X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;fp=pcoacommand.cpp;h=ee0a5462de87049f6b026546492203be630ea8d7;hb=4956d362c5bc6a47cf7a6290258f0e763e3a406e;hp=0000000000000000000000000000000000000000;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
new file mode 100644
index 0000000..ee0a546
--- /dev/null
+++ b/pcoacommand.cpp
@@ -0,0 +1,607 @@
+
+/*
+ *  pcacommand.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 1/4/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "pcacommand.h"
+
+//**********************************************************************************************************************
+vector<string> PCACommand::getValidParameters(){	
+	try {
+		string Array[] =  {"phylip", "outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PCACommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+PCACommand::PCACommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["pcoa"] = tempOutNames;
+		outputTypes["loadings"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PCACommand", "PCACommand");
+		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);
+	}
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PCACommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+PCACommand::PCACommand(string option)  {
+	try {
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"phylip","outputdir", "inputdir"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser. getParameters();
+			
+			ValidParameters validParameter;
+			map<string, string>::iterator it;
+		
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("phylip");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = m->hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["phylip"] = inputDir + it->second;		}
+				}
+			}
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["pcoa"] = tempOutNames;
+			outputTypes["loadings"] = tempOutNames;
+			
+			//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;  }
+			
+			//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 = "";	
+				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; }		
+		}
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PCACommand", "PCACommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+void PCACommand::help(){
+	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; }
+		
+		cout.setf(ios::fixed, ios::floatfield);
+		cout.setf(ios::showpoint);
+		cerr.setf(ios::fixed, ios::floatfield);
+		cerr.setf(ios::showpoint);
+		
+		vector<string> names;
+		vector<vector<double> > D;
+	
+		fbase = outputDir + m->getRootName(m->getSimpleName(filename));
+		
+		read(filename, names, D);
+		
+		if (m->control_pressed) { return 0; }
+   	
+		double offset = 0.0000;
+		vector<double> d;
+		vector<double> e;
+		vector<vector<double> > G = D;
+		vector<vector<double> > copy_G;
+		//int rank = D.size();
+		
+		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; }
+			offset = d[d.size()-1];
+			if(offset > 0.0) break;
+		} 
+		
+		if (m->control_pressed) { return 0; }
+		
+		output(fbase, names, G, d);
+		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+		
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
+		m->mothurOutEndLine();
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PCACommand", "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){
+	try {
+		char d=f.get();
+		while(d != end){	d = f.get();	}
+		d = f.peek();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PCACommand", "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) {
+	try {
+		int rank = name_list.size();
+		double dsum = 0.0000;
+		for(int i=0;i<rank;i++){
+			dsum += d[i];
+			for(int j=0;j<rank;j++){
+				if(d[j] >= 0)	{	G[i][j] *= pow(d[j],0.5);	}
+				else			{	G[i][j] = 0.00000;			}
+			}
+		}
+		
+		ofstream pcaData((fnameRoot+"pcoa").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");
+		
+		ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
+		pcaLoadings.setf(ios::fixed, ios::floatfield);
+		pcaLoadings.setf(ios::showpoint);
+		outputNames.push_back(fnameRoot+"pcoa.loadings");
+		outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");	
+		
+		pcaLoadings << "axis\tloading\n";
+		for(int i=0;i<rank;i++){
+			pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
+		}
+		
+		pcaData << "group";
+		for(int i=0;i<rank;i++){
+			pcaData << '\t' << "axis" << i+1;
+		}
+		pcaData << endl;
+		
+		for(int i=0;i<rank;i++){
+			pcaData << name_list[i] << '\t';
+			for(int j=0;j<rank;j++){
+				pcaData << G[i][j] << '\t';
+			}
+			pcaData << endl;
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PCACommand", "output");
+		exit(1);
+	}
+}
+
+/*********************************************************************************************************************************/
+