#include "sharedutilities.h"
//********************************************************************************************************************
-//sorts highes to lowest
+//sorts highest to lowest
inline bool compareSpearman(spearmanRank left, spearmanRank right){
return (left.score > right.score);
}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
+ return (left.score < right.score);
+}
//**********************************************************************************************************************
vector<string> CorrAxesCommand::getValidParameters(){
try {
int CorrAxesCommand::calcSpearman(map<string, vector<float> >& axes, ofstream& out) {
try {
- bool hasTies = false;
+ /*axes.clear();
+ axes["1a"].push_back(1);
+ axes["1b"].push_back(1);
+ axes["1c"].push_back(1);
+ axes["2a"].push_back(2);
+ axes["2b"].push_back(2);
+ axes["2c"].push_back(2);
+ axes["3a"].push_back(3);
+ axes["3b"].push_back(3);
+ axes["3c"].push_back(3);
+ axes["4a"].push_back(4);
+ axes["4b"].push_back(4);
+ axes["4c"].push_back(4);
+ axes["5a"].push_back(5);
+ axes["5b"].push_back(5);
+ axes["5c"].push_back(5);*/
//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);
}
}
for (int i = 0; i < numaxes; i++) { sort(scores[i].begin(), scores[i].end(), compareSpearman); }
//find ranks of xi in each axis
- vector<float> averageX; averageX.resize(numaxes, 0.0);
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;
+ rankTotal += (j+1);
ties.push_back(scores[i][j]);
- if (j != scores.size()-1) { // you are not the last so you can look ahead
+ 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
- if (ties.size() > 1) { hasTies = true; }
- averageX[i] += rankTotal;
+
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankAxes[ties[k].name].push_back(thisrank);
rankTotal = 0;
}
}else { // you are the last one
- if (ties.size() > 1) { hasTies = true; }
- averageX[i] += rankTotal;
+
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankAxes[ties[k].name].push_back(thisrank);
+
}
}
}
-
- averageX[i] /= (float) scores[i].size();
}
-
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); 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;
- float averageY = 0.0;
int rankTotal = 0;
for (int j = 0; j < otuScores.size(); j++) {
- rankTotal += j;
+ rankTotal += (j+1);
ties.push_back(otuScores[j]);
- if (j != scores.size()-1) { // you are not the last so you can look ahead
+ 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
- if (ties.size() > 1) { hasTies = true; }
- averageY += rankTotal;
+
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankOtus[ties[k].name] = thisrank;
rankTotal = 0;
}
}else { // you are the last one
- if (ties.size() > 1) { hasTies = true; }
- averageY += rankTotal;
+
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
rankOtus[ties[k].name] = thisrank;
}
}
}
-
-
- averageY /= (float) otuScores.size();
- //hasTies = false;
+ vector<double> pValues(numaxes);
//calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
double di = 0.0;
- double denom1 = 0.0;
- double denom2 = 0.0;
for (int k = 0; k < lookupFloat.size(); k++) {
float xi = rankAxes[lookupFloat[k]->getGroup()][j];
float yi = rankOtus[lookupFloat[k]->getGroup()];
- if (hasTies) {
- di += ((xi - averageX[j]) * (yi - averageY));
- denom1 += ((xi - averageX[j]) * (xi - averageX[j]));
- denom2 += ((yi - averageY) * (yi - averageY));
- }else {
- di += ((xi - yi) * (xi - yi));
- }
+ di += ((xi - yi) * (xi - yi));
}
double p = 0.0;
- if (hasTies) {
- double denom = sqrt((denom1 * denom2));
- p = di / denom;
- }else {
- int n = lookupFloat.size();
- p = 1.0 - ((6 * di) / (float) (n * ((n*n) - 1)));
- }
+ 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)));
out << '\t' << p;
+
+ pValues[j] = p;
}
- out << endl;
+ double sum = 0;
+ for(int k=0;k<numaxes;k++){
+ sum += pValues[k] * pValues[k];
+ }
+ out << '\t' << sqrt(sum) << endl;
}
return 0;
int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& out) {
try {
+ numaxes = 1;
+ axes.clear();
+ axes["1a"].push_back(1);
+ axes["1b"].push_back(1);
+ axes["1c"].push_back(1);
+ axes["2a"].push_back(2);
+ axes["2b"].push_back(2);
+ axes["2c"].push_back(2);
+ axes["3a"].push_back(3);
+ axes["3b"].push_back(3);
+ axes["3c"].push_back(3);
+ axes["4a"].push_back(4);
+ axes["4b"].push_back(4);
+ axes["4c"].push_back(4);
+ axes["5a"].push_back(5);
+ axes["5b"].push_back(5);
+ axes["5c"].push_back(5);
+
+
//format data
vector< vector<spearmanRank> > scores; scores.resize(numaxes);
for (map<string, vector<float> >::iterator it = axes.begin(); it != axes.end(); it++) {
vector<spearmanRank*> ties;
int rankTotal = 0;
for (int j = 0; j < scores[i].size(); j++) {
- rankTotal += j;
+ rankTotal += (j+1);
ties.push_back(&(scores[i][j]));
- if (j != scores.size()-1) { // you are not the last so you can look ahead
+ 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();
}
}
}
+ cout << "axes ranks = ";
+ for(int i = 0; i < scores[0].size(); i++) { cout << scores[0][i].score << '\t'; }
+ cout << endl;
+ lookupFloat.clear();
+ lookupFloat.resize(15);
+ for (int i = 0; i < lookupFloat.size(); i++) {
+ lookupFloat[i] = new SharedRAbundFloatVector();
+ }
+ lookupFloat[0]->push_back(0.2288227, "1a"); lookupFloat[0]->setGroup("1a");
+ lookupFloat[1]->push_back(0.7394062, "1b"); lookupFloat[1]->setGroup("1b");
+ lookupFloat[2]->push_back(0.4521187, "1c"); lookupFloat[2]->setGroup("1c");
+ lookupFloat[3]->push_back(0.1598630, "2a"); lookupFloat[3]->setGroup("2a");
+ lookupFloat[4]->push_back(0.09588156, "2b"); lookupFloat[4]->setGroup("2b");
+
+ lookupFloat[5]->push_back(0.933174, "2c"); lookupFloat[5]->setGroup("2c");
+ lookupFloat[6]->push_back(0.3958304, "3a"); lookupFloat[6]->setGroup("3a");;
+ lookupFloat[7]->push_back(0.2364419, "3b"); lookupFloat[7]->setGroup("3b");
+ lookupFloat[8]->push_back(0.1697712, "3c"); lookupFloat[8]->setGroup("3c");
+ lookupFloat[9]->push_back(0.4077173, "4a"); lookupFloat[9]->setGroup("4a");
+
+ lookupFloat[10]->push_back(0.6116547, "4b"); lookupFloat[10]->setGroup("4b");
+ lookupFloat[11]->push_back(0.9374322, "4c"); lookupFloat[11]->setGroup("4c");
+ lookupFloat[12]->push_back(0.852184, "5a"); lookupFloat[12]->setGroup("5a");
+ lookupFloat[13]->push_back(0.845094, "5b"); lookupFloat[13]->setGroup("5b");
+ lookupFloat[14]->push_back(0.5795778, "5c"); lookupFloat[14]->setGroup("5c");
+
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
vector<spearmanRank> ties;
int rankTotal = 0;
for (int j = 0; j < otuScores.size(); j++) {
- rankTotal += j;
+ rankTotal += (j+1);
ties.push_back(otuScores[j]);
- if (j != scores.size()-1) { // you are not the last so you can look ahead
+ 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();
}
}
}
+
+
vector<double> pValues(numaxes);
//calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
- int P = 0;
- //assemble otus ranks in same order as axis ranks
+ int numCoor = 0;
+ int numDisCoor = 0;
+
+ //assemble otus ranks in same order as axis ranks, if ties, put in the best order possible
+ //NOTE: after this ordering the scores[j] indexes may not match the otus indexes within tied sections
+ //since we do not use the axes ranks except to order the otu ranks, I did not take the time to reorder the axes ranks
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);
+ otusTemp.push_back(member);
+
+ if (l != (scores[j].size()-1)) { // you are not the last so you can look ahead
+ if (scores[j][l].score != scores[j][l+1].score) { // you are done with ties, order them and continue
+ //order otus within tied section in the best way possible to make coor pairs
+ sort(otusTemp.begin(), otusTemp.end(), compareSpearmanReverse);
+
+ //save order in otus
+ for (int h = 0; h < otusTemp.size(); h++) { ; otus.push_back(otusTemp[h]); }
+
+ otusTemp.clear();
+ }
+ }else { // you are the last one
+ //order otus within tied section in the best way possible to make coor pairs
+ sort(otusTemp.begin(), otusTemp.end(), compareSpearmanReverse);
+
+ //save order in otus
+ for (int h = 0; h < otusTemp.size(); h++) { otus.push_back(otusTemp[h]); }
+ }
}
+ cout << "otu ranks = ";
+ for (int h = 0; h < otus.size(); h++ ) { cout << otus[h].score << '\t'; }
+ cout << endl;
+
+ 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; u < scores[j].size(); u++) {
if (otus[u].score > thisrank) { numWithHigherRank++; }
+ else if (otus[u].score < thisrank) { numWithLowerRank++; }
+ count++;
}
- P += numWithHigherRank;
+ numCoor += numWithHigherRank;
+ numDisCoor += numWithLowerRank;
}
- int n = lookupFloat.size();
-
- double p = ( (4 * P) / (float) (n * (n - 1)) ) - 1.0;
+ //sample size
+ //int n = lookupFloat.size();
+ //comparing to yourself
+ count -= lookupFloat.size();
+ //double p = ( (4 * P) / (float) ((n * (n - 1)) - numTies) ) - 1.0;
+ double p = (numCoor - numDisCoor) / (float) count;
+ cout << "numCoor = " << numCoor << " numDisCoor = " << numDisCoor << " p = " << p << " count = " << count << endl;
out << '\t' << p;
pValues[j] = p;
projects / mothur.git / blobdiff