1 #ifndef CORRAXESCOMMAND_H
2 #define CORRAXESCOMMAND_H
8 * Created by westcott on 12/22/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "sharedrabundvector.h"
15 #include "sharedrabundfloatvector.h"
16 #include "inputdata.h"
18 /***************************************************************/
23 spearmanRank(string n, float s) : name(n), score(s) {}
25 /***************************************************************/
27 class CorrAxesCommand : public Command {
29 CorrAxesCommand(string);
32 vector<string> getRequiredParameters();
33 vector<string> getValidParameters();
34 vector<string> getRequiredFiles();
35 map<string, vector<string> > getOutputFiles() { return outputTypes; }
42 GlobalData* globaldata;
43 string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
44 bool abort, pickedGroups;
48 vector<string> outputNames, Groups;
49 map<string, vector<string> > outputTypes;
50 vector<SharedRAbundVector*> lookup;
51 vector<SharedRAbundFloatVector*> lookupFloat;
52 vector<string> metadataLabels;
57 int convertToRelabund();
58 int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
59 map<string, vector<float> > readAxes();
60 int calcPearson(map<string, vector<float> >&, ofstream&);
61 int calcSpearman(map<string, vector<float> >&, ofstream&);
62 int calcKendall(map<string, vector<float> >&, ofstream&);