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                 lines.clear();
  21                 labels.clear();
  22
  23                 //allow user to run help
  24                 if(option == "help") { help(); abort = true; }
  25
  26                 else {
  27                         //valid paramters for this command
  28                         string AlignArray[] =  {"groups","line","label","sorted","scale"};
  29                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  30
  31                         parser = new OptionParser();
  32                         parser->parse(option, parameters);  delete parser;
  33
  34                         ValidParameters* validParameter = new ValidParameters();
  35
  36                         //check to make sure all parameters are valid for command
  37                         for (it = parameters.begin(); it != parameters.end(); it++) {
  38                                 if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  39                         }
  40
  41                         //make sure the user has already run the read.otu command
  42                         if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
  43                                  cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap.bin command." << endl; abort = true;
  44                         }
  45
  46                         //check for optional parameter and set defaults
  47                         // ...at some point should added some additional type checking...
  48                         line = validParameter->validFile(parameters, "line", false);
  49                         if (line == "not found") { line = "";  }
  50                         else {
  51                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  52                                 else { allLines = 1;  }
  53                         }
  54
  55                         label = validParameter->validFile(parameters, "label", false);
  56                         if (label == "not found") { label = ""; }
  57                         else {
  58                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  59                                 else { allLines = 1;  }
  60                         }
  61
  62                         //make sure user did not use both the line and label parameters
  63                         if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
  64                         //if the user has not specified any line or labels use the ones from read.otu
  65                         else if ((line == "") && (label == "")) {
  66                                 allLines = globaldata->allLines;
  67                                 labels = globaldata->labels;
  68                                 lines = globaldata->lines;
  69                         }
  70
  71                         groups = validParameter->validFile(parameters, "groups", false);
  72                         if (groups == "not found") { groups = ""; }
  73                         else {
  74                                 splitAtDash(groups, Groups);
  75                                 globaldata->Groups = Groups;
  76                         }
  77
  78                         sorted = validParameter->validFile(parameters, "sorted", false);                        if (sorted == "not found") { sorted = "T"; }
  79
  80                         scale = validParameter->validFile(parameters, "scale", false);                          if (scale == "not found") { scale = "log10"; }
  81
  82
  83                         delete validParameter;
  84
  85                         if (abort == false) {
  86                                 heatmap = new HeatMap(sorted, scale);
  87                                 format = globaldata->getFormat();
  88                         }
  89                 }
  90
  91         }
  92         catch(exception& e) {
  93                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  94                 exit(1);
  95         }
  96         catch(...) {
  97                 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  98                 exit(1);
  99         }
 100 }
 101
 102 //**********************************************************************************************************************
 103
 104 void HeatMapCommand::help(){
 105         try {
 106                 cout << "The heatmap.bin command can only be executed after a successful read.otu command." << "\n";
 107                 cout << "The heatmap.bin command parameters are groups, sorted, scale, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";
 108                 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
 109                 cout << "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";
 110                 cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n";
 111                 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
 112                 cout << "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
 113                 cout << "Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
 114                 cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
 115                 cout << "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";
 116                 cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
 117                 cout << "The heatmap.bin command outputs a .svg file for each line or label you specify." << "\n";
 118                 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 119
 120         }
 121         catch(exception& e) {
 122                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125         catch(...) {
 126                 cout << "An unknown error has occurred in the HeatMapCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 127                 exit(1);
 128         }
 129 }
 130
 131 //**********************************************************************************************************************
 132
 133 HeatMapCommand::~HeatMapCommand(){
 134         delete input;
 135         delete read;
 136         delete heatmap;
 137 }
 138
 139 //**********************************************************************************************************************
 140
 141 int HeatMapCommand::execute(){
 142         try {
 143
 144                 if (abort == true) { return 0; }
 145
 146                 int count = 1;
 147                 RAbundVector* lastRAbund;
 148                 vector<SharedRAbundVector*> lastLookup;
 149
 150                 if (format == "sharedfile") {
 151                         //you have groups
 152                         read = new ReadOTUFile(globaldata->inputFileName);
 153                         read->read(&*globaldata);
 154
 155                         input = globaldata->ginput;
 156                         lookup = input->getSharedRAbundVectors();
 157                         lastLookup = lookup;
 158                 }else if (format == "list") {
 159                         //you are using just a list file and have only one group
 160                         read = new ReadOTUFile(globaldata->inputFileName);
 161                         read->read(&*globaldata);
 162
 163                         rabund = globaldata->rabund;
 164                         lastRAbund = globaldata->rabund;
 165                         input = globaldata->ginput;
 166                 }
 167
 168                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 169                 set<string> processedLabels;
 170                 set<string> userLabels = labels;
 171                 set<int> userLines = lines;
 172
 173                 if (format != "list") {
 174
 175                         //as long as you are not at the end of the file or done wih the lines you want
 176                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 177
 178                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 179
 180                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
 181                                         heatmap->getPic(lookup);
 182
 183                                         processedLabels.insert(lookup[0]->getLabel());
 184                                         userLabels.erase(lookup[0]->getLabel());
 185                                         userLines.erase(count);
 186                                 }
 187
 188                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 189                                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 190                                         heatmap->getPic(lastLookup);
 191
 192                                         processedLabels.insert(lastLookup[0]->getLabel());
 193                                         userLabels.erase(lastLookup[0]->getLabel());
 194                                 }
 195
 196                                 //prevent memory leak
 197                                 if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 198                                 lastLookup = lookup;
 199
 200                                 //get next line to process
 201                                 lookup = input->getSharedRAbundVectors();
 202                                 count++;
 203                         }
 204
 205                         //output error messages about any remaining user labels
 206                         set<string>::iterator it;
 207                         bool needToRun = false;
 208                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 209                                 cout << "Your file does not include the label "<< *it;
 210                                 if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 211                                         cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 212                                         needToRun = true;
 213                                 }else {
 214                                         cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 215                                 }
 216                         }
 217
 218                         //run last line if you need to
 219                         if (needToRun == true)  {
 220                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 221                                 heatmap->getPic(lastLookup);
 222                         }
 223
 224                         for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 225
 226                         //reset groups parameter
 227                         globaldata->Groups.clear();
 228
 229                 }else{
 230
 231                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 232
 233                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){
 234
 235                                         cout << rabund->getLabel() << '\t' << count << endl;
 236                                         heatmap->getPic(rabund);
 237
 238                                         processedLabels.insert(rabund->getLabel());
 239                                         userLabels.erase(rabund->getLabel());
 240                                         userLines.erase(count);
 241                                 }
 242
 243                                 if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
 244
 245                                         cout << lastRAbund->getLabel() << '\t' << count << endl;
 246                                         heatmap->getPic(lastRAbund);
 247
 248                                         processedLabels.insert(lastRAbund->getLabel());
 249                                         userLabels.erase(lastRAbund->getLabel());
 250                                 }
 251
 252                                 if (count != 1) { delete lastRAbund; }
 253                                 lastRAbund = rabund;
 254
 255                                 rabund = input->getRAbundVector();
 256                                 count++;
 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                                 cout << "Your file does not include the label "<< *it;
 264                                 if (processedLabels.count(lastRAbund->getLabel()) != 1) {
 265                                         cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
 266                                         needToRun = true;
 267                                 }else {
 268                                         cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
 269                                 }
 270                         }
 271
 272                         //run last line if you need to
 273                         if (needToRun == true)  {
 274                                 cout << lastRAbund->getLabel() << '\t' << count << endl;
 275                                 heatmap->getPic(lastRAbund);
 276                         }
 277
 278                         delete lastRAbund;
 279
 280                 }
 281
 282                 return 0;
 283         }
 284         catch(exception& e) {
 285                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 286                 exit(1);
 287         }
 288         catch(...) {
 289                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 290                 exit(1);
 291         }
 292 }
 293
 294 //**********************************************************************************************************************
 295
 296