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","fontsize","numotu","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                         string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
  74                         convert(temp, numOTU);
  75
  76                         temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
  77                         convert(temp, fontSize);
  78
  79                         sorted = validParameter.validFile(parameters, "sorted", false);
  80                         if (sorted == "not found") {
  81                                 //if numOTU is used change default
  82                                 if (numOTU != 0) { sorted = "topotu"; }
  83                                 else { sorted = "shared"; }
  84                         }
  85
  86                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
  87
  88                         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;  }
  89                 }
  90
  91         }
  92         catch(exception& e) {
  93                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
  94                 exit(1);
  95         }
  96 }
  97
  98 //**********************************************************************************************************************
  99
 100 void HeatMapCommand::help(){
 101         try {
 102                 m->mothurOut("The heatmap.bin command can only be executed after a successful read.otu command.\n");
 103                 m->mothurOut("The heatmap.bin command parameters are groups, sorted, scale, numotu, fontsize and label.  No parameters are required.\n");
 104                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
 105                 m->mothurOut("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");
 106                 m->mothurOut("topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n");
 107                 m->mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\n");
 108                 m->mothurOut("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");
 109                 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");
 110                 m->mothurOut("The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n");
 111                 m->mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n");
 112                 m->mothurOut("Example heatmap.bin(groups=A-B-C, sorted=F, scale=log10).\n");
 113                 m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
 114                 m->mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
 115                 m->mothurOut("The heatmap.bin command outputs a .svg file for each label you specify.\n");
 116                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 117
 118         }
 119         catch(exception& e) {
 120                 m->errorOut(e, "HeatMapCommand", "help");
 121                 exit(1);
 122         }
 123 }
 124
 125 //**********************************************************************************************************************
 126
 127 HeatMapCommand::~HeatMapCommand(){
 128 }
 129
 130 //**********************************************************************************************************************
 131
 132 int HeatMapCommand::execute(){
 133         try {
 134
 135                 if (abort == true) { return 0; }
 136
 137                 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir);
 138                 format = globaldata->getFormat();
 139
 140                 string lastLabel;
 141
 142                 read = new ReadOTUFile(globaldata->inputFileName);
 143                 read->read(&*globaldata);
 144                 input = globaldata->ginput;
 145
 146                 if (format == "sharedfile") {
 147                         //you have groups
 148                         lookup = input->getSharedRAbundVectors();
 149                         lastLabel = lookup[0]->getLabel();
 150
 151                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 152                         //you are using just a list file and have only one group
 153                         rabund = globaldata->rabund;
 154                         lastLabel = rabund->getLabel();
 155                 }
 156
 157                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 158                 set<string> processedLabels;
 159                 set<string> userLabels = labels;
 160
 161                 if ((format != "list") && (format != "rabund") && (format != "sabund")) {
 162
 163                         //as long as you are not at the end of the file or done wih the lines you want
 164                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 165                                 if (m->control_pressed) {
 166                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 167                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 168                                         globaldata->Groups.clear();
 169                                         delete read; delete heatmap; return 0;
 170                                 }
 171
 172                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 173
 174                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 175                                         outputNames.push_back(heatmap->getPic(lookup));
 176
 177                                         processedLabels.insert(lookup[0]->getLabel());
 178                                         userLabels.erase(lookup[0]->getLabel());
 179                                 }
 180
 181                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 182                                         string saveLabel = lookup[0]->getLabel();
 183
 184                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 185                                         lookup = input->getSharedRAbundVectors(lastLabel);
 186                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 187
 188                                         outputNames.push_back(heatmap->getPic(lookup));
 189
 190                                         processedLabels.insert(lookup[0]->getLabel());
 191                                         userLabels.erase(lookup[0]->getLabel());
 192
 193                                         //restore real lastlabel to save below
 194                                         lookup[0]->setLabel(saveLabel);
 195                                 }
 196
 197                                 lastLabel = lookup[0]->getLabel();
 198                                 //prevent memory leak
 199                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 200
 201                                 //get next line to process
 202                                 lookup = input->getSharedRAbundVectors();
 203                         }
 204
 205
 206                         if (m->control_pressed) {
 207                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 208                                 globaldata->Groups.clear();
 209                                 delete read; delete heatmap; return 0;
 210                         }
 211
 212                         //output error messages about any remaining user labels
 213                         set<string>::iterator it;
 214                         bool needToRun = false;
 215                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 216                                 m->mothurOut("Your file does not include the label " + *it);
 217                                 if (processedLabels.count(lastLabel) != 1) {
 218                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 219                                         needToRun = true;
 220                                 }else {
 221                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 222                                 }
 223                         }
 224
 225                         //run last label if you need to
 226                         if (needToRun == true)  {
 227                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 228                                 lookup = input->getSharedRAbundVectors(lastLabel);
 229
 230                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 231                                 outputNames.push_back(heatmap->getPic(lookup));
 232                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 233                         }
 234
 235                         //reset groups parameter
 236                         globaldata->Groups.clear();
 237
 238                 }else{
 239
 240                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 241                                 if (m->control_pressed) {
 242                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 243                                         delete rabund;  delete read; delete heatmap; return 0;
 244                                 }
 245
 246                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 247
 248                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 249                                         outputNames.push_back(heatmap->getPic(rabund));
 250
 251                                         processedLabels.insert(rabund->getLabel());
 252                                         userLabels.erase(rabund->getLabel());
 253                                 }
 254
 255                                 if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 256                                         string saveLabel = rabund->getLabel();
 257
 258                                         delete rabund;
 259                                         rabund = input->getRAbundVector(lastLabel);
 260                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 261
 262                                         outputNames.push_back(heatmap->getPic(rabund));
 263
 264                                         processedLabels.insert(rabund->getLabel());
 265                                         userLabels.erase(rabund->getLabel());
 266
 267                                         //restore real lastlabel to save below
 268                                         rabund->setLabel(saveLabel);
 269                                 }
 270
 271
 272
 273                                 lastLabel = rabund->getLabel();
 274                                 delete rabund;
 275                                 rabund = input->getRAbundVector();
 276                         }
 277
 278                         if (m->control_pressed) {
 279                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 280                                 delete read; delete heatmap; return 0;
 281                         }
 282
 283                         //output error messages about any remaining user labels
 284                         set<string>::iterator it;
 285                         bool needToRun = false;
 286                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 287                                 m->mothurOut("Your file does not include the label " + *it);
 288                                 if (processedLabels.count(lastLabel) != 1) {
 289                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 290                                         needToRun = true;
 291                                 }else {
 292                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 293                                 }
 294                         }
 295
 296                         //run last label if you need to
 297                         if (needToRun == true)  {
 298
 299                                 if (rabund != NULL) {   delete rabund;  }
 300                                 rabund = input->getRAbundVector(lastLabel);
 301                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 302
 303                                 outputNames.push_back(heatmap->getPic(rabund));
 304                                 delete rabund; globaldata->rabund = NULL;
 305                         }
 306
 307                 }
 308
 309                 globaldata->rabund = NULL;
 310                 delete input; globaldata->ginput = NULL;
 311
 312                 if (m->control_pressed) {
 313                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
 314                         delete read; delete heatmap; return 0;
 315                 }
 316
 317                 m->mothurOutEndLine();
 318                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 319                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 320                 m->mothurOutEndLine();
 321
 322                 delete read;
 323                 delete heatmap;
 324
 325                 return 0;
 326         }
 327         catch(exception& e) {
 328                 m->errorOut(e, "HeatMapCommand", "execute");
 329                 exit(1);
 330         }
 331 }
 332
 333 //**********************************************************************************************************************
 334
 335