2 * heatmapsimcommand.cpp
5 * Created by Sarah Westcott on 6/8/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "heatmapsimcommand.h"
11 #include "sharedjabund.h"
12 #include "sharedsorabund.h"
13 #include "sharedjclass.h"
14 #include "sharedsorclass.h"
15 #include "sharedjest.h"
16 #include "sharedsorest.h"
17 #include "sharedthetayc.h"
18 #include "sharedthetan.h"
19 #include "sharedmorisitahorn.h"
20 #include "sharedbraycurtis.h"
23 //**********************************************************************************************************************
24 vector<string> HeatMapSimCommand::setParameters(){
26 CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
27 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
28 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
29 CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
30 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
31 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
32 CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
33 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
34 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
36 vector<string> myArray;
37 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
41 m->errorOut(e, "HeatMapSimCommand", "setParameters");
45 //**********************************************************************************************************************
46 string HeatMapSimCommand::getHelpString(){
48 string helpString = "";
49 ValidCalculators validCalculator;
50 helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc and label. shared or phylip or column and name are required unless valid current files exist.\n";
51 helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
52 helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
53 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
54 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";
55 helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
56 helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
57 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
58 helpString += validCalculator.printCalc("heat");
59 helpString += "The default value for calc is jclass-thetayc.\n";
60 helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n";
61 helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n";
62 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";
63 helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n";
64 helpString += "Example heatmap.sim(phylip=amazonGroups.dist).\n";
65 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
69 m->errorOut(e, "HeatMapSimCommand", "getHelpString");
73 //**********************************************************************************************************************
74 HeatMapSimCommand::HeatMapSimCommand(){
76 abort = true; calledHelp = true;
78 vector<string> tempOutNames;
79 outputTypes["svg"] = tempOutNames;
82 m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
86 //**********************************************************************************************************************
88 HeatMapSimCommand::HeatMapSimCommand(string option) {
90 abort = false; calledHelp = false;
93 //allow user to run help
94 if(option == "help") { help(); abort = true; calledHelp = true; }
95 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
98 vector<string> myArray = setParameters();
100 OptionParser parser(option);
101 map<string,string> parameters = parser.getParameters();
103 ValidParameters validParameter;
104 map<string,string>::iterator it;
106 //check to make sure all parameters are valid for command
107 for (it = parameters.begin(); it != parameters.end(); it++) {
108 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
111 //initialize outputTypes
112 vector<string> tempOutNames;
113 outputTypes["svg"] = tempOutNames;
116 //if the user changes the output directory command factory will send this info to us in the output parameter
117 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
119 //if the user changes the input directory command factory will send this info to us in the output parameter
120 string inputDir = validParameter.validFile(parameters, "inputdir", false);
121 if (inputDir == "not found"){ inputDir = ""; }
124 it = parameters.find("phylip");
125 //user has given a template file
126 if(it != parameters.end()){
127 path = m->hasPath(it->second);
128 //if the user has not given a path then, add inputdir. else leave path alone.
129 if (path == "") { parameters["phylip"] = inputDir + it->second; }
132 it = parameters.find("column");
133 //user has given a template file
134 if(it != parameters.end()){
135 path = m->hasPath(it->second);
136 //if the user has not given a path then, add inputdir. else leave path alone.
137 if (path == "") { parameters["column"] = inputDir + it->second; }
140 it = parameters.find("name");
141 //user has given a template file
142 if(it != parameters.end()){
143 path = m->hasPath(it->second);
144 //if the user has not given a path then, add inputdir. else leave path alone.
145 if (path == "") { parameters["name"] = inputDir + it->second; }
148 it = parameters.find("shared");
149 //user has given a template file
150 if(it != parameters.end()){
151 path = m->hasPath(it->second);
152 //if the user has not given a path then, add inputdir. else leave path alone.
153 if (path == "") { parameters["shared"] = inputDir + it->second; }
157 //required parameters
158 phylipfile = validParameter.validFile(parameters, "phylip", true);
159 if (phylipfile == "not open") { abort = true; }
160 else if (phylipfile == "not found") { phylipfile = ""; }
161 else { format = "phylip"; inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); } }
163 columnfile = validParameter.validFile(parameters, "column", true);
164 if (columnfile == "not open") { abort = true; }
165 else if (columnfile == "not found") { columnfile = ""; }
166 else { format = "column"; inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
168 sharedfile = validParameter.validFile(parameters, "shared", true);
169 if (sharedfile == "not open") { abort = true; }
170 else if (sharedfile == "not found") { sharedfile = ""; }
171 else { format = "shared"; inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
173 namefile = validParameter.validFile(parameters, "name", true);
174 if (namefile == "not open") { abort = true; }
175 else if (namefile == "not found") { namefile = ""; }
176 else { m->setNameFile(namefile); }
179 //error checking on files
180 if ((sharedfile == "") && ((phylipfile == "") && (columnfile == ""))) {
181 sharedfile = m->getSharedFile();
182 if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
184 //is there are current file available for either of these?
185 //give priority to column, then phylip
186 columnfile = m->getColumnFile();
187 if (columnfile != "") { format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
189 phylipfile = m->getPhylipFile();
190 if (phylipfile != "") { format = "phylip"; inputfile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
192 m->mothurOut("No valid current files. You must provide a shared or phylip or column file."); m->mothurOutEndLine();
198 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; }
200 if (columnfile != "") {
201 if (namefile == "") {
202 namefile = m->getNameFile();
203 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
205 m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
211 //check for optional parameter and set defaults
212 // ...at some point should added some additional type checking...
214 label = validParameter.validFile(parameters, "label", false);
215 if (label == "not found") { label = ""; }
217 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
218 else { allLines = 1; }
221 calc = validParameter.validFile(parameters, "calc", false);
222 if (calc == "not found") { calc = "jest-thetayc"; }
224 if (calc == "default") { calc = "jest-thetayc"; }
226 m->splitAtDash(calc, Estimators);
227 if (m->inUsersGroups("citation", Estimators)) {
228 ValidCalculators validCalc; validCalc.printCitations(Estimators);
229 //remove citation from list of calcs
230 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
233 groups = validParameter.validFile(parameters, "groups", false);
234 if (groups == "not found") { groups = ""; }
236 m->splitAtDash(groups, Groups);
237 m->setGroups(Groups);
241 if (abort == false) {
242 ValidCalculators validCalculator;
245 for (i=0; i<Estimators.size(); i++) {
246 if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) {
247 if (Estimators[i] == "jabund") {
248 heatCalculators.push_back(new JAbund());
249 }else if (Estimators[i] == "sorabund") {
250 heatCalculators.push_back(new SorAbund());
251 }else if (Estimators[i] == "jclass") {
252 heatCalculators.push_back(new Jclass());
253 }else if (Estimators[i] == "sorclass") {
254 heatCalculators.push_back(new SorClass());
255 }else if (Estimators[i] == "jest") {
256 heatCalculators.push_back(new Jest());
257 }else if (Estimators[i] == "sorest") {
258 heatCalculators.push_back(new SorEst());
259 }else if (Estimators[i] == "thetayc") {
260 heatCalculators.push_back(new ThetaYC());
261 }else if (Estimators[i] == "thetan") {
262 heatCalculators.push_back(new ThetaN());
263 }else if (Estimators[i] == "morisitahorn") {
264 heatCalculators.push_back(new MorHorn());
265 }else if (Estimators[i] == "braycurtis") {
266 heatCalculators.push_back(new BrayCurtis());
277 catch(exception& e) {
278 m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
282 //**********************************************************************************************************************
284 int HeatMapSimCommand::execute(){
287 if (abort == true) { if (calledHelp) { return 0; } return 2; }
289 heatmap = new HeatMapSim(outputDir, inputfile);
291 if (format == "shared") {
293 }else{ runCommandDist(); }
297 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
299 m->mothurOutEndLine();
300 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
301 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
302 m->mothurOutEndLine();
306 catch(exception& e) {
307 m->errorOut(e, "HeatMapSimCommand", "execute");
312 //**********************************************************************************************************************
313 int HeatMapSimCommand::runCommandShared() {
315 //if the users entered no valid calculators don't execute command
316 if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
318 input = new InputData(sharedfile, "sharedfile");
319 lookup = input->getSharedRAbundVectors();
320 string lastLabel = lookup[0]->getLabel();
322 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;}
324 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
325 set<string> processedLabels;
326 set<string> userLabels = labels;
328 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
330 //as long as you are not at the end of the file or done wih the lines you want
331 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
333 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
335 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
337 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
338 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
339 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
341 processedLabels.insert(lookup[0]->getLabel());
342 userLabels.erase(lookup[0]->getLabel());
345 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
346 string saveLabel = lookup[0]->getLabel();
348 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
349 lookup = input->getSharedRAbundVectors(lastLabel);
351 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
352 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
353 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
355 processedLabels.insert(lookup[0]->getLabel());
356 userLabels.erase(lookup[0]->getLabel());
358 //restore real lastlabel to save below
359 lookup[0]->setLabel(saveLabel);
362 //prevent memory leak
364 lastLabel = lookup[0]->getLabel();
366 //get next line to process
367 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
368 lookup = input->getSharedRAbundVectors();
373 if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
375 //output error messages about any remaining user labels
376 set<string>::iterator it;
377 bool needToRun = false;
378 for (it = userLabels.begin(); it != userLabels.end(); it++) {
379 m->mothurOut("Your file does not include the label " + *it);
380 if (processedLabels.count(lastLabel) != 1) {
381 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
384 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
388 if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
390 //run last label if you need to
391 if (needToRun == true) {
392 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
393 lookup = input->getSharedRAbundVectors(lastLabel);
395 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
396 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
397 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
399 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
402 if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
404 //reset groups parameter
411 catch(exception& e) {
412 m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
416 //**********************************************************************************************************************
417 int HeatMapSimCommand::runCommandDist() {
420 vector< vector<double> > matrix;
421 vector<string> names;
424 //read distance file and create distance vector and names vector
425 if (format == "phylip") {
427 m->openInputFile(phylipfile, in);
431 in >> numSeqs >> name;
434 names.push_back(name);
436 //resize the matrix and fill with zeros
437 matrix.resize(numSeqs);
438 for(int i = 0; i < numSeqs; i++) {
439 matrix[i].resize(numSeqs, 0.0);
442 //determine if matrix is square or lower triangle
443 //if it is square read the distances for the first sequence
446 while((d=in.get()) != EOF){
448 //is d a number meaning its square
453 for(int i=0;i<numSeqs;i++){
459 //is d a line return meaning its lower triangle
466 //read rest of matrix
467 if (square == true) {
468 for(int i=1;i<numSeqs;i++){
470 names.push_back(name);
472 if (m->control_pressed) { return 0; }
474 for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
479 for(int i=1;i<numSeqs;i++){
481 names.push_back(name);
483 if (m->control_pressed) { return 0; }
485 for(int j=0;j<i;j++){
487 matrix[i][j] = dist; matrix[j][i] = dist;
495 NameAssignment* nameMap = new NameAssignment(namefile);
498 //put names in order in vector
499 for (int i = 0; i < nameMap->size(); i++) {
500 names.push_back(nameMap->get(i));
504 matrix.resize(nameMap->size());
505 for (int i = 0; i < nameMap->size(); i++) {
506 matrix[i].resize(nameMap->size(), 0.0);
510 string first, second;
512 m->openInputFile(columnfile, in);
515 in >> first >> second >> dist; m->gobble(in);
517 if (m->control_pressed) { return 0; }
519 map<string, int>::iterator itA = nameMap->find(first);
520 map<string, int>::iterator itB = nameMap->find(second);
522 if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); }
523 if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); }
526 matrix[itA->second][itB->second] = dist;
527 matrix[itB->second][itA->second] = dist;
535 string outputFileName = heatmap->getPic(matrix, names);
536 outputNames.push_back(outputFileName); //vector<vector<double>>, vector<string>
537 outputTypes["svg"].push_back(outputFileName);
541 catch(exception& e) {
542 m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
546 //**********************************************************************************************************************