[i]->getValues(lookup[0], lookup[2]);
213 vector<double> sharedBC = vCalcs[i]->getValues(lookup[1], lookup[2]);
215 //merge BC and estimate with shared with A
216 SharedRAbundVector* merge = new SharedRAbundVector();
217 for (int j = 0; j < lookup[1]->size(); j++) {
218 merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
221 vector<double> sharedAwithBC = vCalcs[i]->getValues(lookup[0], merge);
224 //merge AC and estimate with shared with B
225 merge = new SharedRAbundVector();
226 for (int j = 0; j < lookup[0]->size(); j++) {
227 merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
230 vector<double> sharedBwithAC = vCalcs[i]->getValues(lookup[1], merge);
233 //merge AB and estimate with shared with C
234 merge = new SharedRAbundVector();
235 for (int j = 0; j < lookup[0]->size(); j++) {
236 merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
239 vector<double> sharedCwithAB = vCalcs[i]->getValues(lookup[2], merge);
242 //in essence you want to run it like a single
243 if (vCalcs[i]->getName() == "sharedsobs") {
245 vCalcs[i] = new Sobs();
246 }else if (vCalcs[i]->getName() == "sharedchao") {
248 vCalcs[i] = new Chao1();
249 }else if (vCalcs[i]->getName() == "sharedace") {
251 vCalcs[i] = new Ace(10);
254 //get estimates for numA
255 vector<double> numA = vCalcs[i]->getValues(sabundA);
257 //get estimates for numB
258 vector<double> numB = vCalcs[i]->getValues(sabundB);
260 //get estimates for numC
261 vector<double> numC = vCalcs[i]->getValues(sabundC);
263 //find possible sharedABC values
264 float sharedABC1, sharedABC2, sharedABC3, sharedABC;
266 sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
267 sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
268 sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
270 //if any of the possible m's are - throw them out
271 if (sharedABC1 < 0.0) { sharedABC1 = 0; }
272 if (sharedABC2 < 0.0) { sharedABC2 = 0; }
273 if (sharedABC3 < 0.0) { sharedABC3 = 0; }
275 //sharedABC is the minimum of the 3 possibilities
276 if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
277 else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
278 else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
281 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
285 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
286 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
287 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
288 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
289 outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
291 //place labels within overlaps
292 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";
293 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
294 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\" y=\"170\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
295 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";
296 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
297 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
298 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";
299 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
300 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
301 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\" y=\"280\">" + toString(sharedABC) + "</text>\n";
303 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";
304 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";
305 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";
306 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";
307 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";
308 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";
309 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]);
310 if (numA.size() == 3) {
311 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
312 }else { outsvg << "</text>\n"; }
314 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]);
315 if (numB.size() == 3) {
316 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
317 }else { outsvg << "</text>\n"; }
319 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + globaldata->Groups[2] + " is " + toString(numC[0]);
320 if (numC.size() == 3) {
321 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
322 }else { outsvg << "</text>\n"; }
324 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";
327 outsvg << "</g>\n</svg>\n";
331 /******************* 4 Groups **************************/
333 }else if (lookup.size() == 4) {
334 //calc the shared otu
336 int numA = 0; int numB = 0; int numC = 0; int numD = 0;
337 int sharedAB = 0; int sharedAC = 0; int sharedBC = 0; int sharedAD = 0; int sharedBD = 0; int sharedCD = 0;
338 int sharedABC = 0; int sharedACD = 0; int sharedBCD = 0; int sharedABD = 0;
340 //A = red, B = green, C = blue, D = yellow
342 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; }
345 for (int i = 0; i < lookup[0]->size(); i++) {
346 //are they only in one
347 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numA++; }
348 if ((lookup[1]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numB++; }
349 if ((lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numC++; }
350 if ((lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0)) { numD++; }
351 //are they shared by 2
352 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAB++; }
353 if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAC++; }
354 if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedBC++; }
355 if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0)) { sharedAD++; }
356 if ((lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBD++; }
357 if ((lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedCD++; }
358 //are they shared by 3
359 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) == 0)) { sharedABC++; }
360 if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0)) { sharedACD++; }
361 if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBCD++; }
362 if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0)) { sharedABD++; }
363 //are they shared by all
364 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0)) { sharedABCD++; }
367 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".venn.sharedsobs.svg";
368 openOutputFile(filenamesvg, outsvg);
371 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
375 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
376 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
377 outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
378 outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
379 outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
380 outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 270 315) \" cx=\"270\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
382 //A = red, B = green, C = blue, D = yellow
384 //place labels within overlaps
385 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)toString(numA).length() / 2)) + "\" y=\"110\">" + toString(numA) + "</text>\n";
386 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[0]->getGroup() + "</text>\n";
387 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedAB).length() / 2)) + "\" y=\"160\">" + toString(sharedAB) + "</text>\n";
388 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)toString(numB).length() / 2)) + "\" y=\"110\">" + toString(numB) + "</text>\n";
389 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[1]->getGroup() + "</text>\n";
390 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(sharedAC).length() / 2)) + "\" y=\"190\">" + toString(sharedAC) + "</text>\n";
391 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(550 - ((int)toString(numC).length() / 2)) + "\" y=\"230\">" + toString(numC) + "</text>\n";
392 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(550 - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"210\">" + lookup[2]->getGroup() + "</text>\n";
393 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(215 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"190\">" + toString(sharedBC) + "</text>\n";
394 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(150 - ((int)toString(numD).length() / 2)) + "\" y=\"230\">" + toString(numD) + "</text>\n";
395 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(150 - ((int)lookup[3]->getGroup().length() / 2)) + "\" y=\"210\">" + lookup[3]->getGroup() + "</text>\n";
396 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(240 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedAD) + "</text>\n";
397 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(470 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedBD) + "</text>\n";
398 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedCD).length() / 2)) + "\" y=\"430\">" + toString(sharedCD) + "</text>\n";
399 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(275 - ((int)toString(sharedABD).length() / 2)) + "\" y=\"240\">" + toString(sharedABD) + "</text>\n";
400 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(400 - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"360\">" + toString(sharedBCD) + "</text>\n";
401 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(305 - ((int)toString(sharedACD).length() / 2)) + "\" y=\"360\">" + toString(sharedACD) + "</text>\n";
402 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(440 - ((int)toString(sharedABC).length() / 2)) + "\" y=\"240\">" + toString(sharedABC) + "</text>\n";
403 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedABCD).length() / 2)) + "\" y=\"320\">" + toString(sharedABCD) + "</text>\n";
404 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";
406 //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";
407 //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";
408 //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";
409 //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";
410 //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";
411 //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";
412 //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";
413 //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";
414 //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";
415 //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";
417 outsvg << "</g>\n</svg>\n";
423 catch(exception& e) {
424 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
428 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";