void CorrAxesCommand::help(){
try {
- m->mothurOut("The corr.axes command reads a shared or relabund file as well as a pcoa file and calculates the correlation coefficient.\n");
+ m->mothurOut("The corr.axes command reads a shared, relabund or metadata file as well as an axes file and calculates the correlation coefficient.\n");
m->mothurOut("The corr.axes command parameters are shared, relabund, axes, metadata, groups, method, numaxes and label. The shared, relabund or metadata and axes parameters are required. If shared is given the relative abundance is calculated.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n");
m->mothurOut("The label parameter allows you to select what distance level you would like used, if none is given the first distance is used.\n");
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
//output headings
- if (metadatafile == "") { out << "OTU\t"; }
- else { out << "Feature\t"; }
+ if (metadatafile == "") { out << "OTU"; }
+ else { out << "Feature"; }
- for (int i = 0; i < numaxes; i++) { out << "axis" << (i+1) << '\t'; }
- out << endl;
+ for (int i = 0; i < numaxes; i++) { out << '\t' << "axis" << (i+1); }
+ out << "\tlength" << endl;
if (method == "pearson") { calcPearson(axes, out); }
else if (method == "spearman") { calcSpearman(axes, out); }
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
- if (metadatafile == "") { out << i+1 << '\t'; }
- else { out << metadataLabels[i] << '\t'; }
-
+ if (metadatafile == "") { out << i+1; }
+ else { out << metadataLabels[i]; }
+
//find the averages this otu - Y
float sumOtu = 0.0;
for (int j = 0; j < lookupFloat.size(); j++) {
}
float Ybar = sumOtu / (float) lookupFloat.size();
+ vector<float> rValues(averageAxes.size());
+
//find r value for each axis
for (int k = 0; k < averageAxes.size(); k++) {
double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
r = numerator / denom;
-
- out << r << '\t';
+ rValues[k] = r;
+ out << '\t' << r;
}
- out << endl;
+ double sum = 0;
+ for(int k=0;k<rValues.size();k++){
+ sum += rValues[k] * rValues[k];
+ }
+ out << '\t' << sqrt(sum) << endl;
}
return 0;
int CorrAxesCommand::calcSpearman(map<string, vector<float> >& axes, ofstream& out) {
try {
+ bool hasTies = false;
+
//format data
vector< vector<spearmanRank> > scores; scores.resize(numaxes);
for (map<string, vector<float> >::iterator it = axes.begin(); it != axes.end(); it++) {
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++) {
if (j != scores.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++) {
- if (metadatafile == "") { out << i+1 << '\t'; }
- else { out << metadataLabels[i] << '\t'; }
+ if (metadatafile == "") { out << i+1; }
+ else { out << metadataLabels[i]; }
//find the ranks of this otu - Y
vector<spearmanRank> otuScores;
map<string, float> rankOtus;
vector<spearmanRank> ties;
+ float averageY = 0.0;
int rankTotal = 0;
for (int j = 0; j < otuScores.size(); j++) {
rankTotal += j;
if (j != scores.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;
+
//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()];
- di += ((xi - yi) * (xi - yi));
+ 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));
+ }
}
- int n = lookupFloat.size();
- double p = 1.0 - ((6 * di) / (float) (n * ((n*n) - 1)));
+ double p = 0.0;
- out << p << '\t';
+ 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)));
+ }
+
+ out << '\t' << p;
}
-
-
+
out << endl;
}
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
- if (metadatafile == "") { out << i+1 << '\t'; }
- else { out << metadataLabels[i] << '\t'; }
+ if (metadatafile == "") { out << i+1; }
+ else { out << metadataLabels[i]; }
//find the ranks of this otu - Y
vector<spearmanRank> otuScores;
}
}
}
+ vector<double> pValues(numaxes);
//calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
double p = ( (4 * P) / (float) (n * (n - 1)) ) - 1.0;
- out << p << '\t';
+ 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;
projects / mothur.git / blobdiff