exit(1);
}
}
+
//**********************************************************************************************************************
+
void HeatMap::getPic(OrderVector* order) {
try {
- colorScale.clear();
- rabund = order->getRAbundVector();
+ RAbundVector rabund = order->getRAbundVector();
//get users scaling method
scaler = globaldata->getScale();
- float maxbin = 0.0;
- for (int i = 0; i < rabund.size(); i++) {
- if (rabund.get(i) != 0) { //don't want log value of 0.
- if (scaler == "log10") {
- colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))] = "";
- if (maxbin < (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))) { maxbin = (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000)); }
- }else if (scaler == "log2") {
- colorScale[(log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))] = "";
- if (maxbin < (log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))) { maxbin = (log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000)); }
- }else if (scaler == "linear") {
- colorScale[rabund.get(i)] = "";
- if (maxbin < rabund.get(i)) { maxbin = rabund.get(i); }
- }else { //if user enters invalid scaler option.
- cout << scaler << " is not a valid scaler option. I will use log10." << endl;
- colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))] = "";
- if (maxbin < (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))) { maxbin = (log10((rabund.get(i)) / (float)rabund.getNumSeqs()) * 1000); }
- }
- }else { colorScale[0] = "00"; }
+ float maxRelAbund = 0.0;
+
+ for(int i=0;i<rabund.size();i++){
+ float relAbund = rabund.get(i) / (float)rabund.getNumSeqs();
+ if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
}
- float scalers = 255 / (float) maxbin;
+ 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) * scalers));
- 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);
//svg image
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 300 " + toString((rabund.getNumBins()*5 + 120)) + "\">\n";
+ outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund.getNumBins()*5 + 120)) + "\">\n";
outsvg << "<g>\n";
//white backround
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"300\" height=\"" + toString((rabund.getNumBins()*5 + 120)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"25\">Heatmap at distance " + order->getLabel() + "</text>\n";
-
+ 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;
int x = 0;
int y = 103 + (rabund.getNumBins()*5);
- printLegend(y, maxbin);
+ printLegend(y, maxRelAbund);
y = 70;
- for (int i = 0; i <= rabund.getNumBins(); i++) {
- if (rabund.get(i) != 0) { //don't want log value of 0.
- if (scaler == "log10") {
- color = colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))];
- }else if (scaler == "log2") {
- color = colorScale[(log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))];
- }else if (scaler == "linear") {
- color = colorScale[rabund.get(i)];
- }else { color = colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))]; }
- }else { color = "OO"; }
+ 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.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) {
try {
- colorScale.clear();
//fills vector of sharedsabunds - lookup
- util->getSharedVectors(globaldata->Groups, lookup, sharedorder); //fills group vectors from order vector.
+ vector<SharedRAbundVector*> lookup;
+ util->getSharedVectors(globaldata->Groups, lookup, sharedorder); //fills group vectors from order vector.
+
//sort lookup so shared bins are on top
- if (sorted == "T") { sortSharedVectors(); }
-
- //get users scaling method
+ if (sorted == "T") { sortSharedVectors(lookup); }
+
+ vector<vector<string> > scaleRelAbund;
+ vector<float> maxRelAbund(lookup.size(), 0.0);
+ float superMaxRelAbund = 0;
+
+ 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();
- float maxbin = 0.0;
- for (int i = 0; i < lookup.size(); i++) {
- for (int j = 0; j < lookup[i]->size(); j++) {
+ 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()) * 1000))] = "";
- if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 1000))) { maxbin = (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 1000)); }
+ 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()) * 1000))] = "";
- if (maxbin < (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 1000))) { maxbin = (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 1000)); }
+ 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); }
+ 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()) * 1000))] = "";
- if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 1000))) { maxbin = (log10((lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()) * 1000); }
+ scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
}
- }else { colorScale[0] = "00"; }
+ }else { scaleRelAbund[i][j] = "FFFFFF"; }
+
}
}
- //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; }
- }
-
string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
openOutputFile(filenamesvg, outsvg);
string color;
int x = 0;
int y = 103 + (lookup[0]->getNumBins()*5);
- printLegend(y, maxbin);
-
+ printLegend(y, superMaxRelAbund);
+
y = 70;
- for (int i = 0; i < lookup[0]->size(); 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()) * 1000))];
- }else if (scaler == "log2") {
- color = colorScale[(log2((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 1000))];
- }else if (scaler == "linear") {
- color = colorScale[lookup[j]->getAbundance(i)];
- }else { color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 1000))]; }
- }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
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 = 0;
- if (maxbin != 0) {
- //convert maxbin to relative abundance again
- if (scaler == "log10") {
- maxbin = pow(10, maxbin) / 1000;
- }else if (scaler == "log2") {
- maxbin = pow(2, maxbin) / 1000;
- }else { maxbin = pow(10, maxbin) / 1000; }
- }else { maxbin = 0.00; }
-
- //5 is the number of boxes in the legend
- float maxbinScaler = maxbin / 10;
- float colorScaler = 255 / 10;
+ int x = 10;
//prints legend
- for (int i = 0; i < 10; i++) {
- color = toHex(int((float)(i+1) * colorScaler));
- outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"30\" height=\"10\"/>\n";
- x += 30;
+ 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 -= 30;
- for (int i = 10; i > 0; i = i-2) {
- string label = toString((i * maxbinScaler));
- //set precision of relative abundance to 3
- int pos = label.find_first_of('.');
- label = label.substr(0,pos+4);
+ 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); }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + label + "</text>\n";
- x -= 60;
+ 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);
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