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