//**********************************************************************************************************************
vector<vector<float> > SparccCommand::driver(vector<vector<float> >& sharedVector, vector<vector<float> >& origCorrMatrix, int numPerms){
try {
int numOTUs = sharedVector[0].size();
vector<vector<float> > sharedShuffled = sharedVector;
vector<vector<float> > pValues(numOTUs);
for(int i=0;i<numOTUs;i++){ pValues[i].assign(numOTUs, 0); }
for(int i=0;i<numPerms;i++){
if (m->control_pressed) { return pValues; }
sharedShuffled = shuffleSharedVector(sharedVector);
CalcSparcc permutedData(sharedShuffled, maxIterations, numSamplings, normalizeMethod);
vector<vector<float> > permuteCorrMatrix = permutedData.getRho();
for(int j=0;j<numOTUs;j++){
for(int k=0;k<j;k++){
//cout << k << endl;
double randValue = permuteCorrMatrix[j][k];
double observedValue = origCorrMatrix[j][k];
if(observedValue >= 0 && randValue > observedValue) { pValues[j][k]++; }//this method seems to deflate the
else if(observedValue < 0 && randValue < observedValue){ pValues[j][k]++; }//pvalues of small rho values
}
}
float done = ceil(numPermutations * 0.05);
if((i+1) % (int)(done) == 0){ cout << i+1 << endl; }
}
return pValues;
}
catch(exception& e) {
m->errorOut(e, "SparccCommand", "driver");
exit(1);
}
}
//**********************************************************************************************************************
int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& out) {
try {
//format data
vector< vector<spearmanRank> > scores; scores.resize(numaxes);
for (map<string, vector<float> >::iterator it = axes.begin(); it != axes.end(); it++) {
vector<float> temp = it->second;
for (int i = 0; i < temp.size(); i++) {
spearmanRank member(it->first, temp[i]);
scores[i].push_back(member);
}
}
//sort each axis
for (int i = 0; i < numaxes; i++) { sort(scores[i].begin(), scores[i].end(), compareSpearman); }
//convert scores to ranks of xi in each axis
for (int i = 0; i < numaxes; i++) {
vector<spearmanRank*> ties;
int rankTotal = 0;
for (int j = 0; j < scores[i].size(); j++) {
rankTotal += (j+1);
ties.push_back(&(scores[i][j]));
if (j != scores[i].size()-1) { // you are not the last so you can look ahead
if (scores[i][j].score != scores[i][j+1].score) { // you are done with ties, rank them and continue
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
(*ties[k]).score = thisrank;
}
ties.clear();
rankTotal = 0;
}
}else { // you are the last one
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
(*ties[k]).score = thisrank;
}
}
}
}
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
if (metadatafile == "") { out << i+1; }
else { out << metadataLabels[i]; }
//find the ranks of this otu - Y
vector<spearmanRank> otuScores;
for (int j = 0; j < lookupFloat.size(); j++) {
spearmanRank member(lookupFloat[j]->getGroup(), lookupFloat[j]->getAbundance(i));
otuScores.push_back(member);
}
sort(otuScores.begin(), otuScores.end(), compareSpearman);
map<string, float> rankOtus;
vector<spearmanRank> ties;
int rankTotal = 0;
for (int j = 0; j < otuScores.size(); j++) {
rankTotal += (j+1);
ties.push_back(otuScores[j]);
if (j != otuScores.size()-1) { // you are not the last so you can look ahead
if (otuScores[j].score != otuScores[j+1].score) { // you are done with ties, rank them and continue
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankOtus[ties[k].name] = thisrank;
}
ties.clear();
rankTotal = 0;
}
}else { // you are the last one
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankOtus[ties[k].name] = thisrank;
}
}
}
vector<double> pValues(numaxes);
//calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
int numCoor = 0;
int numDisCoor = 0;
vector<spearmanRank> otus;
vector<spearmanRank> otusTemp;
for (int l = 0; l < scores[j].size(); l++) {
spearmanRank member(scores[j][l].name, rankOtus[scores[j][l].name]);
otus.push_back(member);
}
int count = 0;
for (int l = 0; l < scores[j].size(); l++) {
int numWithHigherRank = 0;
int numWithLowerRank = 0;
float thisrank = otus[l].score;
for (int u = l+1; u < scores[j].size(); u++) {
if (otus[u].score > thisrank) { numWithHigherRank++; }
else if (otus[u].score < thisrank) { numWithLowerRank++; }
count++;
}
numCoor += numWithHigherRank;
numDisCoor += numWithLowerRank;
}
double p = (numCoor - numDisCoor) / (float) count;
if (isnan(p) || isinf(p)) { p = 0.0; }
out << '\t' << p;
pValues[j] = p;
//calc signif - zA - http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient#Significance_tests
double numer = 3.0 * (numCoor - numDisCoor);
int n = scores[j].size();
double denom = n * (n-1) * (2*n + 5) / (double) 2.0;
denom = sqrt(denom);
double sig = numer / denom;
if (isnan(sig) || isinf(sig)) { sig = 0.0; }
out << '\t' << sig;
}
double sum = 0;
for(int k=0;k<numaxes;k++){
sum += pValues[k] * pValues[k];
}
out << '\t' << sqrt(sum) << endl;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "CorrAxesCommand", "calcKendall");
exit(1);
}
}
//**********************************************************************************************************************
int CorrAxesCommand::calcSpearman(map<string, vector<float> >& axes, ofstream& out) {
try {
//format data
vector< map<float, int> > tableX; tableX.resize(numaxes);
map<float, int>::iterator itTable;
vector< vector<spearmanRank> > scores; scores.resize(numaxes);
for (map<string, vector<float> >::iterator it = axes.begin(); it != axes.end(); it++) {
vector<float> temp = it->second;
for (int i = 0; i < temp.size(); i++) {
spearmanRank member(it->first, temp[i]);
scores[i].push_back(member);
//count number of repeats
itTable = tableX[i].find(temp[i]);
if (itTable == tableX[i].end()) {
tableX[i][temp[i]] = 1;
}else {
tableX[i][temp[i]]++;
}
}
}
//calc LX
//for each axis
vector<double> Lx; Lx.resize(numaxes, 0.0);
for (int i = 0; i < numaxes; i++) {
for (itTable = tableX[i].begin(); itTable != tableX[i].end(); itTable++) {
double tx = (double) itTable->second;
Lx[i] += ((pow(tx, 3.0) - tx) / 12.0);
}
}
//sort each axis
for (int i = 0; i < numaxes; i++) { sort(scores[i].begin(), scores[i].end(), compareSpearman); }
//find ranks of xi in each axis
map<string, vector<float> > rankAxes;
for (int i = 0; i < numaxes; i++) {
vector<spearmanRank> ties;
int rankTotal = 0;
for (int j = 0; j < scores[i].size(); j++) {
rankTotal += (j+1);
ties.push_back(scores[i][j]);
if (j != (scores[i].size()-1)) { // you are not the last so you can look ahead
if (scores[i][j].score != scores[i][j+1].score) { // you are done with ties, rank them and continue
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankAxes[ties[k].name].push_back(thisrank);
}
ties.clear();
rankTotal = 0;
}
}else { // you are the last one
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankAxes[ties[k].name].push_back(thisrank);
}
}
}
}
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
if (metadatafile == "") { out << i+1; }
else { out << metadataLabels[i]; }
//find the ranks of this otu - Y
vector<spearmanRank> otuScores;
map<float, int> tableY;
for (int j = 0; j < lookupFloat.size(); j++) {
spearmanRank member(lookupFloat[j]->getGroup(), lookupFloat[j]->getAbundance(i));
otuScores.push_back(member);
itTable = tableY.find(member.score);
if (itTable == tableY.end()) {
tableY[member.score] = 1;
}else {
tableY[member.score]++;
}
}
//calc Ly
double Ly = 0.0;
for (itTable = tableY.begin(); itTable != tableY.end(); itTable++) {
double ty = (double) itTable->second;
Ly += ((pow(ty, 3.0) - ty) / 12.0);
}
sort(otuScores.begin(), otuScores.end(), compareSpearman);
map<string, float> rankOtus;
vector<spearmanRank> ties;
int rankTotal = 0;
for (int j = 0; j < otuScores.size(); j++) {
rankTotal += (j+1);
ties.push_back(otuScores[j]);
if (j != (otuScores.size()-1)) { // you are not the last so you can look ahead
if (otuScores[j].score != otuScores[j+1].score) { // you are done with ties, rank them and continue
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankOtus[ties[k].name] = thisrank;
}
ties.clear();
rankTotal = 0;
}
}else { // you are the last one
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankOtus[ties[k].name] = thisrank;
}
}
}
vector<double> pValues(numaxes);
//calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
double di = 0.0;
for (int k = 0; k < lookupFloat.size(); k++) {
float xi = rankAxes[lookupFloat[k]->getGroup()][j];
float yi = rankOtus[lookupFloat[k]->getGroup()];
di += ((xi - yi) * (xi - yi));
}
double p = 0.0;
double n = (double) lookupFloat.size();
double SX2 = ((pow(n, 3.0) - n) / 12.0) - Lx[j];
double SY2 = ((pow(n, 3.0) - n) / 12.0) - Ly;
p = (SX2 + SY2 - di) / (2.0 * sqrt((SX2*SY2)));
if (isnan(p) || isinf(p)) { p = 0.0; }
out << '\t' << p;
pValues[j] = p;
//signifigance calc - http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
double temp = (lookupFloat.size()-2) / (double) (1- (p*p));
temp = sqrt(temp);
double sig = p*temp;
if (isnan(sig) || isinf(sig)) { sig = 0.0; }
out << '\t' << sig;
}
double sum = 0;
for(int k=0;k<numaxes;k++){
sum += pValues[k] * pValues[k];
}
out << '\t' << sqrt(sum) << endl;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "CorrAxesCommand", "calcSpearman");
exit(1);
}
}