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){
15 globaldata = GlobalData::getInstance();
16 // format = globaldata->getFormat();
21 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
25 cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
30 //**********************************************************************************************************************
32 void HeatMap::getPic(RAbundVector* rabund) {
36 float maxRelAbund = 0.0;
38 for(int i=0;i<rabund->size();i++){
39 float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
40 if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
44 vector<string> scaleRelAbund(rabund->size(), "");
46 for(int i=0;i<rabund->size();i++){
47 float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
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 = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.bin.svg";
65 openOutputFile(filenamesvg, outsvg);
68 outsvg << "<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++) {
84 outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
88 outsvg << "</g>\n</svg>\n";
94 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
98 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
103 //**********************************************************************************************************************
105 void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
107 //sort lookup so shared bins are on top
108 if (isTrue(sorted) == true) { sortSharedVectors(lookup); }
110 vector<vector<string> > scaleRelAbund;
111 vector<float> maxRelAbund(lookup.size(), 0.0);
112 float superMaxRelAbund = 0;
114 for(int i = 0; i < lookup.size(); i++){
115 for(int j=0; j<lookup[i]->size(); j++){
117 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
118 if(relAbund > maxRelAbund[i]){ maxRelAbund[i] = relAbund; }
120 if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
123 scaleRelAbund.resize(lookup.size());
124 for(int i=0;i<lookup.size();i++){
125 scaleRelAbund[i].assign(lookup[i]->size(), "");
126 for(int j=0;j<lookup[i]->size();j++){
127 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
129 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
130 if (scaler == "log10") {
131 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
132 }else if (scaler == "log2") {
133 scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
134 }else if (scaler == "linear") {
135 scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
136 }else { //if user enters invalid scaler option.
137 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
139 }else { scaleRelAbund[i][j] = "FFFFFF"; }
144 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.bin.svg";
145 openOutputFile(filenamesvg, outsvg);
148 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120)) + "\">\n";
152 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120)) + "\"/>";
153 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
156 for (int h = 0; h < lookup.size(); h++) {
157 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";
160 //output legend and color labels
163 int y = 103 + (lookup[0]->getNumBins()*5);
164 printLegend(y, superMaxRelAbund);
167 for (int i = 0; i < scaleRelAbund[0].size(); i++) {
168 for (int j = 0; j < scaleRelAbund.size(); j++) {
170 outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
177 outsvg << "</g>\n</svg>\n";
181 catch(exception& e) {
182 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
186 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
191 //**********************************************************************************************************************
192 void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
194 //copy lookup and then clear it to refill with sorted.
195 //loop though lookup and determine if they are shared
196 //if they are then insert in the front
197 //if not push to back
199 vector<SharedRAbundVector*> looktemp;
200 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.
201 map<int, int>::iterator it;
204 //create and initialize looktemp as a copy of lookup
205 for (int i = 0; i < lookup.size(); i++) {
206 SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
207 temp->setLabel(lookup[i]->getLabel());
208 temp->setGroup(lookup[i]->getGroup());
209 //copy lookup i's info
210 for (int j = 0; j < lookup[i]->size(); j++) {
211 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
213 looktemp.push_back(temp);
216 //clear out lookup to create sorted lookup -- Sarah look at - this is causing segmentation faults
217 for (int j = 0; j < lookup.size(); j++) {
220 lookup.clear(); //doesn't this do the job?
222 //create and initialize lookup to empty vectors
223 for (int i = 0; i < looktemp.size(); i++) {
224 SharedRAbundVector* temp = new SharedRAbundVector();
225 temp->setLabel(looktemp[i]->getLabel());
226 temp->setGroup(looktemp[i]->getGroup());
227 lookup.push_back(temp);
229 //initialize place map
235 for (int i = 0; i < looktemp[0]->size(); i++) {
237 bool updatePlace = false;
239 for (int j = 0; j < looktemp.size(); j++) {
240 if (looktemp[j]->getAbundance(i) != 0) { count++; }
244 for (int j = 0; j < looktemp.size(); j++) {
245 //if they are not shared then push to back, if they are not insert in front
246 if (count < 2) { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
247 //they are shared by some
248 else { lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup()); updatePlace = true; }
251 if (updatePlace == true) {
252 //move place holders below where you entered up to "make space" for you entry
253 for (it = place.begin(); it!= place.end(); it++) {
254 if (it->first < count) { it->second++; }
259 //delete looktemp -- Sarah look at - this is causing segmentation faults
260 for (int j = 0; j < looktemp.size(); j++) {
261 // delete looktemp[j];
265 catch(exception& e) {
266 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
270 cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
276 //**********************************************************************************************************************
278 void HeatMap::printLegend(int y, float maxbin) {
281 //output legend and color labels
282 //go through map and give each score a color value
287 for (int i = 1; i < 255; i++) {
288 color = toHex(int((float)(i)));
289 outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
293 //prints legend labels
295 for (int i = 1; i<=5; i++) {
297 if(scaler== "log10") { label = maxbin * log10(51*i) / log10(255); }
298 else if(scaler== "log2") { label = maxbin * log2(51*i) / log2(255); }
299 else if(scaler== "linear") { label = maxbin * 51 * i / 255; }
300 else { label = maxbin * log10(51*i) / log10(255); }
301 label = int(label * 1000 + 0.5);
303 string text = toString(label, 3);
305 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
310 catch(exception& e) {
311 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
315 cout << "An unknown error has occurred in the HeatMap class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";