heatmapcommand.cpp

   1 /*
   2  *  heatmapcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/25/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapcommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14
  15 HeatMapCommand::HeatMapCommand(string option) {
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18                 abort = false;
  19                 allLines = 1;
  20                 labels.clear();
  21
  22                 //allow user to run help
  23                 if(option == "help") { help(); abort = true; }
  24
  25                 else {
  26                         //valid paramters for this command
  27                         string AlignArray[] =  {"groups","label","sorted","scale","outputdir","inputdir"};
  28                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  29
  30                         OptionParser parser(option);
  31                         map<string,string> parameters = parser.getParameters();
  32
  33                         ValidParameters validParameter;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         //if the user changes the output directory command factory will send this info to us in the output parameter
  41                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  42                                 outputDir = "";
  43                                 outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  44                         }
  45
  46                         //make sure the user has already run the read.otu command
  47                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "")) {
  48                                  m->mothurOut("You must read a list, rabund, sabund, or a list and a group, or a shared before you can use the heatmap.bin command."); m->mothurOutEndLine(); abort = true;
  49                         }
  50
  51                         //check for optional parameter and set defaults
  52                         // ...at some point should added some additional type checking...
  53                         label = validParameter.validFile(parameters, "label", false);
  54                         if (label == "not found") { label = ""; }
  55                         else {
  56                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  57                                 else { allLines = 1;  }
  58                         }
  59
  60                         //if the user has not specified any labels use the ones from read.otu
  61                         if (label == "") {
  62                                 allLines = globaldata->allLines;
  63                                 labels = globaldata->labels;
  64                         }
  65
  66                         groups = validParameter.validFile(parameters, "groups", false);
  67                         if (groups == "not found") { groups = ""; }
  68                         else {
  69                                 splitAtDash(groups, Groups);
  70                                 globaldata->Groups = Groups;
  71                         }
  72
  73                         sorted = validParameter.validFile(parameters, "sorted", false);                 if (sorted == "not found") { sorted = "T"; }
  74
  75                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
  76
  77                 }
  78
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
  82                 exit(1);
  83         }
  84 }
  85
  86 //**********************************************************************************************************************
  87
  88 void HeatMapCommand::help(){
  89         try {
  90                 m->mothurOut("The heatmap.bin command can only be executed after a successful read.otu command.\n");
  91                 m->mothurOut("The heatmap.bin command parameters are groups, sorted, scale label.  No parameters are required.\n");
  92                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
  93                 m->mothurOut("The sorted parameter allows you to choose to see the file with the shared otus at the top or the otus in the order they appear in your input file. \n");
  94                 m->mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\n");
  95                 m->mothurOut("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");
  96                 m->mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n");
  97                 m->mothurOut("Example heatmap.bin(groups=A-B-C, sorted=F, scale=log10).\n");
  98                 m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
  99                 m->mothurOut("The default value for sorted is T meaning you want the shared otus on top, you may change it to F meaning the exact representation of your input file.\n");
 100                 m->mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
 101                 m->mothurOut("The heatmap.bin command outputs a .svg file for each label you specify.\n");
 102                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 103
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "HeatMapCommand", "help");
 107                 exit(1);
 108         }
 109 }
 110
 111 //**********************************************************************************************************************
 112
 113 HeatMapCommand::~HeatMapCommand(){
 114 }
 115
 116 //**********************************************************************************************************************
 117
 118 int HeatMapCommand::execute(){
 119         try {
 120
 121                 if (abort == true) { return 0; }
 122
 123                 heatmap = new HeatMap(sorted, scale, outputDir);
 124                 format = globaldata->getFormat();
 125
 126                 string lastLabel;
 127
 128                 read = new ReadOTUFile(globaldata->inputFileName);
 129                 read->read(&*globaldata);
 130                 input = globaldata->ginput;
 131
 132                 if (format == "sharedfile") {
 133                         //you have groups
 134                         lookup = input->getSharedRAbundVectors();
 135                         lastLabel = lookup[0]->getLabel();
 136
 137                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 138                         //you are using just a list file and have only one group
 139                         rabund = globaldata->rabund;
 140                         lastLabel = rabund->getLabel();
 141                 }
 142
 143                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 144                 set<string> processedLabels;
 145                 set<string> userLabels = labels;
 146
 147                 if ((format != "list") && (format != "rabund") && (format != "sabund")) {
 148
 149                         //as long as you are not at the end of the file or done wih the lines you want
 150                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 151                                 if (m->control_pressed) {
 152                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 153                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 154                                         globaldata->Groups.clear();
 155                                         delete read; delete heatmap; return 0;
 156                                 }
 157
 158                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 159
 160                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 161                                         outputNames.push_back(heatmap->getPic(lookup));
 162
 163                                         processedLabels.insert(lookup[0]->getLabel());
 164                                         userLabels.erase(lookup[0]->getLabel());
 165                                 }
 166
 167                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 168                                         string saveLabel = lookup[0]->getLabel();
 169
 170                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 171                                         lookup = input->getSharedRAbundVectors(lastLabel);
 172                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 173
 174                                         outputNames.push_back(heatmap->getPic(lookup));
 175
 176                                         processedLabels.insert(lookup[0]->getLabel());
 177                                         userLabels.erase(lookup[0]->getLabel());
 178
 179                                         //restore real lastlabel to save below
 180                                         lookup[0]->setLabel(saveLabel);
 181                                 }
 182
 183                                 lastLabel = lookup[0]->getLabel();
 184                                 //prevent memory leak
 185                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 186
 187                                 //get next line to process
 188                                 lookup = input->getSharedRAbundVectors();
 189                         }
 190
 191
 192                         if (m->control_pressed) {
 193                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 194                                 globaldata->Groups.clear();
 195                                 delete read; delete heatmap; return 0;
 196                         }
 197
 198                         //output error messages about any remaining user labels
 199                         set<string>::iterator it;
 200                         bool needToRun = false;
 201                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 202                                 m->mothurOut("Your file does not include the label " + *it);
 203                                 if (processedLabels.count(lastLabel) != 1) {
 204                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 205                                         needToRun = true;
 206                                 }else {
 207                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 208                                 }
 209                         }
 210
 211                         //run last label if you need to
 212                         if (needToRun == true)  {
 213                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 214                                 lookup = input->getSharedRAbundVectors(lastLabel);
 215
 216                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 217                                 outputNames.push_back(heatmap->getPic(lookup));
 218                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 219                         }
 220
 221                         //reset groups parameter
 222                         globaldata->Groups.clear();
 223
 224                 }else{
 225
 226                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 227                                 if (m->control_pressed) {
 228                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 229                                         delete rabund;  delete read; delete heatmap; return 0;
 230                                 }
 231
 232                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 233
 234                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 235                                         outputNames.push_back(heatmap->getPic(rabund));
 236
 237                                         processedLabels.insert(rabund->getLabel());
 238                                         userLabels.erase(rabund->getLabel());
 239                                 }
 240
 241                                 if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 242                                         string saveLabel = rabund->getLabel();
 243
 244                                         delete rabund;
 245                                         rabund = input->getRAbundVector(lastLabel);
 246                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 247
 248                                         outputNames.push_back(heatmap->getPic(rabund));
 249
 250                                         processedLabels.insert(rabund->getLabel());
 251                                         userLabels.erase(rabund->getLabel());
 252
 253                                         //restore real lastlabel to save below
 254                                         rabund->setLabel(saveLabel);
 255                                 }
 256
 257
 258
 259                                 lastLabel = rabund->getLabel();
 260                                 delete rabund;
 261                                 rabund = input->getRAbundVector();
 262                         }
 263
 264                         if (m->control_pressed) {
 265                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 266                                 delete read; delete heatmap; return 0;
 267                         }
 268
 269                         //output error messages about any remaining user labels
 270                         set<string>::iterator it;
 271                         bool needToRun = false;
 272                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 273                                 m->mothurOut("Your file does not include the label " + *it);
 274                                 if (processedLabels.count(lastLabel) != 1) {
 275                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 276                                         needToRun = true;
 277                                 }else {
 278                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 279                                 }
 280                         }
 281
 282                         //run last label if you need to
 283                         if (needToRun == true)  {
 284
 285                                 if (rabund != NULL) {   delete rabund;  }
 286                                 rabund = input->getRAbundVector(lastLabel);
 287                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 288
 289                                 outputNames.push_back(heatmap->getPic(rabund));
 290                                 delete rabund; globaldata->rabund = NULL;
 291                         }
 292
 293                 }
 294
 295                 globaldata->rabund = NULL;
 296                 delete input; globaldata->ginput = NULL;
 297
 298                 if (m->control_pressed) {
 299                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 300                         delete read; delete heatmap; return 0;
 301                 }
 302
 303                 m->mothurOutEndLine();
 304                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 305                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 306                 m->mothurOutEndLine();
 307
 308                 delete read;
 309                 delete heatmap;
 310
 311                 return 0;
 312         }
 313         catch(exception& e) {
 314                 m->errorOut(e, "HeatMapCommand", "execute");
 315                 exit(1);
 316         }
 317 }
 318
 319 //**********************************************************************************************************************
 320
 321