globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
sorted = globaldata->getSorted();
+ util = new SharedUtil();
}
catch(exception& e) {
if(it->second.length() == 1) { it->second = "0" + it->second; }
}
- string filenamesvg = globaldata->inputFileName + ".heatmap." + order->getLabel() + ".svg";
+ string filenamesvg = getRootName(globaldata->inputFileName) + order->getLabel() + ".heatmap.svg";
openOutputFile(filenamesvg, outsvg);
colorScale.clear();
//fills vector of sharedsabunds - lookup
- getSharedVectors(sharedorder);
+ util->getSharedVectors(globaldata->Groups, lookup, sharedorder); //fills group vectors from order vector.
//sort lookup so shared bins are on top
if (sorted == "1") { sortSharedVectors(); }
- //get maxBin
+ //get users scaling method
+ scaler = globaldata->getScaler();
+
+ int maxbin = 0;
for (int i = 0; i < lookup.size(); i++) {
for (int j = 0; j < lookup[i]->size(); j++) {
- colorScale[lookup[i]->getAbundance(j)] = "";
+ //if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
+ //if (scaler == "log10") {
+ // colorScale[-log((log10(lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()))] = "";
+ //cout << "abundance = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << (lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) << '\t';
+ //cout << -log((log10(lookup[i]->getAbundance(j)) / lookup[i]->getNumSeqs())) << endl;
+ //}else if (scaler == "log2") {
+ //colorScale[-log((log2(lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()))] = ""; //cout << (int)log2(lookup[i]->getAbundance(j)) << endl;
+ //cout << "abundance = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs() << '\t';
+ //cout << -log((log2(lookup[i]->getAbundance(j)) / lookup[i]->getNumSeqs())) << 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) / (float)lookup[i]->getNumSeqs() << '\t';
+ //cout << lookup[i]->getAbundance(j) /(float) lookup[i]->getNumSeqs() << endl;
+ //}else { //if user enters invalid scaler option.
+ // cout << scaler << " is not a valid scaler option. I will use log10." << endl;
+ // colorScale[-log(log10(lookup[i]->getAbundance(j) / lookup[i]->getNumSeqs()))] = "";
+ //}
+ //}else { colorScale[0] = "00"; }
+
}
}
//get scaler
- 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; }
+//cout << it->first << " " << it->second << endl;
}
- string filenamesvg = globaldata->inputFileName + ".heatmap." + sharedorder->getLabel() + "." + groupComb + ".svg";
+ string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
openOutputFile(filenamesvg, outsvg);
//svg image
- outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 15)) + "\">\n";
+ outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->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(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";
+
+ //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;
-
- for (int i = 0; i <= lookup[0]->getNumBins(); i++) {
+ int x = 0;
+ int y = 90 + (lookup[0]->getNumBins()*5);
+ for (it = colorScale.begin(); it != colorScale.end(); it++) {
+ color = it->second;
+ 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) + "\">" + toString(it->first) + "</text>\n";
+ x += 25;
+ }
+
+ 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++) {
-
- color = colorScale[lookup[j]->getAbundance(i)];
-
+
+ //if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
+ //if (scaler == "log10") {
+ // color = colorScale[(int)log10(lookup[j]->getAbundance(i))];
+ //}else if (scaler == "log2") {
+ // color = colorScale[(int)log2(lookup[j]->getAbundance(i))];
+ // }else if (scaler == "linear") {
+ color = colorScale[lookup[j]->getAbundance(i)];
+ //}else { color = colorScale[(int)log10(lookup[j]->getAbundance(i))]; }
+ //}else { color = "OO"; }
+
+
outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
x += 300;
}
- x = 15;
+ x = 0;
y += 5;
}
+
outsvg << "</g>\n</svg>\n";
outsvg.close();
exit(1);
}
}
-//**********************************************************************************************************************
-void HeatMap::getSharedVectors(SharedOrderVector* order){
- try {
-
- //delete lookup
- for (int j = 0; j < lookup.size(); j++) {
- delete lookup[j];
- }
-
- lookup.clear();
-
- groupComb = "";
-
- //create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
- temp->setLabel(order->getLabel());
- temp->setGroup(globaldata->Groups[i]);
- groupComb += globaldata->Groups[i];
- lookup.push_back(temp);
- }
-
- int numSeqs = order->size();
- //sample all the members
- for(int i=0;i<numSeqs;i++){
- //get first sample
- individual chosen = order->get(i);
- int abundance;
-
- //set info for sharedvector in chosens group
- for (int j = 0; j < lookup.size(); j++) {
- if (chosen.group == lookup[j]->getGroup()) {
- abundance = lookup[j]->getAbundance(chosen.bin);
- lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
- break;
- }
- }
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the HeatMap class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-
//**********************************************************************************************************************
void HeatMap::sortSharedVectors(){
//if they are then insert in the front
//if not push to back
- bool shared;
vector<SharedRAbundVector*> looktemp;
+ 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.
+ map<int, int>::iterator it;
+ int count;
//create and initialize looktemp as a copy of lookup
for (int i = 0; i < lookup.size(); i++) {
//create and initialize lookup to empty vectors
for (int i = 0; i < looktemp.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector();
- lookup.push_back(temp);
+ temp->setLabel(looktemp[i]->getLabel());
+ temp->setGroup(looktemp[i]->getGroup());
+ lookup.push_back(temp);
+
+ //initialize place map
+ place[i] = 0;
}
+
//for each bin
for (int i = 0; i < looktemp[0]->size(); i++) {
- shared = true;
+ count = 0;
+ bool updatePlace = false;
//for each group
for (int j = 0; j < looktemp.size(); j++) {
- if (looktemp[j]->getAbundance(i) == 0) { shared = false; }
+ if (looktemp[j]->getAbundance(i) != 0) { count++; }
}
//fill lookup
for (int j = 0; j < looktemp.size(); j++) {
//if they are not shared then push to back, if they are not insert in front
- if (shared == false) { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
- else { lookup[j]->push_front(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
+ if (count < 2) { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
+ //they are shared by some
+ else { lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup()); updatePlace = true; }
+ }
+
+ if (updatePlace == true) {
+ //move place holders below where you entered up to "make space" for you entry
+ for (it = place.begin(); it!= place.end(); it++) {
+ if (it->first < count) { it->second++; }
+ }
}
}
projects / mothur.git / blobdiff