*
*/
-#include "pcacommand.h"
+#include "pcoacommand.h"
+#include "readphylipvector.h"
+
//**********************************************************************************************************************
-vector<string> PCACommand::getValidParameters(){
+vector<string> PCOACommand::setParameters(){
try {
- string Array[] = {"phylip", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","pcoa-loadings",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "getValidParameters");
+ m->errorOut(e, "PCOACommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-PCACommand::PCACommand(){
+string PCOACommand::getHelpString(){
try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["pcoa"] = tempOutNames;
- outputTypes["loadings"] = tempOutNames;
+ string helpString = "";
+ helpString += "The pcoa command parameters are phylip and metric";
+ helpString += "The phylip parameter allows you to enter your distance file.";
+ helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True";
+ helpString += "Example pcoa(phylip=yourDistanceFile).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "PCACommand");
+ m->errorOut(e, "PCOACommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> PCACommand::getRequiredParameters(){
- try {
- string Array[] = {"phylip"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "getRequiredParameters");
- exit(1);
- }
+string PCOACommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "pcoa") { pattern = "[filename],pcoa.axes"; }
+ else if (type == "loadings") { pattern = "[filename],pcoa.loadings"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCOACommand", "getOutputPattern");
+ exit(1);
+ }
}
+
+
//**********************************************************************************************************************
-vector<string> PCACommand::getRequiredFiles(){
+PCOACommand::PCOACommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["pcoa"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "getRequiredFiles");
+ m->errorOut(e, "PCOACommand", "PCOACommand");
exit(1);
}
}
//**********************************************************************************************************************
-PCACommand::PCACommand(string option) {
+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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"phylip","outputdir", "inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser. getParameters();
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; abort = true; }
- else { filename = phylipfile; }
+ else if (phylipfile == "not found") {
+ //if there is a current phylip file, use it
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setPhylipFile(phylipfile); }
+
+ filename = phylipfile;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
}
- //error checking on files
- if (phylipfile == "") { m->mothurOut("You must provide a distance file before running the pca command."); m->mothurOutEndLine(); abort = true; }
+ string temp = validParameter.validFile(parameters, "metric", false); if (temp == "not found"){ temp = "T"; }
+ metric = m->isTrue(temp);
}
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "PCACommand");
+ m->errorOut(e, "PCOACommand", "PCOACommand");
exit(1);
}
}
//**********************************************************************************************************************
-void PCACommand::help(){
+int PCOACommand::execute(){
try {
- m->mothurOut("The pca command..."); m->mothurOutEndLine();
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-PCACommand::~PCACommand(){}
-//**********************************************************************************************************************
-int PCACommand::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; }
vector<double> d;
vector<double> e;
vector<vector<double> > G = D;
- vector<vector<double> > copy_G;
- //int rank = D.size();
-
+ //vector<vector<double> > copy_G;
+
m->mothurOut("\nProcessing...\n");
for(int count=0;count<2;count++){
- recenter(offset, D, G); if (m->control_pressed) { return 0; }
- tred2(G, d, e); if (m->control_pressed) { return 0; }
- qtli(d, e, G); if (m->control_pressed) { return 0; }
+ linearCalc.recenter(offset, D, G); if (m->control_pressed) { return 0; }
+ linearCalc.tred2(G, d, e); if (m->control_pressed) { return 0; }
+ linearCalc.qtli(d, e, G); if (m->control_pressed) { return 0; }
offset = d[d.size()-1];
if(offset > 0.0) break;
}
output(fbase, names, G, d);
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ if (metric) {
+
+ for (int i = 1; i < 4; i++) {
+
+ 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++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
+
+ m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "execute");
+ m->errorOut(e, "PCOACommand", "execute");
exit(1);
}
}
/*********************************************************************************************************************************/
-inline double SIGN(const double a, const double b)
-{
- return b>=0 ? (a>=0 ? a:-a) : (a>=0 ? -a:a);
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::get_comment(istream& f, char begin, char end){
+void PCOACommand::get_comment(istream& f, char begin, char end){
try {
char d=f.get();
while(d != end){ d = f.get(); }
d = f.peek();
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "get_comment");
+ m->errorOut(e, "PCOACommand", "get_comment");
exit(1);
}
}
-
-/*********************************************************************************************************************************/
-
-int PCACommand::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, "PCACommand", "read_phylip");
- exit(1);
- }
-
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::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, "PCACommand", "read");
- exit(1);
- }
-}
-
-/*********************************************************************************************************************************/
-
-double PCACommand::pythag(double a, double b) { return(pow(a*a+b*b,0.5)); }
-
-/*********************************************************************************************************************************/
-
-void PCACommand::matrix_mult(vector<vector<double> > first, vector<vector<double> > second, vector<vector<double> >& product){
- try {
- int first_rows = first.size();
- int first_cols = first[0].size();
- int second_cols = second[0].size();
-
- product.resize(first_rows);
- for(int i=0;i<first_rows;i++){
- product[i].resize(second_cols);
- }
-
- for(int i=0;i<first_rows;i++){
- for(int j=0;j<second_cols;j++){
- product[i][j] = 0.0;
- for(int k=0;k<first_cols;k++){
- product[i][j] += first[i][k] * second[k][j];
- }
- }
- }
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "matrix_mult");
- exit(1);
- }
-
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::recenter(double offset, vector<vector<double> > D, vector<vector<double> >& G){
- try {
- int rank = D.size();
-
- vector<vector<double> > A(rank);
- vector<vector<double> > C(rank);
- for(int i=0;i<rank;i++){
- A[i].resize(rank);
- C[i].resize(rank);
- }
-
- double scale = -1.0000 / (double) rank;
-
- for(int i=0;i<rank;i++){
- A[i][i] = 0.0000;
- C[i][i] = 1.0000 + scale;
- for(int j=i+1;j<rank;j++){
- A[i][j] = A[j][i] = -0.5 * D[i][j] * D[i][j] + offset;
- C[i][j] = C[j][i] = scale;
- }
- }
-
- matrix_mult(C,A,A);
- matrix_mult(A,C,G);
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "recenter");
- exit(1);
- }
-
-}
-
-/*********************************************************************************************************************************/
-
-// This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479
-
-void PCACommand::tred2(vector<vector<double> >& a, vector<double>& d, vector<double>& e){
- try {
- double scale, hh, h, g, f;
-
- int n = a.size();
-
- d.resize(n);
- e.resize(n);
-
- for(int i=n-1;i>0;i--){
- int l=i-1;
- h = scale = 0.0000;
- if(l>0){
- for(int k=0;k<l+1;k++){
- scale += fabs(a[i][k]);
- }
- if(scale == 0.0){
- e[i] = a[i][l];
- }
- else{
- for(int k=0;k<l+1;k++){
- a[i][k] /= scale;
- h += a[i][k] * a[i][k];
- }
- f = a[i][l];
- g = (f >= 0.0 ? -sqrt(h) : sqrt(h));
- e[i] = scale * g;
- h -= f * g;
- a[i][l] = f - g;
- f = 0.0;
- for(int j=0;j<l+1;j++){
- a[j][i] = a[i][j] / h;
- g = 0.0;
- for(int k=0;k<j+1;k++){
- g += a[j][k] * a[i][k];
- }
- for(int k=j+1;k<l+1;k++){
- g += a[k][j] * a[i][k];
- }
- e[j] = g / h;
- f += e[j] * a[i][j];
- }
- hh = f / (h + h);
- for(int j=0;j<l+1;j++){
- f = a[i][j];
- e[j] = g = e[j] - hh * f;
- for(int k=0;k<j+1;k++){
- a[j][k] -= (f * e[k] + g * a[i][k]);
- }
- }
- }
- }
- else{
- e[i] = a[i][l];
- }
-
- d[i] = h;
- }
-
- d[0] = 0.0000;
- e[0] = 0.0000;
-
- for(int i=0;i<n;i++){
- int l = i;
- if(d[i] != 0.0){
- for(int j=0;j<l;j++){
- g = 0.0000;
- for(int k=0;k<l;k++){
- g += a[i][k] * a[k][j];
- }
- for(int k=0;k<l;k++){
- a[k][j] -= g * a[k][i];
- }
- }
- }
- d[i] = a[i][i];
- a[i][i] = 1.0000;
- for(int j=0;j<l;j++){
- a[j][i] = a[i][j] = 0.0;
- }
- }
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "tred2");
- exit(1);
- }
-
-}
-
-/*********************************************************************************************************************************/
-
-// This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479
-
-void PCACommand::qtli(vector<double>& d, vector<double>& e, vector<vector<double> >& z) {
- try {
- int m, i, iter;
- double s, r, p, g, f, dd, c, b;
-
- int n = d.size();
- for(int i=1;i<=n;i++){
- e[i-1] = e[i];
- }
- e[n-1] = 0.0000;
-
- for(int l=0;l<n;l++){
- iter = 0;
- do {
- for(m=l;m<n-1;m++){
- dd = fabs(d[m]) + fabs(d[m+1]);
- if(fabs(e[m])+dd == dd) break;
- }
- if(m != l){
- if(iter++ == 30) cerr << "Too many iterations in tqli\n";
- g = (d[l+1]-d[l]) / (2.0 * e[l]);
- r = pythag(g, 1.0);
- g = d[m] - d[l] + e[l] / (g + SIGN(r,g));
- s = c = 1.0;
- p = 0.0000;
- for(i=m-1;i>=l;i--){
- f = s * e[i];
- b = c * e[i];
- e[i+1] = (r=pythag(f,g));
- if(r==0.0){
- d[i+1] -= p;
- e[m] = 0.0000;
- break;
- }
- s = f / r;
- c = g / r;
- g = d[i+1] - p;
- r = (d[i] - g) * s + 2.0 * c * b;
- d[i+1] = g + ( p = s * r);
- g = c * r - b;
- for(int k=0;k<n;k++){
- f = z[k][i+1];
- z[k][i+1] = s * z[k][i] + c * f;
- z[k][i] = c * z[k][i] - s * f;
- }
- }
- if(r == 0.00 && i >= l) continue;
- d[l] -= p;
- e[l] = g;
- e[m] = 0.0;
- }
- } while (m != l);
- }
-
- int k;
- for(int i=0;i<n;i++){
- p=d[k=i];
- for(int j=i;j<n;j++){
- if(d[j] >= p){
- p=d[k=j];
- }
- }
- if(k!=i){
- d[k]=d[i];
- d[i]=p;
- for(int j=0;j<n;j++){
- p=z[j][i];
- z[j][i] = z[j][k];
- z[j][k] = p;
- }
- }
- }
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "qtli");
- exit(1);
- }
-}
-
/*********************************************************************************************************************************/
-void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> > G, vector<double> d) {
+void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
try {
int rank = name_list.size();
double dsum = 0.0000;
}
}
- ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc);
+ ofstream pcaData;
+ map<string, string> variables;
+ variables["[filename]"] = fnameRoot;
+ string pcoaDataFile = getOutputFileName("pcoa",variables);
+ m->openOutputFile(pcoaDataFile, pcaData);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pcoa");
- outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
+ outputNames.push_back(pcoaDataFile);
+ outputTypes["pcoa"].push_back(pcoaDataFile);
- ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
+ ofstream pcaLoadings;
+ string loadingsFile = getOutputFileName("loadings",variables);
+ m->openOutputFile(loadingsFile, pcaLoadings);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pcoa.loadings");
- outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");
+ outputNames.push_back(loadingsFile);
+ outputTypes["loadings"].push_back(loadingsFile);
pcaLoadings << "axis\tloading\n";
for(int i=0;i<rank;i++){
}
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "output");
+ m->errorOut(e, "PCOACommand", "output");
exit(1);
}
}
projects / mothur.git / blobdiff