*/
#include "command.hpp"
-#include "sharedrabundvector.h"
#include "sharedrabundfloatvector.h"
#include "inputdata.h"
+
class CorrAxesCommand : public Command {
public:
CorrAxesCommand(string);
CorrAxesCommand();
- ~CorrAxesCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~CorrAxesCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "corr.axes"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+ string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Corr.axes"; }
+ string getDescription() { return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; }
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
- string axesfile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
+
+ string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
bool abort, pickedGroups;
int numaxes;
set<string> names;
vector<string> outputNames, Groups;
- map<string, vector<string> > outputTypes;
- vector<SharedRAbundVector*> lookup;
vector<SharedRAbundFloatVector*> lookupFloat;
+ vector<string> metadataLabels;
- int getShared();
- int getSharedFloat();
- int convertToRelabund();
+ int getSharedFloat(InputData*);
+ int getMetadata();
int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
map<string, vector<float> > readAxes();
int calcPearson(map<string, vector<float> >&, ofstream&);
+ int calcSpearman(map<string, vector<float> >&, ofstream&);
+ int calcKendall(map<string, vector<float> >&, ofstream&);
};