X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venn.cpp;h=6f44ed3f366fa6eae8a6c72a85d2c1681046e3f5;hb=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186;hp=6da78bb20c895f70b5e17157ac8281bdd16a8d10;hpb=f20505bcd9f07e0b5f967be0e8d414076d9a5678;p=mothur.git diff --git a/venn.cpp b/venn.cpp index 6da78bb..6f44ed3 100644 --- a/venn.cpp +++ b/venn.cpp @@ -11,6 +11,8 @@ #include "ace.h" #include "sobs.h" #include "chao1.h" +#include "sharedchao1.h" +#include "sharedsobscollectsummary.h" //********************************************************************************************************************** @@ -29,13 +31,11 @@ Venn::Venn(){ } } //********************************************************************************************************************** -void Venn::getPic(OrderVector* order, vector vCalcs) { +void Venn::getPic(SAbundVector* sabund, vector vCalcs) { try { - SAbundVector s; - s = order->getSAbundVector(); sabund = &s; - + for(int i=0;iinputFileName + ".venn." + order->getLabel() + vCalcs[i]->getName() + ".svg"; + string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg"; openOutputFile(filenamesvg, outsvg); vector data = vCalcs[i]->getValues(sabund); @@ -45,7 +45,7 @@ void Venn::getPic(OrderVector* order, vector vCalcs) { outsvg << "\n"; outsvg << ""; - outsvg << "Venn Diagram at distance " + order->getLabel() + "\n"; + outsvg << "Venn Diagram at distance " + sabund->getLabel() + "\n"; outsvg << ""; outsvg << "" + toString(data[0]) + "\n"; @@ -68,44 +68,41 @@ void Venn::getPic(OrderVector* order, vector vCalcs) { } } //********************************************************************************************************************** -void Venn::getPic(SharedOrderVector* sharedorder, vector vCalcs) { +void Venn::getPic(vector lookup, vector vCalcs) { try { - //fills vector of sharedsabunds - lookup - getSharedVectors(sharedorder); + vector 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;iinputFileName + ".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 data = vCalcs[i]->getValues(sabund); + vector data = singleCalc->getValues(sabund); //svg image outsvg << "\n"; outsvg << "\n"; outsvg << ""; - outsvg << "Venn Diagram at distance " + sharedorder->getLabel() + "\n"; + outsvg << "Venn Diagram at distance " + lookup[0]->getLabel() + "\n"; outsvg << ""; + outsvg << "getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "\n"; outsvg << "" + toString(data[0]) + "\n"; if (data.size() == 3) { @@ -115,8 +112,9 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector vCalcs) { outsvg << "\n\n"; outsvg.close(); + delete singleCalc; + } - /******************* 2 Groups **************************/ }else if (lookup.size() == 2) { @@ -124,35 +122,34 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector vCalcs) { //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;iinputFileName + ".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 shared = vCalcs[i]->getValues(lookup[0], lookup[1]); + vector 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 numA = vCalcs[i]->getValues(sabundA); - + vector numA = singleCalc->getValues(sabundA); + //get estimates for numB - vector numB = vCalcs[i]->getValues(sabundB); - + vector numB = singleCalc->getValues(sabundB); //image window outsvg << "\n"; @@ -160,23 +157,33 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector vCalcs) { //draw circles outsvg << ""; - outsvg << "Venn Diagram at distance " + sharedorder->getLabel() + "\n"; + outsvg << "Venn Diagram at distance " + lookup[0]->getLabel() + "\n"; outsvg << ""; outsvg << ""; outsvg << "" + toString(numA[0] - shared[0]) + "\n"; outsvg << "" + toString(numB[0] - shared[0]) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"175\">" + lookup[0]->getGroup() + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"175\">" + lookup[1]->getGroup() + "\n"; outsvg << "" + toString(shared[0]) + "\n"; - outsvg << "The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]) + "\n"; - outsvg << "The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]) + "\n"; + outsvg << "The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]); + if (numA.size() == 3) { + outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "\n"; + }else { outsvg << "\n"; } + + outsvg << "The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]); + if (numB.size() == 3) { + outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "\n"; + }else { outsvg << "\n"; } + outsvg << "The number of sepecies shared between groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(shared[0]) + "\n"; outsvg << "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]))) + "\n"; + outsvg << "The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0])) + "\n"; //close file outsvg << "\n\n"; outsvg.close(); - + delete singleCalc; } - /******************* 3 Groups **************************/ }else if (lookup.size() == 3) { @@ -187,99 +194,129 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector vCalcs) { 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;iinputFileName + ".venn." + sharedorder->getLabel() + vCalcs[i]->getName() + "." + groupComb + ".svg"; - openOutputFile(filenamesvg, outsvg); - - //get estimates for sharedAB, sharedAC and sharedBC - vector sharedAB = vCalcs[i]->getValues(lookup[0], lookup[1]); - vector sharedAC = vCalcs[i]->getValues(lookup[0], lookup[2]); - vector 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 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 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 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 numA = vCalcs[i]->getValues(sabundA); + vector numA = singleCalc->getValues(sabundA); //get estimates for numB - vector numB = vCalcs[i]->getValues(sabundB); + vector numB = singleCalc->getValues(sabundB); //get estimates for numC - vector numC = vCalcs[i]->getValues(sabundC); - + vector 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 sharedAB = vCalcs[i]->getValues(subset); + + subset.clear(); + subset.push_back(lookup[0]); subset.push_back(lookup[2]); + vector sharedAC = vCalcs[i]->getValues(subset); + + subset.clear(); + subset.push_back(lookup[1]); subset.push_back(lookup[2]); + vector sharedBC = vCalcs[i]->getValues(subset); + + vector sharedAwithBC; + vector sharedBwithAC; + vector 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]->getName() != "sharedchao") { + //merge BC and estimate with shared with A + SharedRAbundVector* merge = new SharedRAbundVector(); + for (int j = 0; j < lookup[1]->size(); j++) { + merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, ""); + } + + 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, ""); + } + + 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]; + 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 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 << "\n"; outsvg << "\n"; //draw circles outsvg << ""; - outsvg << "Venn Diagram at distance " + sharedorder->getLabel() + "\n"; + outsvg << "Venn Diagram at distance " + lookup[0]->getLabel() + "\n"; outsvg << ""; outsvg << ""; outsvg << ""; - +//cout << "numA = " << numA[0] << " numB = " << numB[0] << " numC = " << numC[0] << endl; +//cout << "sharedAB = " << sharedAB[0] << " sharedAC = " << sharedAC[0] << " sharedBC = " << sharedBC[0] << endl; +//cout << "sharedAwithBC = " << sharedAwithBC[0] << " sharedBwithAC = " << sharedBwithAC[0] << " sharedCwithAB = " << sharedCwithAB[0] << endl; //place labels within overlaps - outsvg << "" + toString(numA[0]-sharedAwithBC[0]) + "\n"; + outsvg << "" + toString(numA[0]-sharedAwithBC[0]) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "\n"; outsvg << "" + toString(sharedAB[0] - sharedABC) + "\n"; - outsvg << "" + toString(numB[0]-sharedBwithAC[0]) + "\n"; + outsvg << "" + toString(numB[0]-sharedBwithAC[0]) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"150\">" + lookup[1]->getGroup() + "\n"; outsvg << "" + toString(sharedAC[0] - sharedABC) + "\n"; - outsvg << "" + toString(numC[0]-sharedCwithAB[0]) + "\n"; + outsvg << "" + toString(numC[0]-sharedCwithAB[0]) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"410\">" + lookup[2]->getGroup() + "\n"; outsvg << "" + toString(sharedBC[0] - sharedABC) + "\n"; outsvg << "" + toString(sharedABC) + "\n"; @@ -289,106 +326,194 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector vCalcs) { outsvg << "The number of sepecies shared between groups " + globaldata->Groups[0] + " and combined groups " + globaldata->Groups[1] + globaldata->Groups[2] + " is " + toString(sharedAwithBC[0]) + "\n"; outsvg << "The number of sepecies shared between groups " + globaldata->Groups[1] + " and combined groups " + globaldata->Groups[0] + globaldata->Groups[2] + " is " + toString(sharedBwithAC[0]) + "\n"; outsvg << "The number of sepecies shared between groups " + globaldata->Groups[2] + " and combined groups " + globaldata->Groups[0] + globaldata->Groups[1] + " is " + toString(sharedCwithAB[0]) + "\n"; - outsvg << "The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]) + "\n"; - outsvg << "The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]) + "\n"; - outsvg << "The number of species in group " + globaldata->Groups[2] + " is " + toString(numC[0]) + "\n"; - outsvg << "The total number of species in all groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "\n"; + outsvg << "The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]); + if (numA.size() == 3) { + outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "\n"; + }else { outsvg << "\n"; } + + outsvg << "The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]); + if (numB.size() == 3) { + outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "\n"; + }else { outsvg << "\n"; } + + outsvg << "The number of species in group " + globaldata->Groups[2] + " is " + toString(numC[0]); + if (numC.size() == 3) { + outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "\n"; + }else { outsvg << "\n"; } + + outsvg << "The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "\n"; //close file outsvg << "\n\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 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;iinputFileName + ".venn." + sharedorder->getLabel() + "." + groupComb + ".svg"; - openOutputFile(filenamesvg, outsvg); + if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { cout << vCalcs[i]->getName() << " is not a valid calculator with four groups. It will be disregarded. " << endl; } + else{ + 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") { + 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]; + + + //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]; + - //image window - outsvg << "\n"; - outsvg << "\n"; + //image window + outsvg << "\n"; + outsvg << "\n"; - //draw circles - outsvg << ""; - outsvg << "Venn Diagram at distance " + sharedorder->getLabel() + "\n"; - outsvg << "\n "; - outsvg << "\n "; - outsvg << "\n "; - outsvg << "\n "; + //draw circles + outsvg << ""; + outsvg << "Venn Diagram at distance " + lookup[0]->getLabel() + "\n"; + outsvg << "\n "; + outsvg << "\n "; + outsvg << "\n "; + outsvg << "\n "; - //A = red, B = green, C = blue, D = yellow + //A = red, B = green, C = blue, D = yellow - //place labels within overlaps - outsvg << "" + toString(numA) + "\n"; - outsvg << "" + toString(sharedAB) + "\n"; - outsvg << "" + toString(numB) + "\n"; - outsvg << "" + toString(sharedAC) + "\n"; - outsvg << "" + toString(numC) + "\n"; - outsvg << "" + toString(sharedBC) + "\n"; - outsvg << "" + toString(numD) + "\n"; - outsvg << "" + toString(sharedAD) + "\n"; - outsvg << "" + toString(sharedBD) + "\n"; - outsvg << "" + toString(sharedCD) + "\n"; - outsvg << "" + toString(sharedABD) + "\n"; - outsvg << "" + toString(sharedBCD) + "\n"; - outsvg << "" + toString(sharedACD) + "\n"; - outsvg << "" + toString(sharedABC) + "\n"; - outsvg << "" + toString(sharedABCD) + "\n"; + //place labels within overlaps + outsvg << "" + toString(numA) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"90\">" + lookup[0]->getGroup() + "\n"; + outsvg << "" + toString(sharedAB) + "\n"; + outsvg << "" + toString(numB) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"90\">" + lookup[1]->getGroup() + "\n"; + outsvg << "" + toString(sharedAC) + "\n"; + outsvg << "" + toString(numC) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"210\">" + lookup[2]->getGroup() + "\n"; + outsvg << "" + toString(sharedBC) + "\n"; + outsvg << "" + toString(numD) + "\n"; + outsvg << "getGroup().length() / 2)) + "\" y=\"210\">" + lookup[3]->getGroup() + "\n"; + outsvg << "" + toString(sharedAD) + "\n"; + outsvg << "" + toString(sharedBD) + "\n"; + outsvg << "" + toString(sharedCD) + "\n"; + outsvg << "" + toString(sharedABD) + "\n"; + outsvg << "" + toString(sharedBCD) + "\n"; + outsvg << "" + toString(sharedACD) + "\n"; + outsvg << "" + toString(sharedABC) + "\n"; + outsvg << "" + toString(sharedABCD) + "\n"; + outsvg << "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)) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; - //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; + //outsvg << "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))) + "\n"; - outsvg << "\n\n"; - outsvg.close(); - + outsvg << "\n\n"; + outsvg.close(); + delete singleCalc; + } + } } - - - - } catch(exception& e) { @@ -400,54 +525,5 @@ void Venn::getPic(SharedOrderVector* sharedorder, vector vCalcs) { exit(1); } } -//********************************************************************************************************************** -void Venn::getSharedVectors(SharedOrderVector* order){ - try { - - //delete lookup - for (int j = 0; j < lookup.size(); j++) { - delete lookup[j]; - } - 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;iget(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; - } - } - } - - } - 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"; - 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); - } - -}