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; }
88 vector<string> myArray = setParameters();
90 OptionParser parser(option);
91 map<string,string> parameters = parser.getParameters();
92 map<string,string>::iterator it;
94 ValidParameters validParameter;
96 //check to make sure all parameters are valid for command
97 for (it = parameters.begin(); it != parameters.end(); it++) {
98 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
101 //initialize outputTypes
102 vector<string> tempOutNames;
103 outputTypes["svg"] = tempOutNames;
105 //if the user changes the input directory command factory will send this info to us in the output parameter
106 string inputDir = validParameter.validFile(parameters, "inputdir", false);
107 if (inputDir == "not found"){ inputDir = ""; }
110 it = parameters.find("shared");
111 //user has given a template file
112 if(it != parameters.end()){
113 path = m->hasPath(it->second);
114 //if the user has not given a path then, add inputdir. else leave path alone.
115 if (path == "") { parameters["shared"] = inputDir + it->second; }
118 it = parameters.find("rabund");
119 //user has given a template file
120 if(it != parameters.end()){
121 path = m->hasPath(it->second);
122 //if the user has not given a path then, add inputdir. else leave path alone.
123 if (path == "") { parameters["rabund"] = inputDir + it->second; }
126 it = parameters.find("sabund");
127 //user has given a template file
128 if(it != parameters.end()){
129 path = m->hasPath(it->second);
130 //if the user has not given a path then, add inputdir. else leave path alone.
131 if (path == "") { parameters["sabund"] = inputDir + it->second; }
134 it = parameters.find("list");
135 //user has given a template file
136 if(it != parameters.end()){
137 path = m->hasPath(it->second);
138 //if the user has not given a path then, add inputdir. else leave path alone.
139 if (path == "") { parameters["list"] = inputDir + it->second; }
142 it = parameters.find("relabund");
143 //user has given a template file
144 if(it != parameters.end()){
145 path = m->hasPath(it->second);
146 //if the user has not given a path then, add inputdir. else leave path alone.
147 if (path == "") { parameters["relabund"] = inputDir + it->second; }
151 //check for required parameters
152 listfile = validParameter.validFile(parameters, "list", true);
153 if (listfile == "not open") { listfile = ""; abort = true; }
154 else if (listfile == "not found") { listfile = ""; }
155 else { format = "list"; inputfile = listfile; }
157 sabundfile = validParameter.validFile(parameters, "sabund", true);
158 if (sabundfile == "not open") { sabundfile = ""; abort = true; }
159 else if (sabundfile == "not found") { sabundfile = ""; }
160 else { format = "sabund"; inputfile = sabundfile; }
162 rabundfile = validParameter.validFile(parameters, "rabund", true);
163 if (rabundfile == "not open") { rabundfile = ""; abort = true; }
164 else if (rabundfile == "not found") { rabundfile = ""; }
165 else { format = "rabund"; inputfile = rabundfile; }
167 sharedfile = validParameter.validFile(parameters, "shared", true);
168 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
169 else if (sharedfile == "not found") { sharedfile = ""; }
170 else { format = "sharedfile"; inputfile = sharedfile; }
172 relabundfile = validParameter.validFile(parameters, "relabund", true);
173 if (relabundfile == "not open") { relabundfile = ""; abort = true; }
174 else if (relabundfile == "not found") { relabundfile = ""; }
175 else { format = "relabund"; inputfile = relabundfile; }
178 if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
179 //is there are current file available for any of these?
180 //give priority to shared, then list, then rabund, then sabund
181 //if there is a current shared file, use it
182 sharedfile = m->getSharedFile();
183 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
185 listfile = m->getListFile();
186 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
188 rabundfile = m->getRabundFile();
189 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
191 sabundfile = m->getSabundFile();
192 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
194 relabundfile = m->getRelAbundFile();
195 if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
197 m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
207 //if the user changes the output directory command factory will send this info to us in the output parameter
208 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
210 //check for optional parameter and set defaults
211 // ...at some point should added some additional type checking...
212 label = validParameter.validFile(parameters, "label", false);
213 if (label == "not found") { label = ""; }
215 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
216 else { allLines = 1; }
220 groups = validParameter.validFile(parameters, "groups", false);
221 if (groups == "not found") { groups = ""; }
223 m->splitAtDash(groups, Groups);
227 string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; }
228 convert(temp, numOTU);
230 temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
231 convert(temp, fontSize);
233 sorted = validParameter.validFile(parameters, "sorted", false);
234 if (sorted == "not found") {
235 //if numOTU is used change default
236 if (numOTU != 0) { sorted = "topotu"; }
237 else { sorted = "shared"; }
240 scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
242 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; }
246 catch(exception& e) {
247 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
251 //**********************************************************************************************************************
253 int HeatMapCommand::execute(){
256 if (abort == true) { if (calledHelp) { return 0; } return 2; }
258 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
261 input = new InputData(inputfile, format);
263 if (format == "sharedfile") {
265 lookup = input->getSharedRAbundVectors();
266 lastLabel = lookup[0]->getLabel();
268 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
269 //you are using just a list file and have only one group
270 rabund = input->getRAbundVector();
271 lastLabel = rabund->getLabel();
272 }else if (format == "relabund") {
274 lookupFloat = input->getSharedRAbundFloatVectors();
275 lastLabel = lookupFloat[0]->getLabel();
278 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
279 set<string> processedLabels;
280 set<string> userLabels = labels;
282 if (format == "sharedfile") {
284 //as long as you are not at the end of the file or done wih the lines you want
285 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
286 if (m->control_pressed) {
287 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
288 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
290 delete input; delete heatmap; return 0;
293 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
295 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
296 string outputFileName = heatmap->getPic(lookup);
297 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
299 processedLabels.insert(lookup[0]->getLabel());
300 userLabels.erase(lookup[0]->getLabel());
303 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
304 string saveLabel = lookup[0]->getLabel();
306 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
308 lookup = input->getSharedRAbundVectors(lastLabel);
309 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
311 string outputFileName = heatmap->getPic(lookup);
312 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
314 processedLabels.insert(lookup[0]->getLabel());
315 userLabels.erase(lookup[0]->getLabel());
317 //restore real lastlabel to save below
318 lookup[0]->setLabel(saveLabel);
321 lastLabel = lookup[0]->getLabel();
322 //prevent memory leak
323 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
325 //get next line to process
326 lookup = input->getSharedRAbundVectors();
330 if (m->control_pressed) {
331 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
333 delete input; delete heatmap; return 0;
336 //output error messages about any remaining user labels
337 set<string>::iterator it;
338 bool needToRun = false;
339 for (it = userLabels.begin(); it != userLabels.end(); it++) {
340 m->mothurOut("Your file does not include the label " + *it);
341 if (processedLabels.count(lastLabel) != 1) {
342 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
345 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
349 //run last label if you need to
350 if (needToRun == true) {
351 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
352 lookup = input->getSharedRAbundVectors(lastLabel);
354 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
355 string outputFileName = heatmap->getPic(lookup);
356 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
357 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
360 //reset groups parameter
363 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
365 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
366 if (m->control_pressed) {
367 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
368 delete rabund; delete input; delete heatmap; return 0;
371 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
373 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
374 string outputFileName = heatmap->getPic(rabund);
375 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
377 processedLabels.insert(rabund->getLabel());
378 userLabels.erase(rabund->getLabel());
381 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
382 string saveLabel = rabund->getLabel();
385 rabund = input->getRAbundVector(lastLabel);
386 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
388 string outputFileName = heatmap->getPic(rabund);
389 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
391 processedLabels.insert(rabund->getLabel());
392 userLabels.erase(rabund->getLabel());
394 //restore real lastlabel to save below
395 rabund->setLabel(saveLabel);
400 lastLabel = rabund->getLabel();
402 rabund = input->getRAbundVector();
405 if (m->control_pressed) {
406 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
407 delete input; delete heatmap; return 0;
410 //output error messages about any remaining user labels
411 set<string>::iterator it;
412 bool needToRun = false;
413 for (it = userLabels.begin(); it != userLabels.end(); it++) {
414 m->mothurOut("Your file does not include the label " + *it);
415 if (processedLabels.count(lastLabel) != 1) {
416 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
419 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
423 //run last label if you need to
424 if (needToRun == true) {
426 if (rabund != NULL) { delete rabund; }
427 rabund = input->getRAbundVector(lastLabel);
428 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
430 string outputFileName = heatmap->getPic(rabund);
431 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
437 //as long as you are not at the end of the file or done wih the lines you want
438 while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
439 if (m->control_pressed) {
440 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
441 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
443 delete input; delete heatmap; return 0;
446 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
448 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
449 string outputFileName = heatmap->getPic(lookupFloat);
450 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
452 processedLabels.insert(lookupFloat[0]->getLabel());
453 userLabels.erase(lookupFloat[0]->getLabel());
456 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
457 string saveLabel = lookupFloat[0]->getLabel();
459 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
460 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
461 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
463 string outputFileName = heatmap->getPic(lookupFloat);
464 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
466 processedLabels.insert(lookupFloat[0]->getLabel());
467 userLabels.erase(lookupFloat[0]->getLabel());
469 //restore real lastlabel to save below
470 lookupFloat[0]->setLabel(saveLabel);
473 lastLabel = lookupFloat[0]->getLabel();
474 //prevent memory leak
475 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; }
477 //get next line to process
478 lookupFloat = input->getSharedRAbundFloatVectors();
482 if (m->control_pressed) {
483 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear();
485 delete input; delete heatmap; return 0;
488 //output error messages about any remaining user labels
489 set<string>::iterator it;
490 bool needToRun = false;
491 for (it = userLabels.begin(); it != userLabels.end(); it++) {
492 m->mothurOut("Your file does not include the label " + *it);
493 if (processedLabels.count(lastLabel) != 1) {
494 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
497 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
501 //run last label if you need to
502 if (needToRun == true) {
503 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
504 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
506 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
507 string outputFileName = heatmap->getPic(lookupFloat);
508 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
509 for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
512 //reset groups parameter
520 if (m->control_pressed) {
521 for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } } outputTypes.clear(); return 0;
524 m->mothurOutEndLine();
525 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
526 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
527 m->mothurOutEndLine();
531 catch(exception& e) {
532 m->errorOut(e, "HeatMapCommand", "execute");
537 //**********************************************************************************************************************