rabund = order->getRAbundVector();
//get users scaling method
- scaler = globaldata->getScaler();
+ 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()) * 100))] = "";
- if (maxbin < (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))) { maxbin = (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100)); }
+ 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()) * 100))] = "";
- if (maxbin < (log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))) { maxbin = (log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100)); }
+ 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()) * 100))] = "";
- if (maxbin < (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))) { maxbin = (log10((rabund.get(i)) / (float)rabund.getNumSeqs()) * 100); }
+ 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"; }
}
outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"25\">Heatmap at distance " + order->getLabel() + "</text>\n";
//output legend and color labels
- //go through map and give each score a color value
string color;
int x = 0;
int y = 103 + (rabund.getNumBins()*5);
- if (maxbin != 0) {
- //convert maxbin to relative abundance again
- if (scaler == "log10") {
- maxbin = pow(10, maxbin) / 100;
- }else if (scaler == "log2") {
- maxbin = pow(2, maxbin) / 100;
- }else { maxbin = pow(10, maxbin) / 100; }
- }else { maxbin = 0.00; }
+ printLegend(y, maxbin);
- //5 is the number of boxes in the legend
- float maxbinScaler = maxbin / 10;
- float colorScaler = 255 / 10;
-
- for (int i = 0; i < 10; i++) {
- string label = toString(((i+1) * maxbinScaler));
- //set precision of relative abundance to 3
- int pos = label.find_first_of('.');
- label = label.substr(0,pos+4);
- 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";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + label + "</text>\n";
- x += 30;
- }
-
- x = 0;
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()) * 100))];
+ color = colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))];
}else if (scaler == "log2") {
- color = colorScale[(log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))];
+ 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()) * 100))]; }
+ }else { color = colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 1000))]; }
}else { color = "OO"; }
outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
//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(); }
+
//get users scaling method
- scaler = globaldata->getScaler();
+ scaler = globaldata->getScale();
float maxbin = 0.0;
for (int i = 0; i < lookup.size(); i++) {
for (int j = 0; j < lookup[i]->size(); j++) {
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)); }
+ 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)); }
}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)); }
+ 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)); }
}else if (scaler == "linear") {
colorScale[lookup[i]->getAbundance(j)] = "";
if (maxbin < lookup[i]->getAbundance(j)) { maxbin = lookup[i]->getAbundance(j); }
}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); }
+ 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); }
}
}else { colorScale[0] = "00"; }
}
}
//output legend and color labels
- //go through map and give each score a color value
string color;
int x = 0;
int y = 103 + (lookup[0]->getNumBins()*5);
- if (maxbin != 0) {
- //convert maxbin to relative abundance again
- if (scaler == "log10") {
- maxbin = pow(10, maxbin) / 100;
- }else if (scaler == "log2") {
- maxbin = pow(2, maxbin) / 100;
- }else { maxbin = pow(10, maxbin) / 100; }
- }else { maxbin = 0.00; }
-
- //((lookup.size() * 300) / 60) is the number of boxes in the legend
- float maxbinScaler = maxbin / ((lookup.size() * 300) / 60);
- float colorScaler = 255 / ((lookup.size() * 300) / 60);
-
- for (int i = 0; i < ((lookup.size() * 300) / 60); i++) {
- string label = toString(((i+1) * maxbinScaler));
- //set precision of relative abundance to 3
- int pos = label.find_first_of('.');
- label = label.substr(0,pos+4);
+ printLegend(y, maxbin);
- color = toHex(int(((i+1) * colorScaler) + 15));
- outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"30\" height=\"10\"/>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + label + "</text>\n";
- x += 30;
- }
-
- x = 0;
y = 70;
-
- for (int i = 0; i <= lookup[0]->getNumBins(); i++) {
+ for (int i = 0; i < lookup[0]->size(); i++) {
for (int j = 0; j < lookup.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))];
+ 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()) * 100))];
+ 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()) * 100))]; }
+ }else { color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 1000))]; }
}else { color = "OO"; }
}
//**********************************************************************************************************************
+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;
+
+ //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;
+ }
+
+ //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);
+
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + label + "</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