globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
sorted = globaldata->getSorted();
- util = new SharedUtil();
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+
//**********************************************************************************************************************
-void HeatMap::getPic(OrderVector* order) {
+
+void HeatMap::getPic(RAbundVector* rabund) {
try {
- colorScale.clear();
+ //get users scaling method
+ scaler = globaldata->getScale();
- rabund = order->getRAbundVector();
+ float maxRelAbund = 0.0;
- for (int i = 0; i < rabund.size(); i++) {
- colorScale[rabund.get(i)] = "";
+ for(int i=0;i<rabund->size();i++){
+ float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
+ if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
}
- float scaler = 255 / (float) colorScale.size();
+ scaler = globaldata->getScale();
- //go through map and give each score a color value
- for (it = colorScale.begin(); it != colorScale.end(); it++) {
- it->second = toHex(int(float(it->first) * scaler));
- if(it->second.length() == 1) { it->second = "0" + it->second; }
+ vector<string> scaleRelAbund(rabund->size(), "");
+
+ for(int i=0;i<rabund->size();i++){
+ float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
+
+ if (rabund->get(i) != 0) { //don't want log value of 0.
+ if (scaler == "log10") {
+ scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
+ }else if (scaler == "log2") {
+ scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
+ }else if (scaler == "linear") {
+ scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
+ }else { //if user enters invalid scaler option.
+ scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund)))) + "0000";
+ }
+ }
+ else { scaleRelAbund[i] = "FFFFFF"; }
}
-
- string filenamesvg = getRootName(globaldata->inputFileName) + order->getLabel() + ".heatmap.svg";
+
+ string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.svg";
openOutputFile(filenamesvg, outsvg);
- //scale max rank so the maxrank = bright red
-
//svg image
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 300 " + toString((rabund.getNumBins()*5 + 15)) + "\">\n";
+ outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund->getNumBins()*5 + 120)) + "\">\n";
outsvg << "<g>\n";
- int x = 15;
- int y = 15;
+ //white backround
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((rabund->getNumBins()*5 + 120)) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
+
+ //output legend and color labels
string color;
-
- for (int i = 0; i <= rabund.getNumBins(); i++) {
+ int x = 0;
+ int y = 103 + (rabund->getNumBins()*5);
+ printLegend(y, maxRelAbund);
- color = colorScale[rabund.get(i)];
+ y = 70;
+ for (int i = 0; i < scaleRelAbund.size(); i++) {
- outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
+ outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
y += 5;
}
- outsvg << "</g>\n</svg>\n";
+ outsvg << "</g>\n</svg>\n";
outsvg.close();
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+
//**********************************************************************************************************************
-void HeatMap::getPic(SharedOrderVector* sharedorder) {
+
+void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
try {
- colorScale.clear();
-
- //fills vector of sharedsabunds - lookup
- util->getSharedVectors(globaldata->Groups, lookup, sharedorder); //fills group vectors from order vector.
//sort lookup so shared bins are on top
- if (sorted == "1") { sortSharedVectors(); }
+ if (sorted == "T") { sortSharedVectors(lookup); }
- //get users scaling method
- scaler = globaldata->getScaler();
+ vector<vector<string> > scaleRelAbund;
+ vector<float> maxRelAbund(lookup.size(), 0.0);
+ float superMaxRelAbund = 0;
- float maxbin = 0.0;
- for (int i = 0; i < lookup.size(); i++) {
- for (int j = 0; j < lookup[i]->size(); j++) {
+ for(int i = 0; i < lookup.size(); i++){
+ for(int j=0; j<lookup[i]->size(); j++){
+
+ float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
+ if(relAbund > maxRelAbund[i]){ maxRelAbund[i] = relAbund; }
+ }
+ if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
+ }
+
+ scaler = globaldata->getScale();
+
+ scaleRelAbund.resize(lookup.size());
+ for(int i=0;i<lookup.size();i++){
+ scaleRelAbund[i].assign(lookup[i]->size(), "");
+ for(int j=0;j<lookup[i]->size();j++){
+ float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
+
if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
if (scaler == "log10") {
- colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
- if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
- //cout << "abundance = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << (lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) << '\t';
- //cout << (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)) << endl;
+ scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
}else if (scaler == "log2") {
- colorScale[(log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
- if (maxbin < (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
- //cout << "abundance = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs() << '\t';
- //cout << (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)) << endl;
+ scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
}else if (scaler == "linear") {
- colorScale[lookup[i]->getAbundance(j)] = "";
- if (maxbin < lookup[i]->getAbundance(j)) { maxbin = lookup[i]->getAbundance(j); }
- //cout << "abundance = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) << '\t';
- //cout << lookup[i]->getAbundance(j) << endl;
+ scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
}else { //if user enters invalid scaler option.
- cout << scaler << " is not a valid scaler option. I will use log10." << endl;
- colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
- if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()) * 100); }
+ scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
}
- }else { colorScale[0] = "00"; }
+ }else { scaleRelAbund[i][j] = "FFFFFF"; }
}
}
-//cout << "maxbin = " << maxbin << endl;
- //get scaler
- float scalers = 255 / (float) maxbin;
-
-
- //go through map and give each score a color value
- for (it = colorScale.begin(); it != colorScale.end(); it++) {
- it->second = toHex(int(float(it->first) * scalers));
- if(it->second.length() == 1) { it->second = "0" + it->second; }
-//cout << it->first << " " << it->second << endl;
- }
- string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
+ string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.svg";
openOutputFile(filenamesvg, outsvg);
//svg image
//white backround
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + sharedorder->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
//column labels
for (int h = 0; h < lookup.size(); h++) {
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";
}
-
//output legend and color labels
- //go through map and give each score a color value
string color;
int x = 0;
- int y = 90 + (lookup[0]->getNumBins()*5);
- for (it = colorScale.begin(); it != colorScale.end(); it++) {
- color = it->second;
- float value = it->first;
-
- //convert it->first to relative abundance again
- if (scaler == "log10") {
- value = pow(10, value) / 100;
- }else if (scaler == "log2") {
- value = pow(2, value) / 100;
- }else { value = pow(10, value) / 100; }
-
- string itprec = toString(value);
-
- //set precision of relative abundance to 2
- int pos = itprec.find_first_of('.');
- itprec = itprec.substr(0,pos+3);
-
- outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"25\" height=\"10\"/>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + itprec + "</text>\n";
- x += 25;
- }
+ int y = 103 + (lookup[0]->getNumBins()*5);
+ printLegend(y, superMaxRelAbund);
- x = 0;
y = 70;
-
- //start at 1 since bin 0 is nothing
- for (int i = 1; i <= lookup[0]->getNumBins(); i++) {
- for (int j = 0; j < lookup.size(); j++) {
+ for (int i = 0; i < scaleRelAbund[0].size(); i++) {
+ for (int j = 0; j < scaleRelAbund.size(); j++) {
- if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
- if (scaler == "log10") {
- color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];
- }else if (scaler == "log2") {
- color = colorScale[(log2((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];
- }else if (scaler == "linear") {
- color = colorScale[lookup[j]->getAbundance(i)];
- }else { color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))]; }
- }else { color = "OO"; }
-
-
- outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
+ outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
x += 300;
}
x = 0;
y += 5;
}
-
outsvg << "</g>\n</svg>\n";
outsvg.close();
}
//**********************************************************************************************************************
-void HeatMap::sortSharedVectors(){
+void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
try {
//copy lookup and then clear it to refill with sorted.
//loop though lookup and determine if they are shared
}
//clear out lookup to create sorted lookup
+ for (int j = 0; j < lookup.size(); j++) {
+ delete lookup[j];
+ }
lookup.clear();
//create and initialize lookup to empty vectors
cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
+
}
//**********************************************************************************************************************
+void HeatMap::printLegend(int y, float maxbin) {
+ try {
+
+ //output legend and color labels
+ //go through map and give each score a color value
+ string color;
+ int x = 10;
+
+ //prints legend
+ for (int i = 1; i < 255; i++) {
+ color = toHex(int((float)(i)));
+ outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
+ x += 1;
+ }
+
+ //prints legend labels
+ x = 10;
+ for (int i = 1; i<=5; i++) {
+ float label;
+ if(scaler== "log10") { label = maxbin * log10(51*i) / log10(255); }
+ else if(scaler== "log2") { label = maxbin * log2(51*i) / log2(255); }
+ else if(scaler== "linear") { label = maxbin * 51 * i / 255; }
+ else { label = maxbin * log10(51*i) / log10(255); }
+ file://localhost/Users/westcott/Desktop/c.amazon.fn.0.19.rep.fasta
+ label = int(label * 1000 + 0.5);
+ label /= 1000.0;
+ string text = toString(label, 3);
+
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
+ x += 60;
+ }
+ }
+
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMap class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
projects / mothur.git / blobdiff