5 * Created by Sarah Westcott on 3/25/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "heatmapcommand.h"
13 //**********************************************************************************************************************
15 HeatMapCommand::HeatMapCommand(string option){
17 globaldata = GlobalData::getInstance();
23 //allow user to run help
24 if(option == "help") { help(); abort = true; }
27 //valid paramters for this command
28 string AlignArray[] = {"groups","line","label","sorted","scale"};
29 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
31 OptionParser parser(option);
32 map<string,string> parameters = parser.getParameters();
34 ValidParameters validParameter;
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; }
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;
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 = ""; }
51 if(line != "all") { splitAtDash(line, lines); allLines = 0; }
52 else { allLines = 1; }
55 label = validParameter.validFile(parameters, "label", false);
56 if (label == "not found") { label = ""; }
58 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
59 else { allLines = 1; }
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;
71 groups = validParameter.validFile(parameters, "groups", false);
72 if (groups == "not found") { groups = ""; }
74 splitAtDash(groups, Groups);
75 globaldata->Groups = Groups;
78 sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found") { sorted = "T"; }
80 scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
83 heatmap = new HeatMap(sorted, scale);
84 format = globaldata->getFormat();
90 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
94 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
99 //**********************************************************************************************************************
101 void HeatMapCommand::help(){
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";
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";
123 cout << "An unknown error has occurred in the HeatMapCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
128 //**********************************************************************************************************************
130 HeatMapCommand::~HeatMapCommand(){
136 //**********************************************************************************************************************
138 int HeatMapCommand::execute(){
141 if (abort == true) { return 0; }
144 RAbundVector* lastRAbund;
145 vector<SharedRAbundVector*> lastLookup;
147 if (format == "sharedfile") {
149 read = new ReadOTUFile(globaldata->inputFileName);
150 read->read(&*globaldata);
152 input = globaldata->ginput;
153 lookup = input->getSharedRAbundVectors();
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);
160 rabund = globaldata->rabund;
161 lastRAbund = globaldata->rabund;
162 input = globaldata->ginput;
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;
170 if (format != "list") {
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))) {
175 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
177 cout << lookup[0]->getLabel() << '\t' << count << endl;
178 heatmap->getPic(lookup);
180 processedLabels.insert(lookup[0]->getLabel());
181 userLabels.erase(lookup[0]->getLabel());
182 userLines.erase(count);
185 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
186 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
187 heatmap->getPic(lastLookup);
189 processedLabels.insert(lastLookup[0]->getLabel());
190 userLabels.erase(lastLookup[0]->getLabel());
193 //prevent memory leak
194 if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
197 //get next line to process
198 lookup = input->getSharedRAbundVectors();
202 //output error messages about any remaining user labels
203 set<string>::iterator it;
204 bool needToRun = false;
205 for (it = userLabels.begin(); it != userLabels.end(); it++) {
206 cout << "Your file does not include the label "<< *it;
207 if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
208 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
211 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
215 //run last line if you need to
216 if (needToRun == true) {
217 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
218 heatmap->getPic(lastLookup);
221 for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
223 //reset groups parameter
224 globaldata->Groups.clear();
228 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
230 if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){
232 cout << rabund->getLabel() << '\t' << count << endl;
233 heatmap->getPic(rabund);
235 processedLabels.insert(rabund->getLabel());
236 userLabels.erase(rabund->getLabel());
237 userLines.erase(count);
240 if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
242 cout << lastRAbund->getLabel() << '\t' << count << endl;
243 heatmap->getPic(lastRAbund);
245 processedLabels.insert(lastRAbund->getLabel());
246 userLabels.erase(lastRAbund->getLabel());
249 if (count != 1) { delete lastRAbund; }
252 rabund = input->getRAbundVector();
256 //output error messages about any remaining user labels
257 set<string>::iterator it;
258 bool needToRun = false;
259 for (it = userLabels.begin(); it != userLabels.end(); it++) {
260 cout << "Your file does not include the label "<< *it;
261 if (processedLabels.count(lastRAbund->getLabel()) != 1) {
262 cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
265 cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
269 //run last line if you need to
270 if (needToRun == true) {
271 cout << lastRAbund->getLabel() << '\t' << count << endl;
272 heatmap->getPic(lastRAbund);
282 catch(exception& e) {
283 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
287 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
292 //**********************************************************************************************************************