*/
#include "pcoacommand.h"
+#include "readphylipvector.h"
//**********************************************************************************************************************
vector<string> PCOACommand::getValidParameters(){
//**********************************************************************************************************************
PCOACommand::PCOACommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["pcoa"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
- outputTypes["corr"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "PCOACommand", "PCOACommand");
PCOACommand::PCOACommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
vector<string> tempOutNames;
outputTypes["pcoa"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
- outputTypes["corr"] = tempOutNames;
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
int PCOACommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::showpoint);
fbase = outputDir + m->getRootName(m->getSimpleName(filename));
- read(filename, names, D);
+ ReadPhylipVector readFile(filename);
+ names = readFile.read(D);
if (m->control_pressed) { return 0; }
for (int i = 1; i < 4; i++) {
- vector< vector<double> > EuclidDists = calculateEuclidianDistance(G, i); //G is the pcoa file
+ vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- double corr = calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
+ double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
- m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
+ m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
}
}
}
/*********************************************************************************************************************************/
-vector< vector<double> > PCOACommand::calculateEuclidianDistance(vector< vector<double> >& axes, int dimensions){
- try {
- //make square matrix
- vector< vector<double> > dists; dists.resize(axes.size());
- for (int i = 0; i < dists.size(); i++) { dists[i].resize(axes.size(), 0.0); }
-
- if (dimensions == 1) { //one dimension calc = abs(x-y)
-
- for (int i = 0; i < dists.size(); i++) {
-
- if (m->control_pressed) { return dists; }
-
- for (int j = 0; j < i; j++) {
- dists[i][j] = abs(axes[i][0] - axes[j][0]);
- dists[j][i] = dists[i][j];
- }
- }
-
- }else if (dimensions == 2) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2)
-
- for (int i = 0; i < dists.size(); i++) {
-
- if (m->control_pressed) { return dists; }
-
- for (int j = 0; j < i; j++) {
- double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
- double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
-
- dists[i][j] = sqrt((firstDim + secondDim));
- dists[j][i] = dists[i][j];
- }
- }
-
- }else if (dimensions == 3) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2 + (x3 - y3)^2)
-
- for (int i = 0; i < dists.size(); i++) {
-
- if (m->control_pressed) { return dists; }
-
- for (int j = 0; j < i; j++) {
- double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
- double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
- double thirdDim = ((axes[i][2] - axes[j][2]) * (axes[i][2] - axes[j][2]));
-
- dists[i][j] = sqrt((firstDim + secondDim + thirdDim));
- dists[j][i] = dists[i][j];
- }
- }
-
- }else { m->mothurOut("[ERROR]: too many dimensions, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
-
- return dists;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "calculateEuclidianDistance");
- exit(1);
- }
-}
-/*********************************************************************************************************************************/
-double PCOACommand::calcPearson(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
- try {
-
- //find average for - X
- vector<float> averageEuclid; averageEuclid.resize(euclidDists.size(), 0.0);
- for (int i = 0; i < euclidDists.size(); i++) {
- for (int j = 0; j < euclidDists[i].size(); j++) {
- averageEuclid[i] += euclidDists[i][j];
- }
- }
- for (int i = 0; i < averageEuclid.size(); i++) { averageEuclid[i] = averageEuclid[i] / (float) euclidDists.size(); }
-
- //find average for - Y
- vector<float> averageUser; averageUser.resize(userDists.size(), 0.0);
- for (int i = 0; i < userDists.size(); i++) {
- for (int j = 0; j < userDists[i].size(); j++) {
- averageUser[i] += userDists[i][j];
- }
- }
- for (int i = 0; i < averageUser.size(); i++) { averageUser[i] = averageUser[i] / (float) userDists.size(); }
-
- double numerator = 0.0;
- double denomTerm1 = 0.0;
- double denomTerm2 = 0.0;
-
- for (int i = 0; i < euclidDists.size(); i++) {
-
- for (int k = 0; k < i; k++) {
-
- float Yi = userDists[i][k];
- float Xi = euclidDists[i][k];
-
- numerator += ((Xi - averageEuclid[k]) * (Yi - averageUser[k]));
- denomTerm1 += ((Xi - averageEuclid[k]) * (Xi - averageEuclid[k]));
- denomTerm2 += ((Yi - averageUser[k]) * (Yi - averageUser[k]));
- }
- }
-
- double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
- double r = numerator / denom;
-
- return r;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "calculateEuclidianDistance");
- exit(1);
- }
-}
-/*********************************************************************************************************************************/
void PCOACommand::get_comment(istream& f, char begin, char end){
try {
exit(1);
}
}
-
-/*********************************************************************************************************************************/
-
-int PCOACommand::read_phylip(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
- try {
- // int count1=0;
- // int count2=0;
-
- int rank;
- f >> rank;
-
- name_list.resize(rank);
- d.resize(rank);
- if(square_m == 1){
- for(int i=0;i<rank;i++)
- d[i].resize(rank);
- for(int i=0;i<rank;i++) {
- f >> name_list[i];
- // cout << i << "\t" << name_list[i] << endl;
- for(int j=0;j<rank;j++) {
- if (m->control_pressed) { return 0; }
-
- f >> d[i][j];
- if (d[i][j] == -0.0000)
- d[i][j] = 0.0000;
- }
- }
- }
- else if(square_m == 2){
- for(int i=0;i<rank;i++){
- d[i].resize(rank);
- }
- d[0][0] = 0.0000;
- f >> name_list[0];
- for(int i=1;i<rank;i++){
- f >> name_list[i];
- d[i][i]=0.0000;
- for(int j=0;j<i;j++){
- if (m->control_pressed) { return 0; }
- f >> d[i][j];
- if (d[i][j] == -0.0000)
- d[i][j] = 0.0000;
- d[j][i]=d[i][j];
- }
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "read_phylip");
- exit(1);
- }
-
-}
-
-/*********************************************************************************************************************************/
-
-void PCOACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
- try {
- ifstream f;
- m->openInputFile(fname, f);
-
- //check whether matrix is square
- char d;
- int q = 1;
- int numSeqs;
- string name;
-
- f >> numSeqs >> name;
-
- while((d=f.get()) != EOF){
-
- //is d a number meaning its square
- if(isalnum(d)){
- q = 1;
- break;
- }
-
- //is d a line return meaning its lower triangle
- if(d == '\n'){
- q = 2;
- break;
- }
- }
- f.close();
-
- //reopen to get back to beginning
- m->openInputFile(fname, f);
- read_phylip(f, q, names, D);
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "read");
- exit(1);
- }
-}
-
/*********************************************************************************************************************************/
void PCOACommand::recenter(double offset, vector<vector<double> > D, vector<vector<double> >& G){
}
}
- ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc);
+ ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pcoa");
- outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
+ outputNames.push_back(fnameRoot+"pcoa.axes");
+ outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes");
ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
pcaLoadings.setf(ios::fixed, ios::floatfield);