5 * Created by Sarah Westcott on 3/25/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 //**********************************************************************************************************************
13 HeatMap::HeatMap(string sort, string scale, string dir){
15 globaldata = GlobalData::getInstance();
16 m = MothurOut::getInstance();
17 // format = globaldata->getFormat();
23 m->errorOut(e, "HeatMap", "HeatMap");
28 //**********************************************************************************************************************
30 string HeatMap::getPic(RAbundVector* rabund) {
34 float maxRelAbund = 0.0;
36 for(int i=0;i<rabund->size();i++){
37 float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
38 if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
42 vector<string> scaleRelAbund(rabund->size(), "");
44 for(int i=0;i<rabund->size();i++){
45 float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
47 if (m->control_pressed) { return "control"; }
49 if (rabund->get(i) != 0) { //don't want log value of 0.
50 if (scaler == "log10") {
51 scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
52 }else if (scaler == "log2") {
53 scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
54 }else if (scaler == "linear") {
55 scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
56 }else { //if user enters invalid scaler option.
57 scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund)))) + "0000";
60 else { scaleRelAbund[i] = "FFFFFF"; }
64 string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + rabund->getLabel() + ".heatmap.bin.svg";
65 openOutputFile(filenamesvg, outsvg);
68 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund->getNumBins()*5 + 120)) + "\">\n";
72 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((rabund->getNumBins()*5 + 120)) + "\"/>";
73 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
75 //output legend and color labels
78 int y = 103 + (rabund->getNumBins()*5);
79 printLegend(y, maxRelAbund);
82 for (int i = 0; i < scaleRelAbund.size(); i++) {
83 if (m->control_pressed) { outsvg.close(); return "control"; }
85 outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
89 outsvg << "</g>\n</svg>\n";
95 m->errorOut(e, "HeatMap", "getPic");
100 //**********************************************************************************************************************
102 string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
104 //sort lookup so shared bins are on top
105 if (isTrue(sorted) == true) { sortSharedVectors(lookup); }
107 vector<vector<string> > scaleRelAbund;
108 vector<float> maxRelAbund(lookup.size(), 0.0);
109 float superMaxRelAbund = 0;
111 for(int i = 0; i < lookup.size(); i++){
112 for(int j=0; j<lookup[i]->size(); j++){
114 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
115 if(relAbund > maxRelAbund[i]){ maxRelAbund[i] = relAbund; }
117 if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
120 scaleRelAbund.resize(lookup.size());
121 for(int i=0;i<lookup.size();i++){
122 scaleRelAbund[i].assign(lookup[i]->size(), "");
123 for(int j=0;j<lookup[i]->size();j++){
124 if (m->control_pressed) { return "control"; }
125 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
127 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
128 if (scaler == "log10") {
129 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
130 }else if (scaler == "log2") {
131 scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
132 }else if (scaler == "linear") {
133 scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
134 }else { //if user enters invalid scaler option.
135 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
137 }else { scaleRelAbund[i][j] = "FFFFFF"; }
142 string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
143 openOutputFile(filenamesvg, outsvg);
146 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120)) + "\">\n";
150 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120)) + "\"/>";
151 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
154 for (int h = 0; h < lookup.size(); h++) {
155 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
158 //output legend and color labels
161 int y = 103 + (lookup[0]->getNumBins()*5);
162 printLegend(y, superMaxRelAbund);
165 for (int i = 0; i < scaleRelAbund[0].size(); i++) {
166 for (int j = 0; j < scaleRelAbund.size(); j++) {
167 if (m->control_pressed) { outsvg.close(); return "control"; }
169 outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
176 outsvg << "</g>\n</svg>\n";
182 catch(exception& e) {
183 m->errorOut(e, "HeatMap", "getPic");
188 //**********************************************************************************************************************
189 void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
191 //copy lookup and then clear it to refill with sorted.
192 //loop though lookup and determine if they are shared
193 //if they are then insert in the front
194 //if not push to back
196 vector<SharedRAbundVector*> looktemp;
197 map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
198 map<int, int>::iterator it;
201 //create and initialize looktemp as a copy of lookup
202 for (int i = 0; i < lookup.size(); i++) {
203 SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
204 temp->setLabel(lookup[i]->getLabel());
205 temp->setGroup(lookup[i]->getGroup());
206 //copy lookup i's info
207 for (int j = 0; j < lookup[i]->size(); j++) {
208 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
210 looktemp.push_back(temp);
213 //clear out lookup to create sorted lookup -- Sarah look at - this is causing segmentation faults
214 for (int j = 0; j < lookup.size(); j++) {
217 lookup.clear(); //doesn't this do the job?
219 //create and initialize lookup to empty vectors
220 for (int i = 0; i < looktemp.size(); i++) {
221 SharedRAbundVector* temp = new SharedRAbundVector();
222 temp->setLabel(looktemp[i]->getLabel());
223 temp->setGroup(looktemp[i]->getGroup());
224 lookup.push_back(temp);
226 //initialize place map
232 for (int i = 0; i < looktemp[0]->size(); i++) {
234 bool updatePlace = false;
236 for (int j = 0; j < looktemp.size(); j++) {
237 if (looktemp[j]->getAbundance(i) != 0) { count++; }
241 for (int j = 0; j < looktemp.size(); j++) {
242 //if they are not shared then push to back, if they are not insert in front
243 if (count < 2) { lookup[j]->push_back(looktemp[j]->getAbundance(i), looktemp[j]->getGroup()); }
244 //they are shared by some
245 else { lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup()); updatePlace = true; }
248 if (updatePlace == true) {
249 //move place holders below where you entered up to "make space" for you entry
250 for (it = place.begin(); it!= place.end(); it++) {
251 if (it->first < count) { it->second++; }
256 //delete looktemp -- Sarah look at - this is causing segmentation faults
257 for (int j = 0; j < looktemp.size(); j++) {
258 // delete looktemp[j];
262 catch(exception& e) {
263 m->errorOut(e, "HeatMap", "sortSharedVectors");
268 //**********************************************************************************************************************
270 void HeatMap::printLegend(int y, float maxbin) {
273 //output legend and color labels
274 //go through map and give each score a color value
279 for (int i = 1; i < 255; i++) {
280 color = toHex(int((float)(i)));
281 outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
285 //prints legend labels
287 for (int i = 1; i<=5; i++) {
289 if(scaler== "log10") { label = maxbin * log10(51*i) / log10(255); }
290 else if(scaler== "log2") { label = maxbin * log2(51*i) / log2(255); }
291 else if(scaler== "linear") { label = maxbin * 51 * i / 255; }
292 else { label = maxbin * log10(51*i) / log10(255); }
293 label = int(label * 1000 + 0.5);
295 string text = toString(label, 3);
297 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
302 catch(exception& e) {
303 m->errorOut(e, "HeatMap", "printLegend");