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; 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; 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; 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 = ""; }
178 //error checking on files
179 if ((sharedfile == "") && ((phylipfile == "") && (columnfile == ""))) {
180 sharedfile = m->getSharedFile();
181 if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
183 //is there are current file available for either of these?
184 //give priority to column, then phylip
185 columnfile = m->getColumnFile();
186 if (columnfile != "") { format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
188 phylipfile = m->getPhylipFile();
189 if (phylipfile != "") { format = "phylip"; inputfile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
191 m->mothurOut("No valid current files. You must provide a shared or phylip or column file."); m->mothurOutEndLine();
197 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; }
199 if (columnfile != "") {
200 if (namefile == "") {
201 namefile = m->getNameFile();
202 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
204 m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
210 //check for optional parameter and set defaults
211 // ...at some point should added some additional type checking...
213 label = validParameter.validFile(parameters, "label", false);
214 if (label == "not found") { label = ""; }
216 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
217 else { allLines = 1; }
220 calc = validParameter.validFile(parameters, "calc", false);
221 if (calc == "not found") { calc = "jest-thetayc"; }
223 if (calc == "default") { calc = "jest-thetayc"; }
225 m->splitAtDash(calc, Estimators);
226 if (m->inUsersGroups("citation", Estimators)) {
227 ValidCalculators validCalc; validCalc.printCitations(Estimators);
228 //remove citation from list of calcs
229 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
232 groups = validParameter.validFile(parameters, "groups", false);
233 if (groups == "not found") { groups = ""; }
235 m->splitAtDash(groups, Groups);
240 if (abort == false) {
241 ValidCalculators validCalculator;
244 for (i=0; i<Estimators.size(); i++) {
245 if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) {
246 if (Estimators[i] == "jabund") {
247 heatCalculators.push_back(new JAbund());
248 }else if (Estimators[i] == "sorabund") {
249 heatCalculators.push_back(new SorAbund());
250 }else if (Estimators[i] == "jclass") {
251 heatCalculators.push_back(new Jclass());
252 }else if (Estimators[i] == "sorclass") {
253 heatCalculators.push_back(new SorClass());
254 }else if (Estimators[i] == "jest") {
255 heatCalculators.push_back(new Jest());
256 }else if (Estimators[i] == "sorest") {
257 heatCalculators.push_back(new SorEst());
258 }else if (Estimators[i] == "thetayc") {
259 heatCalculators.push_back(new ThetaYC());
260 }else if (Estimators[i] == "thetan") {
261 heatCalculators.push_back(new ThetaN());
262 }else if (Estimators[i] == "morisitahorn") {
263 heatCalculators.push_back(new MorHorn());
264 }else if (Estimators[i] == "braycurtis") {
265 heatCalculators.push_back(new BrayCurtis());
276 catch(exception& e) {
277 m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
281 //**********************************************************************************************************************
283 int HeatMapSimCommand::execute(){
286 if (abort == true) { if (calledHelp) { return 0; } return 2; }
288 heatmap = new HeatMapSim(outputDir, inputfile);
290 if (format == "shared") {
292 }else{ runCommandDist(); }
296 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
298 m->mothurOutEndLine();
299 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
300 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
301 m->mothurOutEndLine();
305 catch(exception& e) {
306 m->errorOut(e, "HeatMapSimCommand", "execute");
311 //**********************************************************************************************************************
312 int HeatMapSimCommand::runCommandShared() {
314 //if the users entered no valid calculators don't execute command
315 if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
317 input = new InputData(sharedfile, "sharedfile");
318 lookup = input->getSharedRAbundVectors();
319 string lastLabel = lookup[0]->getLabel();
321 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;}
323 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
324 set<string> processedLabels;
325 set<string> userLabels = labels;
327 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
329 //as long as you are not at the end of the file or done wih the lines you want
330 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
332 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
334 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
336 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
337 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
338 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
340 processedLabels.insert(lookup[0]->getLabel());
341 userLabels.erase(lookup[0]->getLabel());
344 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
345 string saveLabel = lookup[0]->getLabel();
347 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
348 lookup = input->getSharedRAbundVectors(lastLabel);
350 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
351 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
352 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
354 processedLabels.insert(lookup[0]->getLabel());
355 userLabels.erase(lookup[0]->getLabel());
357 //restore real lastlabel to save below
358 lookup[0]->setLabel(saveLabel);
361 //prevent memory leak
363 lastLabel = lookup[0]->getLabel();
365 //get next line to process
366 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
367 lookup = input->getSharedRAbundVectors();
372 if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
374 //output error messages about any remaining user labels
375 set<string>::iterator it;
376 bool needToRun = false;
377 for (it = userLabels.begin(); it != userLabels.end(); it++) {
378 m->mothurOut("Your file does not include the label " + *it);
379 if (processedLabels.count(lastLabel) != 1) {
380 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
383 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
387 if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
389 //run last label if you need to
390 if (needToRun == true) {
391 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
392 lookup = input->getSharedRAbundVectors(lastLabel);
394 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
395 vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
396 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
398 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
401 if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
403 //reset groups parameter
410 catch(exception& e) {
411 m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
415 //**********************************************************************************************************************
416 int HeatMapSimCommand::runCommandDist() {
419 vector< vector<double> > matrix;
420 vector<string> names;
423 //read distance file and create distance vector and names vector
424 if (format == "phylip") {
426 m->openInputFile(phylipfile, in);
430 in >> numSeqs >> name;
433 names.push_back(name);
435 //resize the matrix and fill with zeros
436 matrix.resize(numSeqs);
437 for(int i = 0; i < numSeqs; i++) {
438 matrix[i].resize(numSeqs, 0.0);
441 //determine if matrix is square or lower triangle
442 //if it is square read the distances for the first sequence
445 while((d=in.get()) != EOF){
447 //is d a number meaning its square
452 for(int i=0;i<numSeqs;i++){
458 //is d a line return meaning its lower triangle
465 //read rest of matrix
466 if (square == true) {
467 for(int i=1;i<numSeqs;i++){
469 names.push_back(name);
471 if (m->control_pressed) { return 0; }
473 for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
478 for(int i=1;i<numSeqs;i++){
480 names.push_back(name);
482 if (m->control_pressed) { return 0; }
484 for(int j=0;j<i;j++){
486 matrix[i][j] = dist; matrix[j][i] = dist;
494 NameAssignment* nameMap = new NameAssignment(namefile);
497 //put names in order in vector
498 for (int i = 0; i < nameMap->size(); i++) {
499 names.push_back(nameMap->get(i));
503 matrix.resize(nameMap->size());
504 for (int i = 0; i < nameMap->size(); i++) {
505 matrix[i].resize(nameMap->size(), 0.0);
509 string first, second;
511 m->openInputFile(columnfile, in);
514 in >> first >> second >> dist; m->gobble(in);
516 if (m->control_pressed) { return 0; }
518 map<string, int>::iterator itA = nameMap->find(first);
519 map<string, int>::iterator itB = nameMap->find(second);
521 if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); }
522 if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); }
525 matrix[itA->second][itB->second] = dist;
526 matrix[itB->second][itA->second] = dist;
534 string outputFileName = heatmap->getPic(matrix, names);
535 outputNames.push_back(outputFileName); //vector<vector<double>>, vector<string>
536 outputTypes["svg"].push_back(outputFileName);
540 catch(exception& e) {
541 m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
545 //**********************************************************************************************************************