#include "ace.h"
#include "sobs.h"
#include "chao1.h"
+#include "nseqs.h"
#include "sharedchao1.h"
#include "sharedsobscollectsummary.h"
singleCalc = new Chao1();
}else if (vCalcs[i]->getName() == "sharedace") {
singleCalc = new Ace(10);
+ }else if (vCalcs[i]->getName() == "nseqs") {
+ singleCalc = new NSeqs();
}
vector<double> data = singleCalc->getValues(sabund);
if (m->control_pressed) { outsvg.close(); return outputNames; }
//get estimates for sharedAB
- vector<double> shared = vCalcs[i]->getValues(subset);
+ vector<double> results = vCalcs[i]->getValues(subset);
//in essence you want to run it like a single
if (vCalcs[i]->getName() == "sharedsobs") {
singleCalc = new Sobs();
}else if (vCalcs[i]->getName() == "sharedchao") {
singleCalc = new Chao1();
+ }else if (vCalcs[i]->getName() == "nseqs") {
+ singleCalc = new NSeqs();
}//else if (vCalcs[i]->getName() == "sharedace") {
//singleCalc = new Ace(10);
//}
//get estimates for numA
- vector<double> numA = singleCalc->getValues(sabundA);
+ vector<double> resultsA = singleCalc->getValues(sabundA);
//get estimates for numB
- vector<double> numB = singleCalc->getValues(sabundB);
+ vector<double> resultsB = singleCalc->getValues(sabundB);
+
+ double numA, numB, shared;
+ if (vCalcs[i]->getName() == "nseqs") {
+ shared = results[0] + results[1]; //add both groups sequences
+ numA = resultsA[0] - results[0]; //what's in A - the number of species in A that are in shared otus
+ numB = resultsB[0] - results[1]; //what's in B - the number of species in B that are in shared otus
+ }else{
+ shared = results[0];
+ numA = resultsA[0] - shared;
+ numB = resultsB[0] - shared;
+ }
//image window
outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(width) + " " + toString(height) + " \" >\n";
outsvg << "<g>\n";
-
+
//draw circles
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.36 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.62 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numA[0] - shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numB[0] - shared[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numA) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numB) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.66 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
- if (numA.size() == 3) {
- outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(shared) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.66 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(resultsA[0]);
+ if (resultsA.size() == 3) {
+ outsvg << " the lci is " + toString(resultsA[1]) + " and the hci is " + toString(resultsA[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.69 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
- if (numB.size() == 3) {
- outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.69 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(resultsB[0]);
+ if (resultsB.size() == 3) {
+ outsvg << " the lci is " + toString(resultsB[1]) + " and the hci is " + toString(resultsB[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.72 * height)) + "\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.78 * height)) + "\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0])) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.72 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared / (float)(numA + numB + shared))*100) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.78 * height)) + "\">The total richness for all groups is " + toString((float)(numA + numB + shared)) + "</text>\n";
//close file
outsvg << "</g>\n</svg>\n";
vector<double> sharedCwithAB;
//find possible sharedABC values
- float sharedABC1 = 0.0; float sharedABC2 = 0.0; float sharedABC3 = 0.0; float sharedABC = 0.0;
+ double sharedABC1 = 0.0; double sharedABC2 = 0.0; double sharedABC3 = 0.0; double sharedABC = 0.0;
+ vector<double> = resultsNseqs;
if (vCalcs[i]->getMultiple() == false) {
//merge BC and estimate with shared with A
else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
}else{
vector<double> data = vCalcs[i]->getValues(lookup);
+ resultsNseqs = data;
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);
}
+ double numA, numB, numC, numAB, numAC, numBC, numABC;
+ if (vCalcs[i]->getName() == "nseqs") {
+ numABC = resultsNseqs[0] + resultsNseqs[1] + resultsNseqs[2];
+ numBC = sharedBC[0] + sharedBC[1] - (resultsNseqs[1] + resultsNseqs[2]);
+
+ }else{
+ numABC = sharedABC;
+ numBC = sharedBC[0] - sharedABC;
+ numAB = sharedAB[0] - sharedABC;
+ numAC = sharedAC[0] - sharedABC;
+ numA = numA[0]-sharedAwithBC[0];
+ numB = numB[0]-sharedBwithAC[0];
+ numC = numC[0]-sharedCwithAB[0];
+ }
+
//image window
outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(width) + " " + toString(height) + " \" >\n";
outsvg << "<g>\n";
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups. It will be disregarded. "); m->mothurOutEndLine(); }
+ if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao") && (vCalcs[i]->getName() != "nseqs")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups. It will be disregarded. "); m->mothurOutEndLine(); }
else{
string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
outputNames.push_back(filenamesvg);
singleCalc = new Sobs();
}else if (vCalcs[i]->getName() == "sharedchao") {
singleCalc = new Chao1();
+ }else if (vCalcs[i]->getName() == "nseqs") {
+ singleCalc = new NSeqs();
}
+
//get estimates for numA
data = singleCalc->getValues(sabundA);
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