#include "heatmap.h"
//**********************************************************************************************************************
-HeatMap::HeatMap(){
+HeatMap::HeatMap(string sort, string scale, int num, int fsize, string dir){
try {
globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
- sorted = globaldata->getSorted();
+ m = MothurOut::getInstance();
+// format = globaldata->getFormat();
+ sorted = sort;
+ scaler = scale;
+ outputDir = dir;
+ numOTU = num;
+ fontSize = fsize;
}
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(RAbundVector* rabund) {
+string HeatMap::getPic(RAbundVector* rabund) {
try {
- //get users scaling method
- scaler = globaldata->getScale();
+
float maxRelAbund = 0.0;
if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
}
- scaler = globaldata->getScale();
vector<string> scaleRelAbund(rabund->size(), "");
for(int i=0;i<rabund->size();i++){
float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
+ 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";
}
- string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.bin.svg";
- openOutputFile(filenamesvg, outsvg);
+ string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + rabund->getLabel() + ".heatmap.bin.svg";
+ m->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 << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
//output legend and color labels
string color;
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(vector<SharedRAbundVector*> lookup) {
+string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
try {
+
+ int numBinsToDisplay = lookup[0]->size();
+
+ if (numOTU != 0) { //user want to display a portion of the otus
+ if (numOTU < numBinsToDisplay) { numBinsToDisplay = numOTU; }
+ }
+
//sort lookup so shared bins are on top
- if (isTrue(sorted) == true) { sortSharedVectors(lookup); }
+ if (sorted != "none") { 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.
}
}
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.bin.svg";
- openOutputFile(filenamesvg, outsvg);
+ string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
+ m->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 " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" text-anchor=\"middle\" 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";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" 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;
printLegend(y, superMaxRelAbund);
y = 70;
- for (int i = 0; i < scaleRelAbund[0].size(); i++) {
+ for (int i = 0; i < numBinsToDisplay; 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);
}
}
//**********************************************************************************************************************
-void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
+int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
try {
- //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;
+ /****************** find order of otus **********************/
+ if (sorted == "shared") {
+ place = orderShared(lookup);
+ }else if (sorted == "topotu") {
+ place = orderTopOtu(lookup);
+ }else if (sorted == "topgroup") {
+ place = orderTopGroup(lookup);
+ }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine(); return 1; }
+
+
+ /******************* create copy of lookup *********************/
//create and initialize looktemp as a copy of lookup
for (int i = 0; i < lookup.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
}
looktemp.push_back(temp);
}
+
+ /************************ fill lookup in order given by place *********************/
+ //for each bin
+ for (int i = 0; i < looktemp[0]->size(); i++) { //place
+ //fill lookup // 2 -> 1
+ for (int j = 0; j < looktemp.size(); j++) { // 3 -> 2
+ int newAbund = looktemp[j]->getAbundance(i); // 1 -> 3
+ lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
+ }
+ }
- //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];
+ //delete looktemp -- Sarah look at - this is causing segmentation faults
+ for (int j = 0; j < looktemp.size(); j++) {
+// delete looktemp[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);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMap", "sortSharedVectors");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+map<int, int> HeatMap::orderShared(vector<SharedRAbundVector*>& lookup){
+ try {
+
+ 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;
+
+ vector<int> sharedBins;
+ vector<int> uniqueBins;
+
+ //for each bin
+ for (int i = 0; i < lookup[0]->size(); i++) {
+ int count = 0;
- //initialize place map
- place[i] = 0;
+ //is this bin shared
+ for (int j = 0; j < lookup.size(); j++) { if (lookup[j]->getAbundance(i) != 0) { count++; } }
+
+ if (count < 2) { uniqueBins.push_back(i); }
+ else { sharedBins.push_back(i); }
}
+ //fill place
+ for (int i = 0; i < sharedBins.size(); i++) { place[sharedBins[i]] = i; }
+ for (int i = 0; i < uniqueBins.size(); i++) { place[uniqueBins[i]] = (sharedBins.size() + i); }
+
+ return place;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMap", "orderShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+map<int, int> HeatMap::orderTopOtu(vector<SharedRAbundVector*>& lookup){
+ try {
+
+ 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;
+
+ vector<binCount> totals;
//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++; }
- }
+ for (int i = 0; i < lookup[0]->size(); i++) {
+ int total = 0;
- //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; }
- }
+ for (int j = 0; j < lookup.size(); j++) { total += lookup[j]->getAbundance(i); }
- 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++; }
- }
- }
+ binCount temp(i, total);
+
+ totals.push_back(temp);
}
- //delete looktemp -- Sarah look at - this is causing segmentation faults
- for (int j = 0; j < looktemp.size(); j++) {
-// delete looktemp[j];
- }
+ sort(totals.begin(), totals.end(), comparebinCounts);
+
+ //fill place
+ for (int i = 0; i < totals.size(); i++) { place[totals[i].bin] = i; }
+
+ return place;
}
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", "orderTopOtu");
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";
+}
+//**********************************************************************************************************************
+map<int, int> HeatMap::orderTopGroup(vector<SharedRAbundVector*>& lookup){
+ try {
+
+ 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;
+
+ vector < vector<binCount> > totals; //totals[0] = bin totals for group 0, totals[1] = bin totals for group 1, ...
+ totals.resize(lookup.size());
+
+ //for each bin
+ for (int i = 0; i < lookup[0]->size(); i++) {
+ for (int j = 0; j < lookup.size(); j++) {
+ binCount temp(i, (lookup[j]->getAbundance(i)));
+ totals[j].push_back(temp);
+ }
+ }
+
+ for (int i = 0; i < totals.size(); i++) { sort(totals[i].begin(), totals[i].end(), comparebinCounts); }
+
+ //fill place
+ //grab the top otu for each group adding it if its not already added
+ int count = 0;
+ for (int i = 0; i < totals[0].size(); i++) {
+
+ for (int j = 0; j < totals.size(); j++) {
+ it = place.find(totals[j][i].bin);
+
+ if (it == place.end()) { //not added yet
+ place[totals[j][i].bin] = count;
+ count++;
+ }
+ }
+ }
+
+ return place;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMap", "orderTopGroup");
exit(1);
}
-
}
-
//**********************************************************************************************************************
void HeatMap::printLegend(int y, float maxbin) {
}
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";
- 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";
+ m->errorOut(e, "HeatMap", "printLegend");
exit(1);
}
-
}
+//**********************************************************************************************************************
+
projects / mothur.git / blobdiff