try {
globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
-
- if (format != "list") { setGroups(); }
+ sorted = globaldata->getSorted();
+ util = new SharedUtil();
}
catch(exception& e) {
//**********************************************************************************************************************
void HeatMap::getPic(OrderVector* order) {
try {
- sabund = order->getSAbundVector();
- string filename = getRootName(globaldata->inputFileName) + "heatmap" + 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 = 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 << "<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);
+ 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 users scaling method
+ scaler = globaldata->getScaler();
+
+ 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)); }
+ //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;
+
+
+ //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; }
+//cout << it->first << " " << it->second << endl;
+ }
+
+ 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 + 120)) + "\">\n";
+ outsvg << "<g>\n";
+
+ //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;
+ 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
+ if (scaler == "log10") {
+ value = pow(10, value) / 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);
+
+ 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;
+ }
- string filename = getRootName(globaldata->inputFileName) + "heatmap" + sharedorder->getLabel();
+ 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++) {
+
+ 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))];
+ }else if (scaler == "log2") {
+ color = colorScale[(log2((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];
+ }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 = "OO"; }
+
+
+ outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
+ x += 300;
+ }
+ x = 0;
+ y += 5;
+ }
+
+
+ outsvg << "</g>\n</svg>\n";
+ outsvg.close();
}
catch(exception& e) {
exit(1);
}
}
+
//**********************************************************************************************************************
-void HeatMap::getSharedVectors(SharedOrderVector* order){
+void HeatMap::sortSharedVectors(){
try {
- lookup.clear();
+ //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
+
+ 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++) {
+ 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());
+ }
+ looktemp.push_back(temp);
+ }
- vector<SharedRAbundVector*> templookup;
+ //clear out lookup to create sorted lookup
+ lookup.clear();
- //create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(order->getMaxRank());
- temp->setLabel(order->getLabel());
- temp->setGroup(globaldata->Groups[i]);
- templookup.push_back(temp);
+ //create and initialize lookup to empty vectors
+ for (int i = 0; i < looktemp.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(looktemp[i]->getLabel());
+ temp->setGroup(looktemp[i]->getGroup());
+ lookup.push_back(temp);
+
+ //initialize place map
+ place[i] = 0;
}
- 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 < templookup.size(); j++) {
- if (chosen.group == templookup[j]->getGroup()) {
- abundance = templookup[j]->getAbundance(chosen.bin);
- templookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
- break;
+
+ //for each bin
+ for (int i = 0; i < looktemp[0]->size(); i++) {
+ count = 0;
+ bool updatePlace = false;
+ //for each group
+ for (int j = 0; j < looktemp.size(); j++) {
+ 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 (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++; }
}
}
}
- //convert templookups rabunds to lookups sabunds
- for (int j = 0; j < templookup.size(); j++) {
- lookup.push_back(templookup[j]->getSharedSAbundVector());
- delete templookup[j];
+ //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 getSharedVectors. 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 getSharedVectors. 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);
}
}
//**********************************************************************************************************************
-void HeatMap::setGroups() {
- 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("");
- }
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
-
- }
- 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";
- 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";
- exit(1);
- }
-}
-/***********************************************************/
+
+
+
+
projects / mothur.git / blobdiff