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","svg",false,false,true); parameters.push_back(plist);
16 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
17 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
18 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
19 CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",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 string HeatMapCommand::getOutputPattern(string type) {
69 if (type == "svg") { pattern = "[filename],svg"; }
70 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
75 m->errorOut(e, "HeatMapCommand", "getOutputPattern");
80 //**********************************************************************************************************************
81 HeatMapCommand::HeatMapCommand(){
83 abort = true; calledHelp = true;
85 vector<string> tempOutNames;
86 outputTypes["svg"] = tempOutNames;
89 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
93 //**********************************************************************************************************************
95 HeatMapCommand::HeatMapCommand(string option) {
97 abort = false; calledHelp = false;
100 //allow user to run help
101 if(option == "help") { help(); abort = true; calledHelp = true; }
102 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
105 vector<string> myArray = setParameters();
107 OptionParser parser(option);
108 map<string,string> parameters = parser.getParameters();
109 map<string,string>::iterator it;
111 ValidParameters validParameter;
113 //check to make sure all parameters are valid for command
114 for (it = parameters.begin(); it != parameters.end(); it++) {
115 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
118 //initialize outputTypes
119 vector<string> tempOutNames;
120 outputTypes["svg"] = tempOutNames;
122 //if the user changes the input directory command factory will send this info to us in the output parameter
123 string inputDir = validParameter.validFile(parameters, "inputdir", false);
124 if (inputDir == "not found"){ inputDir = ""; }
127 it = parameters.find("shared");
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["shared"] = inputDir + it->second; }
135 it = parameters.find("rabund");
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["rabund"] = inputDir + it->second; }
143 it = parameters.find("sabund");
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["sabund"] = inputDir + it->second; }
151 it = parameters.find("list");
152 //user has given a template file
153 if(it != parameters.end()){
154 path = m->hasPath(it->second);
155 //if the user has not given a path then, add inputdir. else leave path alone.
156 if (path == "") { parameters["list"] = inputDir + it->second; }
159 it = parameters.find("relabund");
160 //user has given a template file
161 if(it != parameters.end()){
162 path = m->hasPath(it->second);
163 //if the user has not given a path then, add inputdir. else leave path alone.
164 if (path == "") { parameters["relabund"] = inputDir + it->second; }
168 //check for required parameters
169 listfile = validParameter.validFile(parameters, "list", true);
170 if (listfile == "not open") { abort = true; }
171 else if (listfile == "not found") { listfile = ""; }
172 else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
174 sabundfile = validParameter.validFile(parameters, "sabund", true);
175 if (sabundfile == "not open") { abort = true; }
176 else if (sabundfile == "not found") { sabundfile = ""; }
177 else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
179 rabundfile = validParameter.validFile(parameters, "rabund", true);
180 if (rabundfile == "not open") { abort = true; }
181 else if (rabundfile == "not found") { rabundfile = ""; }
182 else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
184 sharedfile = validParameter.validFile(parameters, "shared", true);
185 if (sharedfile == "not open") { abort = true; }
186 else if (sharedfile == "not found") { sharedfile = ""; }
187 else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
189 relabundfile = validParameter.validFile(parameters, "relabund", true);
190 if (relabundfile == "not open") { abort = true; }
191 else if (relabundfile == "not found") { relabundfile = ""; }
192 else { format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
195 if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
196 //is there are current file available for any of these?
197 //give priority to shared, then list, then rabund, then sabund
198 //if there is a current shared file, use it
199 sharedfile = m->getSharedFile();
200 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
202 listfile = m->getListFile();
203 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
205 rabundfile = m->getRabundFile();
206 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
208 sabundfile = m->getSabundFile();
209 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
211 relabundfile = m->getRelAbundFile();
212 if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
214 m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
224 //if the user changes the output directory command factory will send this info to us in the output parameter
225 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
227 //check for optional parameter and set defaults
228 // ...at some point should added some additional type checking...
229 label = validParameter.validFile(parameters, "label", false);
230 if (label == "not found") { label = ""; }
232 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
233 else { allLines = 1; }
237 groups = validParameter.validFile(parameters, "groups", false);
238 if (groups == "not found") { groups = ""; }
240 m->splitAtDash(groups, Groups);
241 m->setGroups(Groups);
244 string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; }
245 m->mothurConvert(temp, numOTU);
247 temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
248 m->mothurConvert(temp, fontSize);
250 sorted = validParameter.validFile(parameters, "sorted", false);
251 if (sorted == "not found") {
252 //if numOTU is used change default
253 if (numOTU != 0) { sorted = "topotu"; }
254 else { sorted = "shared"; }
257 scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
259 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; }
263 catch(exception& e) {
264 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
268 //**********************************************************************************************************************
270 int HeatMapCommand::execute(){
273 if (abort == true) { if (calledHelp) { return 0; } return 2; }
275 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
278 input = new InputData(inputfile, format);
280 if (format == "sharedfile") {
282 lookup = input->getSharedRAbundVectors();
283 lastLabel = lookup[0]->getLabel();
285 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
286 //you are using just a list file and have only one group
287 rabund = input->getRAbundVector();
288 lastLabel = rabund->getLabel();
289 }else if (format == "relabund") {
291 lookupFloat = input->getSharedRAbundFloatVectors();
292 lastLabel = lookupFloat[0]->getLabel();
295 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
296 set<string> processedLabels;
297 set<string> userLabels = labels;
299 if (format == "sharedfile") {
301 //as long as you are not at the end of the file or done wih the lines you want
302 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
303 if (m->control_pressed) {
304 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
305 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
307 delete input; delete heatmap; return 0;
310 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
312 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
313 string outputFileName = heatmap->getPic(lookup);
314 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
316 processedLabels.insert(lookup[0]->getLabel());
317 userLabels.erase(lookup[0]->getLabel());
320 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
321 string saveLabel = lookup[0]->getLabel();
323 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
325 lookup = input->getSharedRAbundVectors(lastLabel);
326 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
328 string outputFileName = heatmap->getPic(lookup);
329 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
331 processedLabels.insert(lookup[0]->getLabel());
332 userLabels.erase(lookup[0]->getLabel());
334 //restore real lastlabel to save below
335 lookup[0]->setLabel(saveLabel);
338 lastLabel = lookup[0]->getLabel();
339 //prevent memory leak
340 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
342 //get next line to process
343 lookup = input->getSharedRAbundVectors();
347 if (m->control_pressed) {
348 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
350 delete input; delete heatmap; return 0;
353 //output error messages about any remaining user labels
354 set<string>::iterator it;
355 bool needToRun = false;
356 for (it = userLabels.begin(); it != userLabels.end(); it++) {
357 m->mothurOut("Your file does not include the label " + *it);
358 if (processedLabels.count(lastLabel) != 1) {
359 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
362 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
366 //run last label if you need to
367 if (needToRun == true) {
368 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
369 lookup = input->getSharedRAbundVectors(lastLabel);
371 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
372 string outputFileName = heatmap->getPic(lookup);
373 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
374 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
377 //reset groups parameter
380 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
382 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
383 if (m->control_pressed) {
384 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
385 delete rabund; delete input; delete heatmap; return 0;
388 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
390 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
391 string outputFileName = heatmap->getPic(rabund);
392 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
394 processedLabels.insert(rabund->getLabel());
395 userLabels.erase(rabund->getLabel());
398 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
399 string saveLabel = rabund->getLabel();
402 rabund = input->getRAbundVector(lastLabel);
403 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
405 string outputFileName = heatmap->getPic(rabund);
406 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
408 processedLabels.insert(rabund->getLabel());
409 userLabels.erase(rabund->getLabel());
411 //restore real lastlabel to save below
412 rabund->setLabel(saveLabel);
417 lastLabel = rabund->getLabel();
419 rabund = input->getRAbundVector();
422 if (m->control_pressed) {
423 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
424 delete input; delete heatmap; return 0;
427 //output error messages about any remaining user labels
428 set<string>::iterator it;
429 bool needToRun = false;
430 for (it = userLabels.begin(); it != userLabels.end(); it++) {
431 m->mothurOut("Your file does not include the label " + *it);
432 if (processedLabels.count(lastLabel) != 1) {
433 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
436 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
440 //run last label if you need to
441 if (needToRun == true) {
443 if (rabund != NULL) { delete rabund; }
444 rabund = input->getRAbundVector(lastLabel);
445 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
447 string outputFileName = heatmap->getPic(rabund);
448 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
454 //as long as you are not at the end of the file or done wih the lines you want
455 while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
456 if (m->control_pressed) {
457 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
458 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
460 delete input; delete heatmap; return 0;
463 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
465 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
466 string outputFileName = heatmap->getPic(lookupFloat);
467 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
469 processedLabels.insert(lookupFloat[0]->getLabel());
470 userLabels.erase(lookupFloat[0]->getLabel());
473 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
474 string saveLabel = lookupFloat[0]->getLabel();
476 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
477 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
478 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
480 string outputFileName = heatmap->getPic(lookupFloat);
481 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
483 processedLabels.insert(lookupFloat[0]->getLabel());
484 userLabels.erase(lookupFloat[0]->getLabel());
486 //restore real lastlabel to save below
487 lookupFloat[0]->setLabel(saveLabel);
490 lastLabel = lookupFloat[0]->getLabel();
491 //prevent memory leak
492 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; }
494 //get next line to process
495 lookupFloat = input->getSharedRAbundFloatVectors();
499 if (m->control_pressed) {
500 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
502 delete input; delete heatmap; return 0;
505 //output error messages about any remaining user labels
506 set<string>::iterator it;
507 bool needToRun = false;
508 for (it = userLabels.begin(); it != userLabels.end(); it++) {
509 m->mothurOut("Your file does not include the label " + *it);
510 if (processedLabels.count(lastLabel) != 1) {
511 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
514 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
518 //run last label if you need to
519 if (needToRun == true) {
520 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
521 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
523 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
524 string outputFileName = heatmap->getPic(lookupFloat);
525 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
526 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
529 //reset groups parameter
537 if (m->control_pressed) {
538 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); return 0;
541 m->mothurOutEndLine();
542 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
543 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
544 m->mothurOutEndLine();
548 catch(exception& e) {
549 m->errorOut(e, "HeatMapCommand", "execute");
554 //**********************************************************************************************************************