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                         OptionParser parser(option);
  32                         map<string,string> parameters = parser.getParameters();
  33
  34                         ValidParameters validParameter;
  35
  36                         //check to make sure all parameters are valid for command
  37                         for (map<string,string>::iterator 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                         if (abort == false) {
  83                                 heatmap = new HeatMap(sorted, scale);
  84                                 format = globaldata->getFormat();
  85                         }
  86                 }
  87
  88         }
  89         catch(exception& e) {
  90                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  91                 exit(1);
  92         }
  93         catch(...) {
  94                 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  95                 exit(1);
  96         }
  97 }
  98
  99 //**********************************************************************************************************************
 100
 101 void HeatMapCommand::help(){
 102         try {
 103                 cout << "The heatmap.bin command can only be executed after a successful read.otu command." << "\n";
 104                 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";
 105                 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
 106                 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";
 107                 cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n";
 108                 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";
 109                 cout << "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
 110                 cout << "Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
 111                 cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
 112                 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";
 113                 cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
 114                 cout << "The heatmap.bin command outputs a .svg file for each line or label you specify." << "\n";
 115                 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 116
 117         }
 118         catch(exception& e) {
 119                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 120                 exit(1);
 121         }
 122         catch(...) {
 123                 cout << "An unknown error has occurred in the HeatMapCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126 }
 127
 128 //**********************************************************************************************************************
 129
 130 HeatMapCommand::~HeatMapCommand(){
 131         if (abort == false) {
 132                 delete read;
 133                 delete heatmap;
 134         }
 135 }
 136
 137 //**********************************************************************************************************************
 138
 139 int HeatMapCommand::execute(){
 140         try {
 141
 142                 if (abort == true) { return 0; }
 143
 144                 int count = 1;
 145                 string lastLabel;
 146
 147                 if (format == "sharedfile") {
 148                         //you have groups
 149                         read = new ReadOTUFile(globaldata->inputFileName);
 150                         read->read(&*globaldata);
 151
 152                         input = globaldata->ginput;
 153                         lookup = input->getSharedRAbundVectors();
 154                         lastLabel = lookup[0]->getLabel();
 155                 }else if (format == "list") {
 156                         //you are using just a list file and have only one group
 157                         read = new ReadOTUFile(globaldata->inputFileName);
 158                         read->read(&*globaldata);
 159
 160                         rabund = globaldata->rabund;
 161                         lastLabel = rabund->getLabel();
 162                         input = globaldata->ginput;
 163                 }
 164
 165                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 166                 set<string> processedLabels;
 167                 set<string> userLabels = labels;
 168                 set<int> userLines = lines;
 169
 170                 if (format != "list") {
 171
 172                         //as long as you are not at the end of the file or done wih the lines you want
 173                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 174
 175                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 176
 177                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
 178                                         heatmap->getPic(lookup);
 179
 180                                         processedLabels.insert(lookup[0]->getLabel());
 181                                         userLabels.erase(lookup[0]->getLabel());
 182                                         userLines.erase(count);
 183                                 }
 184
 185                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 186                                         cout << lastLabel << '\t' << count << endl;
 187                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 188                                         lookup = input->getSharedRAbundVectors(lastLabel);
 189
 190                                         heatmap->getPic(lookup);
 191
 192                                         processedLabels.insert(lookup[0]->getLabel());
 193                                         userLabels.erase(lookup[0]->getLabel());
 194                                 }
 195
 196                                 lastLabel = lookup[0]->getLabel();
 197                                 //prevent memory leak
 198                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 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(lastLabel) != 1) {
 211                                         cout << ". I will use " << lastLabel << "." << endl;
 212                                         needToRun = true;
 213                                 }else {
 214                                         cout << ". Please refer to " << lastLabel << "." << endl;
 215                                 }
 216                         }
 217
 218                         //run last line if you need to
 219                         if (needToRun == true)  {
 220                                 cout << lastLabel << '\t' << count << endl;
 221                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 222                                 lookup = input->getSharedRAbundVectors(lastLabel);
 223
 224                                 heatmap->getPic(lookup);
 225                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 226                         }
 227
 228
 229
 230                         //reset groups parameter
 231                         globaldata->Groups.clear();
 232
 233                 }else{
 234
 235                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 236
 237                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){
 238
 239                                         cout << rabund->getLabel() << '\t' << count << endl;
 240                                         heatmap->getPic(rabund);
 241
 242                                         processedLabels.insert(rabund->getLabel());
 243                                         userLabels.erase(rabund->getLabel());
 244                                         userLines.erase(count);
 245                                 }
 246
 247                                 if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 248
 249                                         cout << lastLabel << '\t' << count << endl;
 250                                         delete rabund;
 251                                         rabund = input->getRAbundVector(lastLabel);
 252
 253                                         heatmap->getPic(rabund);
 254
 255                                         processedLabels.insert(rabund->getLabel());
 256                                         userLabels.erase(rabund->getLabel());
 257                                 }
 258
 259
 260
 261                                 lastLabel = rabund->getLabel();
 262                                 delete rabund;
 263                                 rabund = input->getRAbundVector();
 264                                 count++;
 265                         }
 266
 267                         //output error messages about any remaining user labels
 268                         set<string>::iterator it;
 269                         bool needToRun = false;
 270                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 271                                 cout << "Your file does not include the label "<< *it;
 272                                 if (processedLabels.count(lastLabel) != 1) {
 273                                         cout << ". I will use " << lastLabel << "." << endl;
 274                                         needToRun = true;
 275                                 }else {
 276                                         cout << ". Please refer to " << lastLabel << "." << endl;
 277                                 }
 278                         }
 279
 280                         //run last line if you need to
 281                         if (needToRun == true)  {
 282                                 cout << lastLabel << '\t' << count << endl;
 283                                 delete rabund;
 284                                 rabund = input->getRAbundVector(lastLabel);
 285
 286                                 heatmap->getPic(rabund);
 287                                 delete rabund; globaldata->rabund = NULL;
 288                         }
 289
 290                 }
 291
 292                 delete input; globaldata->ginput = NULL;
 293                 return 0;
 294         }
 295         catch(exception& e) {
 296                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 297                 exit(1);
 298         }
 299         catch(...) {
 300                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 301                 exit(1);
 302         }
 303 }
 304
 305 //**********************************************************************************************************************
 306
 307