globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
- if (format != "list") { setGroups(); }
-
}
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";
//**********************************************************************************************************************
void HeatMap::getPic(OrderVector* order) {
try {
- sabund = order->getSAbundVector();
- string filename = getRootName(globaldata->inputFileName) + order->getLabel();
+ colorScale.clear();
+
+ rabund = order->getRAbundVector();
+
+ for (int i = 0; i < rabund.size(); i++) {
+ colorScale[rabund.get(i)] = "";
+ }
+
+ float scaler = 255 / (float) colorScale.size();
+
+ //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; }
+ }
+
+ string filenamesvg = globaldata->inputFileName + ".heatmap." + order->getLabel() + ".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 << "<g>\n";
+
+ int x = 15;
+ int y = 15;
+ string color;
+
+ for (int i = 0; i <= rabund.getNumBins(); i++) {
+
+ color = colorScale[rabund.get(i)];
+
+ 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.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";
//**********************************************************************************************************************
void HeatMap::getPic(SharedOrderVector* sharedorder) {
try {
+ colorScale.clear();
+
+ //fills vector of sharedsabunds - lookup
getSharedVectors(sharedorder);
+ //sort lookup so shared bins are on top
+ sortSharedVectors();
+
+ //get maxBin
+ for (int i = 0; i < lookup.size(); i++) {
+ for (int j = 0; j < lookup[i]->size(); j++) {
+ colorScale[lookup[i]->getAbundance(j)] = "";
+ }
+ }
+
+ //get scaler
+ float scaler = 255 / (float) colorScale.size();
+
+ //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; }
+ }
+
+ string filenamesvg = globaldata->inputFileName + ".heatmap." + sharedorder->getLabel() + "." + groupComb + ".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 << "<g>\n";
+
+ int x = 15;
+ int y = 15;
+ string color;
+
+ for (int i = 0; i <= lookup[0]->getNumBins(); i++) {
+
+ for (int j = 0; j < lookup.size(); j++) {
+
+ color = colorScale[lookup[j]->getAbundance(i)];
+
+ outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
+ x += 300;
+ }
+ x = 15;
+ y += 5;
+ }
+ outsvg << "</g>\n</svg>\n";
+
+ outsvg.close();
+
+
}
catch(exception& e) {
//**********************************************************************************************************************
void HeatMap::getSharedVectors(SharedOrderVector* order){
try {
+
+ //delete lookup
+ for (int j = 0; j < lookup.size(); j++) {
+ delete lookup[j];
+ }
+
lookup.clear();
- vector<SharedRAbundVector*> templookup;
+ 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]);
- templookup.push_back(temp);
+ groupComb += globaldata->Groups[i];
+ lookup.push_back(temp);
}
int numSeqs = order->size();
int abundance;
//set info for sharedvector in chosens group
- for (int j = 0; j < templookup.size(); j++) {
- if (chosen.group == templookup[j]->getGroup()) {
- abundance = templookup[j]->getAbundance(chosen.bin);
- templookup[j]->set(chosen.bin, (abundance + 1), chosen.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;
}
}
}
- //convert templookups rabunds to lookups sabunds
- for (int j = 0; j < templookup.size(); j++) {
- lookup.push_back(templookup[j]->getSharedSAbundVector());
- delete templookup[j];
- }
-
-
}
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";
}
+
//**********************************************************************************************************************
-void HeatMap::setGroups() {
+void HeatMap::sortSharedVectors(){
try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
- }else{//user has enter "all" and wants the default groups
- globaldata->Groups.clear();
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- globaldata->setGroups("");
+ //copy lookup and then clear it to refill with sorted.
+ //loop though lookup and determine if they are shared
+ //if they are then insert in the front
+ //if not push to back
+
+ bool shared;
+ vector<SharedRAbundVector*> looktemp;
+
+ //create and initialize looktemp as a copy of lookup
+ for (int i = 0; i < lookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
+ temp->setLabel(lookup[i]->getLabel());
+ temp->setGroup(lookup[i]->getGroup());
+ //copy lookup i's info
+ for (int j = 0; j < lookup[i]->size(); j++) {
+ temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
}
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ looktemp.push_back(temp);
+ }
+
+ //clear out lookup to create sorted lookup
+ lookup.clear();
+
+ //create and initialize lookup to empty vectors
+ for (int i = 0; i < looktemp.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ lookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < looktemp[0]->size(); i++) {
+ shared = true;
+ //for each group
+ for (int j = 0; j < looktemp.size(); j++) {
+ if (looktemp[j]->getAbundance(i) == 0) { shared = false; }
}
+
+ //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()); }
+ }
+ }
+
+ //delete looktemp
+ for (int j = 0; j < looktemp.size(); j++) {
+ delete looktemp[j];
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the HeatMap class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
- }
+ }
}
-/***********************************************************/
+
+//**********************************************************************************************************************
+
+
+
+
+
projects / mothur.git / blobdiff