X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.cpp;h=f8083cc01c10a23b4626c6ea2ccd285a15f59c87;hb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1;hp=10669e580998797222fd785b6d80608fd87ba036;hpb=ecd4f324189cf1cb49a3eb49d5cff58562f27b7f;p=mothur.git diff --git a/corraxescommand.cpp b/corraxescommand.cpp index 10669e5..f8083cc 100644 --- a/corraxescommand.cpp +++ b/corraxescommand.cpp @@ -9,6 +9,7 @@ #include "corraxescommand.h" #include "sharedutilities.h" +#include "linearalgebra.h" //********************************************************************************************************************** vector CorrAxesCommand::setParameters(){ @@ -55,12 +56,32 @@ string CorrAxesCommand::getHelpString(){ } } //********************************************************************************************************************** +string CorrAxesCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "corraxes") { outputFileName = "corr.axes"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "CorrAxesCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** CorrAxesCommand::CorrAxesCommand(){ try { abort = true; calledHelp = true; setParameters(); vector tempOutNames; - outputTypes["corr.axes"] = tempOutNames; + outputTypes["corraxes"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "CorrAxesCommand", "CorrAxesCommand"); @@ -91,7 +112,7 @@ CorrAxesCommand::CorrAxesCommand(string option) { } vector tempOutNames; - outputTypes["corr.axes"] = tempOutNames; + outputTypes["corraxes"] = tempOutNames; //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); @@ -265,8 +286,8 @@ int CorrAxesCommand::execute(){ // calc the r values // /************************************************************************************/ - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + ".corr.axes"; - outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName); + string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + "." + getOutputFileNameTag("corraxes"); + outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName); ofstream out; m->openOutputFile(outputFileName, out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); @@ -304,6 +325,8 @@ int CorrAxesCommand::execute(){ int CorrAxesCommand::calcPearson(map >& axes, ofstream& out) { try { + LinearAlgebra linear; + //find average of each axis - X vector averageAxes; averageAxes.resize(numaxes, 0.0); for (map >::iterator it = axes.begin(); it != axes.end(); it++) { @@ -318,7 +341,7 @@ int CorrAxesCommand::calcPearson(map >& axes, ofstream& ou //for each otu for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) { - if (metadatafile == "") { out << i+1; } + if (metadatafile == "") { out << m->currentBinLabels[i]; } else { out << metadataLabels[i]; } //find the averages this otu - Y @@ -355,11 +378,7 @@ int CorrAxesCommand::calcPearson(map >& axes, ofstream& ou rValues[k] = r; out << '\t' << r; - //signifigance calc - http://faculty.vassar.edu/lowry/ch4apx.html - double temp = (1- (r*r)) / (double) (lookupFloat.size()-2); - temp = sqrt(temp); - double sig = r / temp; - if (isnan(sig) || isinf(sig)) { sig = 0.0; } + double sig = linear.calcPearsonSig(lookupFloat.size(), r); out << '\t' << sig; } @@ -382,6 +401,9 @@ int CorrAxesCommand::calcPearson(map >& axes, ofstream& ou int CorrAxesCommand::calcSpearman(map >& axes, ofstream& out) { try { + LinearAlgebra linear; + vector sf; + //format data vector< map > tableX; tableX.resize(numaxes); map::iterator itTable; @@ -421,6 +443,7 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o vector ties; int rankTotal = 0; + double sfTemp = 0.0; for (int j = 0; j < scores[i].size(); j++) { rankTotal += (j+1); ties.push_back(scores[i][j]); @@ -432,6 +455,8 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o float thisrank = rankTotal / (float) ties.size(); rankAxes[ties[k].name].push_back(thisrank); } + int t = ties.size(); + sfTemp += (t*t*t-t); ties.clear(); rankTotal = 0; } @@ -444,13 +469,14 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o } } } + sf.push_back(sfTemp); } //for each otu for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) { - if (metadatafile == "") { out << i+1; } + if (metadatafile == "") { out << m->currentBinLabels[i]; } else { out << metadataLabels[i]; } //find the ranks of this otu - Y @@ -478,6 +504,7 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o sort(otuScores.begin(), otuScores.end(), compareSpearman); + double sg = 0.0; map rankOtus; vector ties; int rankTotal = 0; @@ -492,6 +519,8 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o float thisrank = rankTotal / (float) ties.size(); rankOtus[ties[k].name] = thisrank; } + int t = ties.size(); + sg += (t*t*t-t); ties.clear(); rankTotal = 0; } @@ -532,12 +561,7 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o pValues[j] = p; - //signifigance calc - http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient - double temp = (lookupFloat.size()-2) / (double) (1- (p*p)); - temp = sqrt(temp); - double sig = p*temp; - if (isnan(sig) || isinf(sig)) { sig = 0.0; } - + double sig = linear.calcSpearmanSig(n, sf[j], sg, di); out << '\t' << sig; } @@ -560,6 +584,8 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o int CorrAxesCommand::calcKendall(map >& axes, ofstream& out) { try { + LinearAlgebra linear; + //format data vector< vector > scores; scores.resize(numaxes); for (map >::iterator it = axes.begin(); it != axes.end(); it++) { @@ -603,7 +629,7 @@ int CorrAxesCommand::calcKendall(map >& axes, ofstream& ou //for each otu for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) { - if (metadatafile == "") { out << i+1; } + if (metadatafile == "") { out << m->currentBinLabels[i]; } else { out << metadataLabels[i]; } //find the ranks of this otu - Y @@ -678,14 +704,7 @@ int CorrAxesCommand::calcKendall(map >& axes, ofstream& ou out << '\t' << p; pValues[j] = p; - //calc signif - zA - http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient#Significance_tests - double numer = 3.0 * (numCoor - numDisCoor); - int n = scores[j].size(); - double denom = n * (n-1) * (2*n + 5) / (double) 2.0; - denom = sqrt(denom); - double sig = numer / denom; - - if (isnan(sig) || isinf(sig)) { sig = 0.0; } + double sig = linear.calcKendallSig(scores[j].size(), p); out << '\t' << sig; }