changed heatmap and venn command to use vector of sharedrabunds instead of order...

[mothur.git] / heatmap.cpp

diff --git a/heatmap.cpp b/heatmap.cpp
index 187c953fcaf49501f9985d669cfd7645d7294355..0b1a80e6e9dca67a794653ce171d1b4011287b4a 100644 (file)
--- a/heatmap.cpp
+++ b/heatmap.cpp
@@ -15,8 +15,6 @@ HeatMap::HeatMap(){
                globaldata = GlobalData::getInstance();
                format = globaldata->getFormat();
                sorted = globaldata->getSorted();
-               util = new SharedUtil();
-               
        }
        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";
@@ -30,29 +28,26 @@ HeatMap::HeatMap(){
 
 //**********************************************************************************************************************
 
-void HeatMap::getPic(OrderVector* order) {
+void 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 (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") {
@@ -67,21 +62,21 @@ void HeatMap::getPic(OrderVector* order) {
                }
                
                
-               string filenamesvg = getRootName(globaldata->inputFileName) + rabund.getLabel() + ".heatmap.svg";
+               string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.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 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;
@@ -108,14 +103,9 @@ void HeatMap::getPic(OrderVector* order) {
 
 //**********************************************************************************************************************
 
-void HeatMap::getPic(SharedOrderVector* sharedorder) {
+void 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);  }
                
@@ -155,7 +145,7 @@ void HeatMap::getPic(SharedOrderVector* sharedorder) {
                        }
                }
                
-               string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
+               string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.svg";
                openOutputFile(filenamesvg, outsvg);
                
                //svg image
@@ -164,7 +154,7 @@ void HeatMap::getPic(SharedOrderVector* sharedorder) {
                
                //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++) {
@@ -309,7 +299,7 @@ void HeatMap::printLegend(int y, float maxbin) {
                        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);      }
-                       
+                       file://localhost/Users/westcott/Desktop/c.amazon.fn.0.19.rep.fasta
                        label = int(label * 1000 + 0.5);
                        label /= 1000.0;
                        string text = toString(label, 3);