#include "heatmap.h"
//**********************************************************************************************************************
-HeatMap::HeatMap(){
+HeatMap::HeatMap(string sort, string scale, string dir){
try {
globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
- sorted = globaldata->getSorted();
- util = new SharedUtil();
-
+ m = MothurOut::getInstance();
+// format = globaldata->getFormat();
+ sorted = sort;
+ scaler = scale;
+ outputDir = dir;
}
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";
+ m->errorOut(e, "HeatMap", "HeatMap");
exit(1);
}
}
//**********************************************************************************************************************
-void HeatMap::getPic(OrderVector* order) {
+string HeatMap::getPic(RAbundVector* rabund) {
try {
- RAbundVector rabund = order->getRAbundVector();
-
- //get users scaling method
- scaler = globaldata->getScale();
float maxRelAbund = 0.0;
- for(int i=0;i<rabund.size();i++){
- float relAbund = rabund.get(i) / (float)rabund.getNumSeqs();
+ for(int i=0;i<rabund->size();i++){
+ float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
}
- scaler = globaldata->getScale();
- vector<string> scaleRelAbund(rabund.size(), "");
+ vector<string> scaleRelAbund(rabund->size(), "");
- for(int i=0;i<rabund.size();i++){
- float relAbund = rabund.get(i) / (float)rabund.getNumSeqs();
+ 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 (m->control_pressed) { return "control"; }
+
+ 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") {
}
- string filenamesvg = getRootName(globaldata->inputFileName) + rabund.getLabel() + ".heatmap.svg";
+ string filenamesvg = outputDir + getRootName(getSimpleName(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 << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/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";
+ 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);
+ int y = 103 + (rabund->getNumBins()*5);
printLegend(y, maxRelAbund);
y = 70;
for (int i = 0; i < scaleRelAbund.size(); i++) {
+ if (m->control_pressed) { outsvg.close(); return "control"; }
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();
-
+ return filenamesvg;
}
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";
+ m->errorOut(e, "HeatMap", "getPic");
exit(1);
}
}
//**********************************************************************************************************************
-void HeatMap::getPic(SharedOrderVector* sharedorder) {
+string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
try {
-
- //fills vector of sharedsabunds - lookup
- vector<SharedRAbundVector*> lookup;
-
- util->getSharedVectors(globaldata->Groups, lookup, sharedorder); //fills group vectors from order vector.
-
//sort lookup so shared bins are on top
- if (sorted == "T") { sortSharedVectors(lookup); }
+ if (isTrue(sorted) == true) { sortSharedVectors(lookup); }
vector<vector<string> > scaleRelAbund;
vector<float> maxRelAbund(lookup.size(), 0.0);
if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
}
- scaler = globaldata->getScale();
-
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++){
+ if (m->control_pressed) { return "control"; }
float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
}
}else { scaleRelAbund[i][j] = "FFFFFF"; }
-
+
}
}
-
- string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
+
+ string filenamesvg = outputDir + getRootName(getSimpleName(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 << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/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";
+ 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++) {
y = 70;
for (int i = 0; i < scaleRelAbund[0].size(); i++) {
for (int j = 0; j < scaleRelAbund.size(); j++) {
+ if (m->control_pressed) { outsvg.close(); return "control"; }
outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
x += 300;
outsvg << "</g>\n</svg>\n";
outsvg.close();
+ return filenamesvg;
+
}
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";
+ m->errorOut(e, "HeatMap", "getPic");
exit(1);
}
}
looktemp.push_back(temp);
}
- //clear out lookup to create sorted lookup
- lookup.clear();
+ //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++) {
//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()); }
+ if (count < 2) { lookup[j]->push_back(looktemp[j]->getAbundance(i), looktemp[j]->getGroup()); }
//they are shared by some
else { lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup()); updatePlace = true; }
}
}
}
- //delete looktemp
+ //delete looktemp -- Sarah look at - this is causing segmentation faults
for (int j = 0; j < looktemp.size(); j++) {
- delete looktemp[j];
+// delete looktemp[j];
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMap", "sortSharedVectors");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************
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);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMap", "printLegend");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMap class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
projects / mothur.git / blobdiff