#include "heatmap.h"
//**********************************************************************************************************************
-HeatMap::HeatMap(){
+HeatMap::HeatMap(string sort, string scale){
try {
globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
-
- if (format != "list") { setGroups(); }
-
+// format = globaldata->getFormat();
+ sorted = sort;
+ scaler = scale;
}
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";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "HeatMap", "HeatMap");
exit(1);
}
}
+
//**********************************************************************************************************************
-void HeatMap::getPic(OrderVector* order) {
+
+void HeatMap::getPic(RAbundVector* rabund) {
try {
- sabund = order->getSAbundVector();
- string filename = getRootName(globaldata->inputFileName) + order->getLabel();
+
+
+ float maxRelAbund = 0.0;
+
+ for(int i=0;i<rabund->size();i++){
+ float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
+ if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
+ }
+
+
+ vector<string> scaleRelAbund(rabund->size(), "");
+
+ for(int i=0;i<rabund->size();i++){
+ float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
+
+ if (rabund->get(i) != 0) { //don't want log value of 0.
+ if (scaler == "log10") {
+ scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
+ }else if (scaler == "log2") {
+ scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
+ }else if (scaler == "linear") {
+ scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
+ }else { //if user enters invalid scaler option.
+ scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund)))) + "0000";
+ }
+ }
+ else { scaleRelAbund[i] = "FFFFFF"; }
+ }
+
+
+ string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.bin.svg";
+ openOutputFile(filenamesvg, outsvg);
+
+ //svg image
+ outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund->getNumBins()*5 + 120)) + "\">\n";
+ outsvg << "<g>\n";
+
+ //white backround
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((rabund->getNumBins()*5 + 120)) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
+
+ //output legend and color labels
+ string color;
+ int x = 0;
+ int y = 103 + (rabund->getNumBins()*5);
+ printLegend(y, maxRelAbund);
+
+ y = 70;
+ for (int i = 0; i < scaleRelAbund.size(); i++) {
+
+ outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" 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";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "HeatMap", "getPic");
exit(1);
}
}
+
//**********************************************************************************************************************
-void HeatMap::getPic(SharedOrderVector* sharedorder) {
+
+void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
try {
- getSharedVectors(sharedorder);
+ //sort lookup so shared bins are on top
+ if (isTrue(sorted) == true) { sortSharedVectors(lookup); }
+
+ vector<vector<string> > scaleRelAbund;
+ vector<float> maxRelAbund(lookup.size(), 0.0);
+ float superMaxRelAbund = 0;
+
+ for(int i = 0; i < lookup.size(); i++){
+ for(int j=0; j<lookup[i]->size(); j++){
+
+ float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
+ if(relAbund > maxRelAbund[i]){ maxRelAbund[i] = relAbund; }
+ }
+ if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
+ }
+
+ scaleRelAbund.resize(lookup.size());
+ for(int i=0;i<lookup.size();i++){
+ scaleRelAbund[i].assign(lookup[i]->size(), "");
+ for(int j=0;j<lookup[i]->size();j++){
+ float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
+
+ if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
+ if (scaler == "log10") {
+ scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
+ }else if (scaler == "log2") {
+ scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
+ }else if (scaler == "linear") {
+ scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
+ }else { //if user enters invalid scaler option.
+ scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
+ }
+ }else { scaleRelAbund[i][j] = "FFFFFF"; }
+
+ }
+ }
+
+ string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.bin.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 " + lookup[0]->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
+ string color;
+ int x = 0;
+ int y = 103 + (lookup[0]->getNumBins()*5);
+ printLegend(y, superMaxRelAbund);
+
+ y = 70;
+ for (int i = 0; i < scaleRelAbund[0].size(); i++) {
+ for (int j = 0; j < scaleRelAbund.size(); j++) {
+
+ outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "HeatMap", "getPic");
exit(1);
}
}
+
//**********************************************************************************************************************
-void HeatMap::getSharedVectors(SharedOrderVector* order){
+void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
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*> templookup;
+ 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 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);
+ //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);
}
- 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;
+ //clear out lookup to create sorted lookup -- Sarah look at - this is causing segmentation faults
+ for (int j = 0; j < lookup.size(); j++) {
+// delete lookup[j];
+ }
+ lookup.clear(); //doesn't this do the job?
+
+ //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;
+ }
+
+
+ //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 -- Sarah look at - this is causing segmentation faults
+ 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";
+ errorOut(e, "HeatMap", "sortSharedVectors");
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::setGroups() {
+
+void HeatMap::printLegend(int y, float maxbin) {
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]);
- }
+
+ //output legend and color labels
+ //go through map and give each score a color value
+ string color;
+ int x = 10;
+
+ //prints legend
+ for (int i = 1; i < 255; i++) {
+ color = toHex(int((float)(i)));
+ outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
+ x += 1;
}
+ //prints legend labels
+ x = 10;
+ for (int i = 1; i<=5; i++) {
+ float label;
+ if(scaler== "log10") { label = maxbin * log10(51*i) / log10(255); }
+ else if(scaler== "log2") { label = maxbin * log2(51*i) / log2(255); }
+ else if(scaler== "linear") { label = maxbin * 51 * i / 255; }
+ else { label = maxbin * log10(51*i) / log10(255); }
+ label = int(label * 1000 + 0.5);
+ label /= 1000.0;
+ string text = toString(label, 3);
+
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
+ x += 60;
+ }
}
+
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";
+ errorOut(e, "HeatMap", "printLegend");
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