1 #ifndef HEATMAPCOMMAND_H
2 #define HEATMAPCOMMAND_H
8 * Created by Sarah Westcott on 3/25/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "command.hpp"
15 #include "inputdata.h"
16 #include "sharedlistvector.h"
18 #include "rabundvector.hpp"
21 class HeatMapCommand : public Command {
24 HeatMapCommand(string);
28 vector<string> setParameters();
29 string getCommandName() { return "heatmap.bin"; }
30 string getCommandCategory() { return "OTU-Based Approaches"; }
32 string getHelpString();
33 string getOutputPattern(string);
34 string getCitation() { return "http://www.mothur.org/wiki/Heatmap.bin"; }
35 string getDescription() { return "generate a heatmap where the color represents the relative abundanceof an OTU"; }
39 void help() { m->mothurOut(getHelpString()); }
45 vector<SharedRAbundVector*> lookup;
46 vector<SharedRAbundFloatVector*> lookupFloat;
50 set<string> labels; //holds labels to be used
51 string format, groups, sorted, scale, label, outputDir, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
52 vector<string> Groups, outputNames;