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"};
  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                         //make sure the user has already run the read.otu command
  41                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "")) {
  42                                  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;
  43                         }
  44
  45                         //check for optional parameter and set defaults
  46                         // ...at some point should added some additional type checking...
  47                         label = validParameter.validFile(parameters, "label", false);
  48                         if (label == "not found") { label = ""; }
  49                         else {
  50                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  51                                 else { allLines = 1;  }
  52                         }
  53
  54                         //if the user has not specified any labels use the ones from read.otu
  55                         if (label == "") {
  56                                 allLines = globaldata->allLines;
  57                                 labels = globaldata->labels;
  58                         }
  59
  60                         groups = validParameter.validFile(parameters, "groups", false);
  61                         if (groups == "not found") { groups = ""; }
  62                         else {
  63                                 splitAtDash(groups, Groups);
  64                                 globaldata->Groups = Groups;
  65                         }
  66
  67                         sorted = validParameter.validFile(parameters, "sorted", false);                 if (sorted == "not found") { sorted = "T"; }
  68
  69                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
  70
  71                         if (abort == false) {
  72                                 heatmap = new HeatMap(sorted, scale);
  73                                 format = globaldata->getFormat();
  74                         }
  75                 }
  76
  77         }
  78         catch(exception& e) {
  79                 errorOut(e, "HeatMapCommand", "HeatMapCommand");
  80                 exit(1);
  81         }
  82 }
  83
  84 //**********************************************************************************************************************
  85
  86 void HeatMapCommand::help(){
  87         try {
  88                 mothurOut("The heatmap.bin command can only be executed after a successful read.otu command.\n");
  89                 mothurOut("The heatmap.bin command parameters are groups, sorted, scale label.  No parameters are required.\n");
  90                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
  91                 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");
  92                 mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\n");
  93                 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");
  94                 mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n");
  95                 mothurOut("Example heatmap.bin(groups=A-B-C, sorted=F, scale=log10).\n");
  96                 mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
  97                 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");
  98                 mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
  99                 mothurOut("The heatmap.bin command outputs a .svg file for each label you specify.\n");
 100                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 101
 102         }
 103         catch(exception& e) {
 104                 errorOut(e, "HeatMapCommand", "help");
 105                 exit(1);
 106         }
 107 }
 108
 109 //**********************************************************************************************************************
 110
 111 HeatMapCommand::~HeatMapCommand(){
 112         if (abort == false) {
 113                 delete read;
 114                 delete heatmap;
 115         }
 116 }
 117
 118 //**********************************************************************************************************************
 119
 120 int HeatMapCommand::execute(){
 121         try {
 122
 123                 if (abort == true) { return 0; }
 124
 125                 string lastLabel;
 126
 127                 if (format == "sharedfile") {
 128                         //you have groups
 129                         read = new ReadOTUFile(globaldata->inputFileName);
 130                         read->read(&*globaldata);
 131
 132                         input = globaldata->ginput;
 133                         lookup = input->getSharedRAbundVectors();
 134                         lastLabel = lookup[0]->getLabel();
 135
 136                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 137                         //you are using just a list file and have only one group
 138                         read = new ReadOTUFile(globaldata->inputFileName);
 139                         read->read(&*globaldata);
 140
 141                         rabund = globaldata->rabund;
 142                         lastLabel = rabund->getLabel();
 143                         input = globaldata->ginput;
 144
 145                 }
 146
 147                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 148                 set<string> processedLabels;
 149                 set<string> userLabels = labels;
 150
 151                 if ((format != "list") && (format != "rabund") && (format != "sabund")) {
 152
 153                         //as long as you are not at the end of the file or done wih the lines you want
 154                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 155
 156                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 157
 158                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 159                                         heatmap->getPic(lookup);
 160
 161                                         processedLabels.insert(lookup[0]->getLabel());
 162                                         userLabels.erase(lookup[0]->getLabel());
 163                                 }
 164
 165                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 166                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 167                                         lookup = input->getSharedRAbundVectors(lastLabel);
 168                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 169
 170                                         heatmap->getPic(lookup);
 171
 172                                         processedLabels.insert(lookup[0]->getLabel());
 173                                         userLabels.erase(lookup[0]->getLabel());
 174                                 }
 175
 176                                 lastLabel = lookup[0]->getLabel();
 177                                 //prevent memory leak
 178                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 179
 180                                 //get next line to process
 181                                 lookup = input->getSharedRAbundVectors();
 182                         }
 183
 184                         //output error messages about any remaining user labels
 185                         set<string>::iterator it;
 186                         bool needToRun = false;
 187                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 188                                 mothurOut("Your file does not include the label " + *it);
 189                                 if (processedLabels.count(lastLabel) != 1) {
 190                                         mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 191                                         needToRun = true;
 192                                 }else {
 193                                         mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 194                                 }
 195                         }
 196
 197                         //run last label if you need to
 198                         if (needToRun == true)  {
 199                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 200                                 lookup = input->getSharedRAbundVectors(lastLabel);
 201
 202                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 203                                 heatmap->getPic(lookup);
 204                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 205                         }
 206
 207
 208
 209                         //reset groups parameter
 210                         globaldata->Groups.clear();
 211
 212                 }else{
 213
 214                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 215
 216                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 217
 218                                         mothurOut(rabund->getLabel()); mothurOutEndLine();
 219                                         heatmap->getPic(rabund);
 220
 221                                         processedLabels.insert(rabund->getLabel());
 222                                         userLabels.erase(rabund->getLabel());
 223                                 }
 224
 225                                 if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 226
 227                                         delete rabund;
 228                                         rabund = input->getRAbundVector(lastLabel);
 229                                         mothurOut(rabund->getLabel()); mothurOutEndLine();
 230
 231                                         heatmap->getPic(rabund);
 232
 233                                         processedLabels.insert(rabund->getLabel());
 234                                         userLabels.erase(rabund->getLabel());
 235                                 }
 236
 237
 238
 239                                 lastLabel = rabund->getLabel();
 240                                 delete rabund;
 241                                 rabund = input->getRAbundVector();
 242                         }
 243
 244                         //output error messages about any remaining user labels
 245                         set<string>::iterator it;
 246                         bool needToRun = false;
 247                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 248                                 mothurOut("Your file does not include the label " + *it);
 249                                 if (processedLabels.count(lastLabel) != 1) {
 250                                         mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 251                                         needToRun = true;
 252                                 }else {
 253                                         mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 254                                 }
 255                         }
 256
 257                         //run last label if you need to
 258                         if (needToRun == true)  {
 259
 260                                 if (rabund != NULL) {   delete rabund;  }
 261                                 rabund = input->getRAbundVector(lastLabel);
 262                                 mothurOut(rabund->getLabel()); mothurOutEndLine();
 263
 264                                 heatmap->getPic(rabund);
 265                                 delete rabund; globaldata->rabund = NULL;
 266                         }
 267
 268                 }
 269
 270                 globaldata->rabund = NULL;
 271                 delete input; globaldata->ginput = NULL;
 272                 return 0;
 273         }
 274         catch(exception& e) {
 275                 errorOut(e, "HeatMapCommand", "execute");
 276                 exit(1);
 277         }
 278 }
 279
 280 //**********************************************************************************************************************
 281
 282