5 * Created by Sarah Westcott on 3/25/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "heatmapcommand.h"
12 //**********************************************************************************************************************
13 vector<string> HeatMapCommand::setParameters(){
15 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
16 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
17 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
18 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
19 CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
20 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
21 CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "",false,false); parameters.push_back(pscale);
22 CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "",false,false); parameters.push_back(psorted);
23 CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnumotu);
24 CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
25 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
26 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
27 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
29 vector<string> myArray;
30 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
34 m->errorOut(e, "HeatMapCommand", "setParameters");
38 //**********************************************************************************************************************
39 string HeatMapCommand::getHelpString(){
41 string helpString = "";
42 helpString += "The heatmap.bin command parameters are shared, relabund, list, rabund, sabund, groups, sorted, scale, numotu, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
43 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
44 helpString += "The sorted parameter allows you to order the otus displayed, default=shared, meaning display the shared otus first. Other options for sorted are none, meaning the exact representation of your otus, \n";
45 helpString += "topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n";
46 helpString += "The scale parameter allows you to choose the range of color your bin information will be displayed with.\n";
47 helpString += "The numotu parameter allows you to display only the top N otus, by default all the otus are displayed. You could choose to look at the top 10, by setting numotu=10. The default for sorted is topotu when numotu is used.\n";
48 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 are also separated by dashes.\n";
49 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
50 helpString += "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n";
51 helpString += "Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n";
52 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
53 helpString += "The default value for scale is log10; your other options are log2 and linear.\n";
54 helpString += "The heatmap.bin command outputs a .svg file for each label you specify.\n";
55 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
59 m->errorOut(e, "HeatMapCommand", "getHelpString");
64 //**********************************************************************************************************************
65 HeatMapCommand::HeatMapCommand(){
67 abort = true; calledHelp = true;
69 vector<string> tempOutNames;
70 outputTypes["svg"] = tempOutNames;
73 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
77 //**********************************************************************************************************************
79 HeatMapCommand::HeatMapCommand(string option) {
81 abort = false; calledHelp = false;
84 //allow user to run help
85 if(option == "help") { help(); abort = true; calledHelp = true; }
86 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
89 vector<string> myArray = setParameters();
91 OptionParser parser(option);
92 map<string,string> parameters = parser.getParameters();
93 map<string,string>::iterator it;
95 ValidParameters validParameter;
97 //check to make sure all parameters are valid for command
98 for (it = parameters.begin(); it != parameters.end(); it++) {
99 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
102 //initialize outputTypes
103 vector<string> tempOutNames;
104 outputTypes["svg"] = tempOutNames;
106 //if the user changes the input directory command factory will send this info to us in the output parameter
107 string inputDir = validParameter.validFile(parameters, "inputdir", false);
108 if (inputDir == "not found"){ inputDir = ""; }
111 it = parameters.find("shared");
112 //user has given a template file
113 if(it != parameters.end()){
114 path = m->hasPath(it->second);
115 //if the user has not given a path then, add inputdir. else leave path alone.
116 if (path == "") { parameters["shared"] = inputDir + it->second; }
119 it = parameters.find("rabund");
120 //user has given a template file
121 if(it != parameters.end()){
122 path = m->hasPath(it->second);
123 //if the user has not given a path then, add inputdir. else leave path alone.
124 if (path == "") { parameters["rabund"] = inputDir + it->second; }
127 it = parameters.find("sabund");
128 //user has given a template file
129 if(it != parameters.end()){
130 path = m->hasPath(it->second);
131 //if the user has not given a path then, add inputdir. else leave path alone.
132 if (path == "") { parameters["sabund"] = inputDir + it->second; }
135 it = parameters.find("list");
136 //user has given a template file
137 if(it != parameters.end()){
138 path = m->hasPath(it->second);
139 //if the user has not given a path then, add inputdir. else leave path alone.
140 if (path == "") { parameters["list"] = inputDir + it->second; }
143 it = parameters.find("relabund");
144 //user has given a template file
145 if(it != parameters.end()){
146 path = m->hasPath(it->second);
147 //if the user has not given a path then, add inputdir. else leave path alone.
148 if (path == "") { parameters["relabund"] = inputDir + it->second; }
152 //check for required parameters
153 listfile = validParameter.validFile(parameters, "list", true);
154 if (listfile == "not open") { listfile = ""; abort = true; }
155 else if (listfile == "not found") { listfile = ""; }
156 else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
158 sabundfile = validParameter.validFile(parameters, "sabund", true);
159 if (sabundfile == "not open") { sabundfile = ""; abort = true; }
160 else if (sabundfile == "not found") { sabundfile = ""; }
161 else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
163 rabundfile = validParameter.validFile(parameters, "rabund", true);
164 if (rabundfile == "not open") { rabundfile = ""; abort = true; }
165 else if (rabundfile == "not found") { rabundfile = ""; }
166 else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
168 sharedfile = validParameter.validFile(parameters, "shared", true);
169 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
170 else if (sharedfile == "not found") { sharedfile = ""; }
171 else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
173 relabundfile = validParameter.validFile(parameters, "relabund", true);
174 if (relabundfile == "not open") { relabundfile = ""; abort = true; }
175 else if (relabundfile == "not found") { relabundfile = ""; }
176 else { format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
179 if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
180 //is there are current file available for any of these?
181 //give priority to shared, then list, then rabund, then sabund
182 //if there is a current shared file, use it
183 sharedfile = m->getSharedFile();
184 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
186 listfile = m->getListFile();
187 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
189 rabundfile = m->getRabundFile();
190 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
192 sabundfile = m->getSabundFile();
193 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
195 relabundfile = m->getRelAbundFile();
196 if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
198 m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
208 //if the user changes the output directory command factory will send this info to us in the output parameter
209 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
211 //check for optional parameter and set defaults
212 // ...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; }
221 groups = validParameter.validFile(parameters, "groups", false);
222 if (groups == "not found") { groups = ""; }
224 m->splitAtDash(groups, Groups);
225 m->setGroups(Groups);
228 string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; }
229 m->mothurConvert(temp, numOTU);
231 temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
232 m->mothurConvert(temp, fontSize);
234 sorted = validParameter.validFile(parameters, "sorted", false);
235 if (sorted == "not found") {
236 //if numOTU is used change default
237 if (numOTU != 0) { sorted = "topotu"; }
238 else { sorted = "shared"; }
241 scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
243 if ((sorted != "none") && (sorted != "shared") && (sorted != "topotu") && (sorted != "topgroup")) { m->mothurOut(sorted + " is not a valid sorting option. Sorted options are: none, shared, topotu, topgroup"); m->mothurOutEndLine(); abort=true; }
247 catch(exception& e) {
248 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
252 //**********************************************************************************************************************
254 int HeatMapCommand::execute(){
257 if (abort == true) { if (calledHelp) { return 0; } return 2; }
259 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
262 input = new InputData(inputfile, format);
264 if (format == "sharedfile") {
266 lookup = input->getSharedRAbundVectors();
267 lastLabel = lookup[0]->getLabel();
269 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
270 //you are using just a list file and have only one group
271 rabund = input->getRAbundVector();
272 lastLabel = rabund->getLabel();
273 }else if (format == "relabund") {
275 lookupFloat = input->getSharedRAbundFloatVectors();
276 lastLabel = lookupFloat[0]->getLabel();
279 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
280 set<string> processedLabels;
281 set<string> userLabels = labels;
283 if (format == "sharedfile") {
285 //as long as you are not at the end of the file or done wih the lines you want
286 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
287 if (m->control_pressed) {
288 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
289 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
291 delete input; delete heatmap; return 0;
294 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
296 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
297 string outputFileName = heatmap->getPic(lookup);
298 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
300 processedLabels.insert(lookup[0]->getLabel());
301 userLabels.erase(lookup[0]->getLabel());
304 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
305 string saveLabel = lookup[0]->getLabel();
307 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
309 lookup = input->getSharedRAbundVectors(lastLabel);
310 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
312 string outputFileName = heatmap->getPic(lookup);
313 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
315 processedLabels.insert(lookup[0]->getLabel());
316 userLabels.erase(lookup[0]->getLabel());
318 //restore real lastlabel to save below
319 lookup[0]->setLabel(saveLabel);
322 lastLabel = lookup[0]->getLabel();
323 //prevent memory leak
324 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
326 //get next line to process
327 lookup = input->getSharedRAbundVectors();
331 if (m->control_pressed) {
332 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
334 delete input; delete heatmap; return 0;
337 //output error messages about any remaining user labels
338 set<string>::iterator it;
339 bool needToRun = false;
340 for (it = userLabels.begin(); it != userLabels.end(); it++) {
341 m->mothurOut("Your file does not include the label " + *it);
342 if (processedLabels.count(lastLabel) != 1) {
343 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
346 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
350 //run last label if you need to
351 if (needToRun == true) {
352 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
353 lookup = input->getSharedRAbundVectors(lastLabel);
355 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
356 string outputFileName = heatmap->getPic(lookup);
357 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
358 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
361 //reset groups parameter
364 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
366 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
367 if (m->control_pressed) {
368 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
369 delete rabund; delete input; delete heatmap; return 0;
372 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
374 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
375 string outputFileName = heatmap->getPic(rabund);
376 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
378 processedLabels.insert(rabund->getLabel());
379 userLabels.erase(rabund->getLabel());
382 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
383 string saveLabel = rabund->getLabel();
386 rabund = input->getRAbundVector(lastLabel);
387 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
389 string outputFileName = heatmap->getPic(rabund);
390 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
392 processedLabels.insert(rabund->getLabel());
393 userLabels.erase(rabund->getLabel());
395 //restore real lastlabel to save below
396 rabund->setLabel(saveLabel);
401 lastLabel = rabund->getLabel();
403 rabund = input->getRAbundVector();
406 if (m->control_pressed) {
407 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
408 delete input; delete heatmap; return 0;
411 //output error messages about any remaining user labels
412 set<string>::iterator it;
413 bool needToRun = false;
414 for (it = userLabels.begin(); it != userLabels.end(); it++) {
415 m->mothurOut("Your file does not include the label " + *it);
416 if (processedLabels.count(lastLabel) != 1) {
417 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
420 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
424 //run last label if you need to
425 if (needToRun == true) {
427 if (rabund != NULL) { delete rabund; }
428 rabund = input->getRAbundVector(lastLabel);
429 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
431 string outputFileName = heatmap->getPic(rabund);
432 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
438 //as long as you are not at the end of the file or done wih the lines you want
439 while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
440 if (m->control_pressed) {
441 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
442 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
444 delete input; delete heatmap; return 0;
447 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
449 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
450 string outputFileName = heatmap->getPic(lookupFloat);
451 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
453 processedLabels.insert(lookupFloat[0]->getLabel());
454 userLabels.erase(lookupFloat[0]->getLabel());
457 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
458 string saveLabel = lookupFloat[0]->getLabel();
460 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
461 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
462 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
464 string outputFileName = heatmap->getPic(lookupFloat);
465 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
467 processedLabels.insert(lookupFloat[0]->getLabel());
468 userLabels.erase(lookupFloat[0]->getLabel());
470 //restore real lastlabel to save below
471 lookupFloat[0]->setLabel(saveLabel);
474 lastLabel = lookupFloat[0]->getLabel();
475 //prevent memory leak
476 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; }
478 //get next line to process
479 lookupFloat = input->getSharedRAbundFloatVectors();
483 if (m->control_pressed) {
484 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
486 delete input; delete heatmap; return 0;
489 //output error messages about any remaining user labels
490 set<string>::iterator it;
491 bool needToRun = false;
492 for (it = userLabels.begin(); it != userLabels.end(); it++) {
493 m->mothurOut("Your file does not include the label " + *it);
494 if (processedLabels.count(lastLabel) != 1) {
495 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
498 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
502 //run last label if you need to
503 if (needToRun == true) {
504 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
505 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
507 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
508 string outputFileName = heatmap->getPic(lookupFloat);
509 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
510 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
513 //reset groups parameter
521 if (m->control_pressed) {
522 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); return 0;
525 m->mothurOutEndLine();
526 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
527 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
528 m->mothurOutEndLine();
532 catch(exception& e) {
533 m->errorOut(e, "HeatMapCommand", "execute");
538 //**********************************************************************************************************************