//**********************************************************************************************************************
vector<string> OTUAssociationCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false); parameters.push_back(prelabund);
+ CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ 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); }
string helpString = "";
helpString += "The otu.association command reads a shared or relabund file and calculates the correlation coefficients between otus.\n";
helpString += "If you provide a metadata file, mothur will calculate te correlation bewteen the metadata and the otus.\n";
- helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method and label. The shared or relabund parameter is required.\n";
+ helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method, cutoff and label. The shared or relabund parameter is required.\n";
helpString += "The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n";
helpString += "The label parameter allows you to select what distances level you would like used, and are also separated by dashes.\n";
+ helpString += "The cutoff parameter allows you to set a pvalue at which the otu will be reported.\n";
helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n";
helpString += "The otu.association command should be in the following format: otu.association(shared=yourSharedFile, method=yourMethod).\n";
helpString += "Example otu.association(shared=genus.pool.shared, method=kendall).\n";
}
}
//**********************************************************************************************************************
+string OTUAssociationCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "otucorr") { pattern = "[filename],[distance],[tag],otu.corr"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
OTUAssociationCommand::OTUAssociationCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["otu.corr"] = tempOutNames;
+ outputTypes["otucorr"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand");
}
vector<string> tempOutNames;
- outputTypes["otu.corr"] = tempOutNames;
+ outputTypes["otucorr"] = 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);
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
+ string temp = validParameter.validFile(parameters, "cutoff", false);
+ if (temp == "not found") { temp = "10"; }
+ m->mothurConvert(temp, cutoff);
+
if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
}
//**********************************************************************************************************************
int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
- outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[distance]"] = lookup[0]->getLabel();
+ variables["[tag]"] = method;
+ string outputFileName = getOutputFileName("otucorr",variables);
+ outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << m->currentSharedBinLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}else { //compare otus to metadata
else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
try {
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
- outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[distance]"] = lookup[0]->getLabel();
+ variables["[tag]"] = method;
+ string outputFileName = getOutputFileName("otucorr",variables);
+ outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << m->currentSharedBinLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
}else { //compare otus to metadata
else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); }
else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
- out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl;
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
}
//save names of columns you are reading
while (!iss.eof()) {
iss >> columnLabel; m->gobble(iss);
+ if (m->debug) { m->mothurOut("[DEBUG]: metadata column Label = " + columnLabel + "\n"); }
metadataLabels.push_back(columnLabel);
}
int count = metadataLabels.size();
string group = "";
in >> group; m->gobble(in);
+ if (m->debug) { m->mothurOut("[DEBUG]: metadata group = " + group + "\n"); }
SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
tempLookup->setGroup(group);
for (int i = 0; i < count; i++) {
float temp = 0.0;
- in >> temp;
+ in >> temp;
+ if (m->debug) { m->mothurOut("[DEBUG]: metadata value = " + toString(temp) + "\n"); }
tempLookup->push_back(temp, group);
}
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