X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapsimcommand.cpp;fp=heatmapsimcommand.cpp;h=de35075e98ee938e67f1880cada0ebfb1e0ba26a;hp=0000000000000000000000000000000000000000;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
new file mode 100644
index 0000000..de35075
--- /dev/null
+++ b/heatmapsimcommand.cpp
@@ -0,0 +1,558 @@
+/*
+ *  heatmapsimcommand.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "heatmapsimcommand.h"
+#include "sharedjabund.h"
+#include "sharedsorabund.h"
+#include "sharedjclass.h"
+#include "sharedsorclass.h"
+#include "sharedjest.h"
+#include "sharedsorest.h"
+#include "sharedthetayc.h"
+#include "sharedthetan.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+
+
+//**********************************************************************************************************************
+vector<string> HeatMapSimCommand::setParameters(){	
+	try {
+		CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);	
+		CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
+		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+		CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);		
+		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+		CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+		CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
+		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);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapSimCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string HeatMapSimCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		ValidCalculators validCalculator;
+		helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc, fontsize and label.  shared or phylip or column and name are required unless valid current files exist.\n";
+		helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
+		helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
+		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
+		helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n";
+		helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
+		helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
+		helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
+		helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
+		helpString +=  validCalculator.printCalc("heat");
+		helpString += "The default value for calc is jclass-thetayc.\n";
+		helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n";
+		helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n";
+		helpString += "Using the command this way, the phylip or column parameter are required, and only one may be used.  If you use a column file the name filename is required. \n";
+		helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n";
+		helpString += "Example heatmap.sim(phylip=amazonGroups.dist).\n";
+		helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapSimCommand", "getHelpString");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+HeatMapSimCommand::HeatMapSimCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["svg"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+HeatMapSimCommand::HeatMapSimCommand(string option)  {
+	try {
+		abort = false; calledHelp = false;   
+		allLines = 1;
+			
+		//allow user to run help
+		if(option == "help") {  help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+		
+		else {
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			map<string,string>::iterator it;
+			
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["svg"] = tempOutNames;
+			
+			format = "";
+				
+			//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 (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("phylip");
+				//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["phylip"] = inputDir + it->second;		}
+				}
+				
+				it = parameters.find("column");
+				//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["column"] = inputDir + it->second;		}
+				}
+				
+				it = parameters.find("name");
+				//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["name"] = inputDir + it->second;		}
+				}
+				
+				it = parameters.find("shared");
+				//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["shared"] = inputDir + it->second;		}
+				}
+			}
+
+			//required parameters
+			phylipfile = validParameter.validFile(parameters, "phylip", true);
+			if (phylipfile == "not open") { abort = true; }
+			else if (phylipfile == "not found") { phylipfile = ""; }	
+			else {  format = "phylip"; 	inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
+			
+			columnfile = validParameter.validFile(parameters, "column", true);
+			if (columnfile == "not open") { abort = true; }	
+			else if (columnfile == "not found") { columnfile = ""; }
+			else {  format = "column";	inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
+			
+			sharedfile = validParameter.validFile(parameters, "shared", true);
+			if (sharedfile == "not open") { abort = true; }	
+			else if (sharedfile == "not found") { sharedfile = ""; }
+			else {  format = "shared";	inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
+			
+			namefile = validParameter.validFile(parameters, "name", true);
+			if (namefile == "not open") { abort = true; }	
+			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
+			
+			
+			//error checking on files			
+			if ((sharedfile == "") && ((phylipfile == "") && (columnfile == "")))	{ 
+				sharedfile = m->getSharedFile(); 
+				if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+				else { 
+					//is there are current file available for either of these?
+					//give priority to column, then phylip
+					columnfile = m->getColumnFile(); 
+					if (columnfile != "") {  format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+					else { 
+						phylipfile = m->getPhylipFile(); 
+						if (phylipfile != "") { format = "phylip";  inputfile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+						else { 
+							m->mothurOut("No valid current files. You must provide a shared or phylip or column file."); m->mothurOutEndLine(); 
+							abort = true;
+						}
+					}
+				}
+			}
+			else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
+			
+			if (columnfile != "") {
+				if (namefile == "") { 
+					namefile = m->getNameFile(); 
+					if (namefile != "") {  m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+					else { 
+						m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); 
+						abort = true; 
+					}	
+				}
+			}
+			
+			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(inputfile);		}
+
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+							
+			label = validParameter.validFile(parameters, "label", false);			
+			if (label == "not found") { label = ""; }
+			else { 
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
+				else { allLines = 1;  }
+			}
+				
+			calc = validParameter.validFile(parameters, "calc", false);			
+			if (calc == "not found") { calc = "jest-thetayc";  }
+			else { 
+				if (calc == "default")  {  calc = "jest-thetayc";  }
+			}
+			m->splitAtDash(calc, Estimators);
+			if (m->inUsersGroups("citation", Estimators)) { 
+				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+				//remove citation from list of calcs
+				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+			}
+				
+			groups = validParameter.validFile(parameters, "groups", false);			
+			if (groups == "not found") { groups = ""; }
+			else { 
+				m->splitAtDash(groups, Groups);
+				m->setGroups(Groups);
+			}
+			
+			string temp = validParameter.validFile(parameters, "fontsize", false);				if (temp == "not found") { temp = "24"; }
+			m->mothurConvert(temp, fontsize);
+			
+			if (abort == false) {
+				ValidCalculators validCalculator;
+			
+				int i;
+				for (i=0; i<Estimators.size(); i++) {
+					if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) { 
+						if (Estimators[i] == "jabund") { 	
+							heatCalculators.push_back(new JAbund());
+						}else if (Estimators[i] == "sorabund") { 
+							heatCalculators.push_back(new SorAbund());
+						}else if (Estimators[i] == "jclass") { 
+							heatCalculators.push_back(new Jclass());
+						}else if (Estimators[i] == "sorclass") { 
+							heatCalculators.push_back(new SorClass());
+						}else if (Estimators[i] == "jest") { 
+							heatCalculators.push_back(new Jest());
+						}else if (Estimators[i] == "sorest") { 
+							heatCalculators.push_back(new SorEst());
+						}else if (Estimators[i] == "thetayc") { 
+							heatCalculators.push_back(new ThetaYC());
+						}else if (Estimators[i] == "thetan") { 
+							heatCalculators.push_back(new ThetaN());
+						}else if (Estimators[i] == "morisitahorn") { 
+							heatCalculators.push_back(new MorHorn());
+						}else if (Estimators[i] == "braycurtis") { 
+							heatCalculators.push_back(new BrayCurtis());
+						}
+					}
+				}
+				
+			}
+		}
+
+				
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+int HeatMapSimCommand::execute(){
+	try {
+	
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		
+		heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
+		
+		if (format == "shared") {
+			runCommandShared();
+		}else{	runCommandDist();	}
+		
+		delete heatmap;
+		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear(); return 0; }
+		
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
+		m->mothurOutEndLine();
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapSimCommand", "execute");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandShared() {
+	try {
+		//if the users entered no valid calculators don't execute command
+		if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
+		
+		input = new InputData(sharedfile, "sharedfile");
+		lookup = input->getSharedRAbundVectors();
+		string lastLabel = lookup[0]->getLabel();
+			
+		if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); return 0;}
+				
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = labels;
+		
+		if (m->control_pressed) {  delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  m->clearGroups(); return 0; }
+		
+		//as long as you are not at the end of the file or done wih the lines you want
+		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+			
+			if (m->control_pressed) { delete input;  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0; }
+
+			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
+	
+				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+				vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+				for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]);  outputTypes["svg"].push_back(outfilenames[i]); }
+					
+				processedLabels.insert(lookup[0]->getLabel());
+				userLabels.erase(lookup[0]->getLabel());
+			}
+				
+			if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+				string saveLabel = lookup[0]->getLabel();
+			
+				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+				lookup = input->getSharedRAbundVectors(lastLabel);				
+
+				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+				vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+				for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]);  }
+					
+				processedLabels.insert(lookup[0]->getLabel());
+				userLabels.erase(lookup[0]->getLabel());
+				
+				//restore real lastlabel to save below
+				lookup[0]->setLabel(saveLabel);
+			}
+				
+			//prevent memory leak
+			 
+			lastLabel = lookup[0]->getLabel();			
+
+			//get next line to process
+			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+			lookup = input->getSharedRAbundVectors();
+
+		}
+		
+			
+		if (m->control_pressed) {  delete input;  m->clearGroups();  return 0; }
+
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			m->mothurOut("Your file does not include the label " + *it); 
+			if (processedLabels.count(lastLabel) != 1) {
+				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+				needToRun = true;
+			}else {
+				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+			}
+		}
+		
+		if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
+		
+		//run last label if you need to
+		if (needToRun == true)  {
+			for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) { delete lookup[i]; } } 
+			lookup = input->getSharedRAbundVectors(lastLabel);				
+
+			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+			vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
+			for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]);  }
+			
+			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+		}
+		
+		if (m->control_pressed) {  delete input;  m->clearGroups(); return 0; }
+			
+		//reset groups parameter
+		m->clearGroups();  
+			
+		delete input;  
+	
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandDist() {
+	try {
+	
+		vector< vector<double> > matrix;
+		vector<string> names;
+		ifstream in;
+		
+		//read distance file and create distance vector and names vector
+		if (format == "phylip") {
+			//read phylip file
+			m->openInputFile(phylipfile, in);
+			
+			string name;
+			int numSeqs;
+			in >> numSeqs >> name; 
+			
+			//save name
+			names.push_back(name);
+		
+			//resize the matrix and fill with zeros
+			matrix.resize(numSeqs); 
+			for(int i = 0; i < numSeqs; i++) {
+				matrix[i].resize(numSeqs, 0.0);
+			}
+					
+			//determine if matrix is square or lower triangle
+			//if it is square read the distances for the first sequence
+			char d;
+			bool square;
+			while((d=in.get()) != EOF){
+				
+				//is d a number meaning its square
+				if(isalnum(d)){ 
+					square = true;
+					in.putback(d);
+					
+					for(int i=0;i<numSeqs;i++){
+						in >> matrix[0][i];
+					}
+					break;
+				}
+				
+				//is d a line return meaning its lower triangle
+				if(d == '\n'){
+					square = false;
+					break;
+				}
+			}
+			
+			//read rest of matrix
+			if (square == true) { 
+				for(int i=1;i<numSeqs;i++){
+					in >> name;		
+					names.push_back(name);
+					
+					if (m->control_pressed) { return 0; }
+					
+					for(int j=0;j<numSeqs;j++) { in >> matrix[i][j];  }
+					m->gobble(in);
+				}
+			}else { 
+				double dist;
+				for(int i=1;i<numSeqs;i++){
+					in >> name;	
+					names.push_back(name);	
+					
+					if (m->control_pressed) { return 0; }
+					
+					for(int j=0;j<i;j++){
+						in >> dist;
+						matrix[i][j] = dist;  matrix[j][i] = dist;
+					}
+					m->gobble(in);
+				}
+			}
+			in.close();
+		}else {
+			//read names file
+			NameAssignment* nameMap = new NameAssignment(namefile);
+			nameMap->readMap();
+			
+			//put names in order in vector
+			for (int i = 0; i < nameMap->size(); i++) {
+				names.push_back(nameMap->get(i));
+			}
+			
+			//resize matrix
+			matrix.resize(nameMap->size());
+			for (int i = 0; i < nameMap->size(); i++) {
+				matrix[i].resize(nameMap->size(), 0.0);
+			}
+			
+			//read column file
+			string first, second;
+			double dist;
+			m->openInputFile(columnfile, in);
+			
+			while (!in.eof()) {
+				in >> first >> second >> dist; m->gobble(in);
+				
+				if (m->control_pressed) { return 0; }
+				
+				map<string, int>::iterator itA = nameMap->find(first);
+				map<string, int>::iterator itB = nameMap->find(second);
+				
+				if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1);  }
+				if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1);  }
+				
+				//save distance
+				matrix[itA->second][itB->second] = dist;
+				matrix[itB->second][itA->second] = dist;
+			}
+			in.close();
+			
+			delete nameMap;
+		}
+		
+		
+		string outputFileName = heatmap->getPic(matrix, names);
+		outputNames.push_back(outputFileName); //vector<vector<double>>, vector<string>
+		outputTypes["svg"].push_back(outputFileName);
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+
+
+
+
+