5 * Created by Sarah Westcott on 3/25/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 //**********************************************************************************************************************
15 globaldata = GlobalData::getInstance();
16 format = globaldata->getFormat();
17 sorted = globaldata->getSorted();
20 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
24 cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
29 //**********************************************************************************************************************
31 void HeatMap::getPic(RAbundVector* rabund) {
33 //get users scaling method
34 scaler = globaldata->getScale();
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; }
43 scaler = globaldata->getScale();
45 vector<string> scaleRelAbund(rabund->size(), "");
47 for(int i=0;i<rabund->size();i++){
48 float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
50 if (rabund->get(i) != 0) { //don't want log value of 0.
51 if (scaler == "log10") {
52 scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
53 }else if (scaler == "log2") {
54 scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
55 }else if (scaler == "linear") {
56 scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
57 }else { //if user enters invalid scaler option.
58 scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund)))) + "0000";
61 else { scaleRelAbund[i] = "FFFFFF"; }
65 string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.svg";
66 openOutputFile(filenamesvg, outsvg);
69 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund->getNumBins()*5 + 120)) + "\">\n";
73 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((rabund->getNumBins()*5 + 120)) + "\"/>";
74 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
76 //output legend and color labels
79 int y = 103 + (rabund->getNumBins()*5);
80 printLegend(y, maxRelAbund);
83 for (int i = 0; i < scaleRelAbund.size(); i++) {
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 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
99 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
104 //**********************************************************************************************************************
106 void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
108 //sort lookup so shared bins are on top
109 if (isTrue(sorted) == true) { sortSharedVectors(lookup); }
111 vector<vector<string> > scaleRelAbund;
112 vector<float> maxRelAbund(lookup.size(), 0.0);
113 float superMaxRelAbund = 0;
115 for(int i = 0; i < lookup.size(); i++){
116 for(int j=0; j<lookup[i]->size(); j++){
118 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
119 if(relAbund > maxRelAbund[i]){ maxRelAbund[i] = relAbund; }
121 if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
124 scaler = globaldata->getScale();
126 scaleRelAbund.resize(lookup.size());
127 for(int i=0;i<lookup.size();i++){
128 scaleRelAbund[i].assign(lookup[i]->size(), "");
129 for(int j=0;j<lookup[i]->size();j++){
130 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
132 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
133 if (scaler == "log10") {
134 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
135 }else if (scaler == "log2") {
136 scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
137 }else if (scaler == "linear") {
138 scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
139 }else { //if user enters invalid scaler option.
140 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
142 }else { scaleRelAbund[i][j] = "FFFFFF"; }
147 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.svg";
148 openOutputFile(filenamesvg, outsvg);
151 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120)) + "\">\n";
155 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120)) + "\"/>";
156 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
159 for (int h = 0; h < lookup.size(); h++) {
160 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";
163 //output legend and color labels
166 int y = 103 + (lookup[0]->getNumBins()*5);
167 printLegend(y, superMaxRelAbund);
170 for (int i = 0; i < scaleRelAbund[0].size(); i++) {
171 for (int j = 0; j < scaleRelAbund.size(); j++) {
173 outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
180 outsvg << "</g>\n</svg>\n";
184 catch(exception& e) {
185 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
189 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
194 //**********************************************************************************************************************
195 void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
197 //copy lookup and then clear it to refill with sorted.
198 //loop though lookup and determine if they are shared
199 //if they are then insert in the front
200 //if not push to back
202 vector<SharedRAbundVector*> looktemp;
203 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.
204 map<int, int>::iterator it;
207 //create and initialize looktemp as a copy of lookup
208 for (int i = 0; i < lookup.size(); i++) {
209 SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
210 temp->setLabel(lookup[i]->getLabel());
211 temp->setGroup(lookup[i]->getGroup());
212 //copy lookup i's info
213 for (int j = 0; j < lookup[i]->size(); j++) {
214 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
216 looktemp.push_back(temp);
219 //clear out lookup to create sorted lookup -- Sarah look at - this is causing segmentation faults
220 for (int j = 0; j < lookup.size(); j++) {
223 lookup.clear(); //doesn't this do the job?
225 //create and initialize lookup to empty vectors
226 for (int i = 0; i < looktemp.size(); i++) {
227 SharedRAbundVector* temp = new SharedRAbundVector();
228 temp->setLabel(looktemp[i]->getLabel());
229 temp->setGroup(looktemp[i]->getGroup());
230 lookup.push_back(temp);
232 //initialize place map
238 for (int i = 0; i < looktemp[0]->size(); i++) {
240 bool updatePlace = false;
242 for (int j = 0; j < looktemp.size(); j++) {
243 if (looktemp[j]->getAbundance(i) != 0) { count++; }
247 for (int j = 0; j < looktemp.size(); j++) {
248 //if they are not shared then push to back, if they are not insert in front
249 if (count < 2) { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
250 //they are shared by some
251 else { lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup()); updatePlace = true; }
254 if (updatePlace == true) {
255 //move place holders below where you entered up to "make space" for you entry
256 for (it = place.begin(); it!= place.end(); it++) {
257 if (it->first < count) { it->second++; }
262 //delete looktemp -- Sarah look at - this is causing segmentation faults
263 for (int j = 0; j < looktemp.size(); j++) {
264 // delete looktemp[j];
268 catch(exception& e) {
269 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
273 cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
279 //**********************************************************************************************************************
281 void HeatMap::printLegend(int y, float maxbin) {
284 //output legend and color labels
285 //go through map and give each score a color value
290 for (int i = 1; i < 255; i++) {
291 color = toHex(int((float)(i)));
292 outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
296 //prints legend labels
298 for (int i = 1; i<=5; i++) {
300 if(scaler== "log10") { label = maxbin * log10(51*i) / log10(255); }
301 else if(scaler== "log2") { label = maxbin * log2(51*i) / log2(255); }
302 else if(scaler== "linear") { label = maxbin * 51 * i / 255; }
303 else { label = maxbin * log10(51*i) / log10(255); }
304 label = int(label * 1000 + 0.5);
306 string text = toString(label, 3);
308 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
313 catch(exception& e) {
314 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
318 cout << "An unknown error has occurred in the HeatMap class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";