//**********************************************************************************************************************
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 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); }
try {
string helpString = "";
helpString += "The otu.association command reads a shared or relabund file and calculates the correlation coefficients between otus.\n";
- helpString += "The otu.association command parameters are shared, relabund, groups, method and label. The shared or relabund parameter is required.\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, 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);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["relabund"] = inputDir + it->second; }
}
+
+ it = parameters.find("metadata");
+ //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["metadata"] = inputDir + it->second; }
+ }
}
else if (relabundfile == "not found") { relabundfile = ""; }
else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
+ metadatafile = validParameter.validFile(parameters, "metadata", true);
+ if (metadatafile == "not open") { abort = true; metadatafile = ""; }
+ else if (metadatafile == "not found") { metadatafile = ""; }
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; pickedGroups = false; }
else {
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; }
}
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if (metadatafile != "") { readMetadata(); }
//function are identical just different datatypes
if (sharedfile != "") { processShared(); }
InputData* input = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
+
+ if (metadatafile != "") {
+ getMetadata();
+ bool error = false;
+ if (metadata[0].size() != lookup.size()) { m->mothurOut("[ERROR]: You have selected to use " + toString(metadata[0].size()) + " data rows from the metadata file, but " + toString(lookup.size()) + " from the shared file.\n"); m->control_pressed = true; error=true;}
+ if (error) {
+ //maybe add extra info here?? compare groups in each file??
+ }
+ }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
//**********************************************************************************************************************
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);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
//column headings
- out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n";
+ if (metadatafile == "") { out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n"; }
+ else { out << "OTUA\tMetadata\t" << method << "Coef\tSignificance\n"; }
+
vector< vector<double> > xy; xy.resize(lookup[0]->getNumBins());
for (int i = 0; i < lookup[0]->getNumBins(); i++) { for (int j = 0; j < lookup.size(); j++) { xy[i].push_back(lookup[j]->getAbundance(i)); } }
LinearAlgebra linear;
- for (int i = 0; i < xy.size(); i++) {
-
- for (int k = 0; k < i; k++) {
-
- if (m->control_pressed) { out.close(); return 0; }
-
- /*cout << m->binLabelsInFile[i] << " <- c(" << xy[i][0];
- for (int l = 1; l < xy[i].size(); l++){
- cout << ", " << xy[i][l];
+ if (metadatafile == "") {//compare otus
+ for (int i = 0; i < xy.size(); i++) {
+
+ for (int k = 0; k < i; k++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ double coef = 0.0;
+ double sig = 0.0;
+ if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); }
+ else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); }
+ 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; }
+
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << m->currentSharedBinLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
- cout << ")\n";
+ }
+ }else { //compare otus to metadata
+ for (int i = 0; i < xy.size(); i++) {
- cout << m->binLabelsInFile[k] << " <- c(" << xy[k][0];
- for (int l = 1; l < xy[k].size(); l++){
- cout << ", " << xy[k][l];
+ for (int k = 0; k < metadata.size(); k++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ double coef = 0.0;
+ double sig = 0.0;
+ if (method == "spearman") { coef = linear.calcSpearman(xy[i], metadata[k], sig); }
+ else if (method == "pearson") { coef = linear.calcPearson(xy[i], metadata[k], sig); }
+ 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; }
+
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
}
- cout << ")\n";*/
+ }
- double coef = 0.0;
- double sig = 0.0;
- if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); }
- else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); }
- 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;
- }
- }
-
+ }
out.close();
InputData* input = new InputData(relabundfile, "relabund");
vector<SharedRAbundFloatVector*> lookup = input->getSharedRAbundFloatVectors();
string lastLabel = lookup[0]->getLabel();
+
+ if (metadatafile != "") {
+ getMetadata();
+ bool error = false;
+ if (metadata[0].size() != lookup.size()) { m->mothurOut("[ERROR]: You have selected to use " + toString(metadata[0].size()) + " data rows from the metadata file, but " + toString(lookup.size()) + " from the relabund file.\n"); m->control_pressed = true; error=true;}
+ if (error) {
+ //maybe add extra info here?? compare groups in each file??
+ }
+ }
+
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
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);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
//column headings
- out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n";
+ if (metadatafile == "") { out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n"; }
+ else { out << "OTUA\tMetadata\t" << method << "Coef\tSignificance\n"; }
vector< vector<double> > xy; xy.resize(lookup[0]->getNumBins());
for (int i = 0; i < lookup[0]->getNumBins(); i++) { for (int j = 0; j < lookup.size(); j++) { xy[i].push_back(lookup[j]->getAbundance(i)); } }
LinearAlgebra linear;
- for (int i = 0; i < xy.size(); i++) {
-
- for (int k = 0; k < i; k++) {
-
- if (m->control_pressed) { out.close(); return 0; }
-
- double coef = 0.0;
- double sig = 0.0;
- if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); }
- else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); }
- 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] << coef << '\t' << sig << endl;
- }
- }
+ if (metadatafile == "") {//compare otus
+ for (int i = 0; i < xy.size(); i++) {
+
+ for (int k = 0; k < i; k++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ double coef = 0.0;
+ double sig = 0.0;
+ if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); }
+ else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); }
+ 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; }
+
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << m->currentSharedBinLabels[k] << '\t' << coef << '\t' << sig << endl; }
+ }
+ }
+ }else { //compare otus to metadata
+ for (int i = 0; i < xy.size(); i++) {
+
+ for (int k = 0; k < metadata.size(); k++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ double coef = 0.0;
+ double sig = 0.0;
+ if (method == "spearman") { coef = linear.calcSpearman(xy[i], metadata[k], sig); }
+ else if (method == "pearson") { coef = linear.calcPearson(xy[i], metadata[k], sig); }
+ 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; }
+
+ if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
+ }
+ }
+
+ }
out.close();
}
}
/*****************************************************************/
+int OTUAssociationCommand::readMetadata(){
+ try {
+ ifstream in;
+ m->openInputFile(metadatafile, in);
+
+ string headerLine = m->getline(in); m->gobble(in);
+ istringstream iss (headerLine,istringstream::in);
+
+ //read the first label, because it refers to the groups
+ string columnLabel;
+ iss >> columnLabel; m->gobble(iss);
+
+ //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();
+
+ //read rest of file
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ string group = "";
+ in >> group; m->gobble(in);
+ if (m->debug) { m->mothurOut("[DEBUG]: metadata group = " + group + "\n"); }
+
+ SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
+ tempLookup->setGroup(group);
+ tempLookup->setLabel("1");
+
+ for (int i = 0; i < count; i++) {
+ float temp = 0.0;
+ in >> temp;
+ if (m->debug) { m->mothurOut("[DEBUG]: metadata value = " + toString(temp) + "\n"); }
+ tempLookup->push_back(temp, group);
+ }
+
+ metadataLookup.push_back(tempLookup);
+
+ m->gobble(in);
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "readMetadata");
+ exit(1);
+ }
+}
+/*****************************************************************/
+//eliminate groups user did not pick, remove zeroed out otus, fill metadata vector.
+int OTUAssociationCommand::getMetadata(){
+ try {
+
+ vector<string> mGroups = m->getGroups();
+
+ bool remove = false;
+ for (int i = 0; i < metadataLookup.size(); i++) {
+ //if this sharedrabund is not from a group the user wants then delete it.
+ if (!(m->inUsersGroups(metadataLookup[i]->getGroup(), mGroups))) {
+ delete metadataLookup[i]; metadataLookup[i] = NULL;
+ metadataLookup.erase(metadataLookup.begin()+i);
+ i--;
+ remove = true;
+ }
+ }
+
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int i = 0; i < metadataLookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(metadataLookup[i]->getLabel());
+ temp->setGroup(metadataLookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ vector<string> newBinLabels;
+ for (int i = 0; i < metadataLookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < metadataLookup.size(); j++) {
+ if (metadataLookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < metadataLookup.size(); j++) {
+ newLookup[j]->push_back(metadataLookup[j]->getAbundance(i), metadataLookup[j]->getGroup());
+ }
+ newBinLabels.push_back(metadataLabels[i]);
+ }
+ }
+
+ metadataLabels = newBinLabels;
+
+ for (int j = 0; j < metadataLookup.size(); j++) { delete metadataLookup[j]; }
+ metadataLookup.clear();
+
+ metadata.resize(newLookup[0]->getNumBins());
+ for (int i = 0; i < newLookup[0]->getNumBins(); i++) { for (int j = 0; j < newLookup.size(); j++) { metadata[i].push_back(newLookup[j]->getAbundance(i)); } }
+
+ for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "getMetadata");
+ exit(1);
+ }
+}
+/*****************************************************************/
projects / mothur.git / blobdiff