rabund = order->getRAbundVector();
+ //get users scaling method
+ scaler = globaldata->getScaler();
+
+ float maxbin = 0.0;
for (int i = 0; i < rabund.size(); i++) {
- colorScale[rabund.get(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)); }
+ }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)); }
+ }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); }
+ }
+ }else { colorScale[0] = "00"; }
}
- float scaler = 255 / (float) colorScale.size();
+ 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) * scaler));
+ it->second = toHex(int(float(it->first) * scalers));
if(it->second.length() == 1) { it->second = "0" + it->second; }
}
string filenamesvg = getRootName(globaldata->inputFileName) + order->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 0 300 " + 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=\"300\" height=\"" + toString((rabund.getNumBins()*5 + 120)) + "\"/>";
+ 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; }
+
+ //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++) {
-
- color = colorScale[rabund.get(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))];
+ }else if (scaler == "log2") {
+ color = colorScale[(log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))];
+ }else if (scaler == "linear") {
+ color = colorScale[rabund.get(i)];
+ }else { color = colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))]; }
+ }else { color = "OO"; }
outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" 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();
}
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;
}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;
}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;
}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); }
}
}else { colorScale[0] = "00"; }
-
}
}
-//cout << "maxbin = " << maxbin << endl;
+
//get scaler
float scalers = 255 / (float) maxbin;
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";
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
+ int y = 103 + (lookup[0]->getNumBins()*5);
+ if (maxbin != 0) {
+ //convert maxbin to relative abundance again
if (scaler == "log10") {
- value = pow(10, value) / 100;
+ maxbin = pow(10, maxbin) / 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);
+ 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);
- 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;
+ 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;
- //start at 1 since bin 0 is nothing
- for (int i = 1; i <= lookup[0]->getNumBins(); i++) {
+ for (int i = 0; i <= lookup[0]->getNumBins(); i++) {
for (int j = 0; j < lookup.size(); j++) {
if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
projects / mothur.git / blobdiff