working on pam

[mothur.git] / heatmap.cpp

diff --git a/heatmap.cpp b/heatmap.cpp
index 7d6eeaa146b84db4233974a70c16dc482bc12ef9..514c7af15312b60d4787bb0aa659dbd9f1ccaf08 100644 (file)
--- a/heatmap.cpp
+++ b/heatmap.cpp
@@ -10,9 +10,8 @@
 #include "heatmap.h"
 
 //**********************************************************************************************************************
-HeatMap::HeatMap(string sort, string scale, int num, int fsize, string dir){
+HeatMap::HeatMap(string sort, string scale, int num, int fsize, string dir, string i){
        try {
-               globaldata = GlobalData::getInstance();
                m = MothurOut::getInstance();
 //             format = globaldata->getFormat();
                sorted = sort;
@@ -20,6 +19,7 @@ HeatMap::HeatMap(string sort, string scale, int num, int fsize, string dir){
                outputDir = dir;
                numOTU = num;
                fontSize = fsize;
+               inputfile = i;
        }
        catch(exception& e) {
                m->errorOut(e, "HeatMap", "HeatMap");
@@ -70,7 +70,7 @@ string HeatMap::getPic(RAbundVector* rabund) {
                }
                
                
-               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + rabund->getLabel() + ".heatmap.bin.svg";
+               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + rabund->getLabel() + ".heatmap.bin.svg";
                m->openOutputFile(filenamesvg, outsvg);
                
                //svg image
@@ -119,7 +119,8 @@ string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
                }
                
                //sort lookup so shared bins are on top
-               if (sorted != "none") {  sortSharedVectors(lookup);  }
+        vector<string> sortedLabels = m->currentSharedBinLabels;
+               if (sorted != "none") {  sortedLabels = sortSharedVectors(lookup);  }
                
                vector<vector<string> > scaleRelAbund;
                vector<float> maxRelAbund(lookup[0]->size(), 0.0);              
@@ -156,38 +157,48 @@ string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
                        }
                }
 
-               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
+               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
                m->openOutputFile(filenamesvg, outsvg);
+        int binHeight = 20;
+        int labelBump = 100;
+        int binWidth = 300;
                
                //svg image
-               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((numBinsToDisplay*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() * binWidth + labelBump) + " " + toString((numBinsToDisplay*binHeight + 120))  + "\">\n";
                outsvg << "<g>\n";
                
                //white backround
-               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((numBinsToDisplay*5 + 120))  + "\"/>"; 
+               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * binWidth+labelBump) + "\" height=\"" + toString((numBinsToDisplay*binHeight + 120))  + "\"/>";
                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\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n"; 
+               for (int h = 0; h < lookup.size()+1; h++) {
+            if (h == 0) {
+                string tempLabel = "OTU";
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(labelBump-labelBump/2+1) + "\" y=\"50\">" + tempLabel + "</text>\n";
+            }else {
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((binWidth * h) - 150) - ((int)lookup[h-1]->getGroup().length() / 2)+labelBump/2) + "\" y=\"50\">" + lookup[h-1]->getGroup() + "</text>\n";
+            }
                }
 
                //output legend and color labels
                string color;
                int x = 0;
-               int y = 103 + (numBinsToDisplay*5);
+               int y = 103 + (numBinsToDisplay*binHeight);
                printLegend(y, superMaxRelAbund);
                
                y = 70;
                for (int i = 0; i < numBinsToDisplay; i++) {
+            outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + sortedLabels[i] + "</text>\n";
+            x += labelBump;
                        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 << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"" + toString(binWidth) +  "\" height=\"" + toString(binHeight) +  "\"/>\n";
+                               x += binWidth;
                        }
                        x = 0;
-                       y += 5;
+                       y += binHeight;
                }
                
                outsvg << "</g>\n</svg>\n";
@@ -203,12 +214,14 @@ string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 }
 
 //**********************************************************************************************************************
-int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
+vector<string> HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
        try {
                                
                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;
+        
+        vector<string> sortedLabels = m->currentSharedBinLabels;
                
                /****************** find order of otus **********************/
                if (sorted == "shared") {
@@ -217,7 +230,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
                        place = orderTopOtu(lookup);    
                }else if (sorted == "topgroup") {
                        place = orderTopGroup(lookup);  
-               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return 1; }
+               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return sortedLabels; }
                                
                
                /******************* create copy of lookup *********************/
@@ -241,6 +254,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
                                int newAbund = looktemp[j]->getAbundance(i);                                                                                            // 1 -> 3
                                lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
                        }
+            sortedLabels[place[i]] = m->currentSharedBinLabels[i];
                }
                
                //delete looktemp -- Sarah look at - this is causing segmentation faults
@@ -248,7 +262,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
 //                     delete looktemp[j];
                }
                
-               return 0;
+               return sortedLabels;
                
        }
        catch(exception& e) {
@@ -416,7 +430,8 @@ string HeatMap::getPic(vector<SharedRAbundFloatVector*> lookup) {
                }
                
                //sort lookup so shared bins are on top
-               if (sorted != "none") {  sortSharedVectors(lookup);  }
+               vector<string> sortedLabels = m->currentSharedBinLabels;
+               if (sorted != "none") {  sortedLabels = sortSharedVectors(lookup);  }
                
                vector<vector<string> > scaleRelAbund;
                vector<float> maxRelAbund(lookup.size(), 0.0);          
@@ -453,38 +468,49 @@ string HeatMap::getPic(vector<SharedRAbundFloatVector*> lookup) {
                        }
                }
 
-               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
+               string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
                m->openOutputFile(filenamesvg, outsvg);
+        
+        int binHeight = 20;
+        int labelBump = 100;
+        int binWidth = 300;
                
                //svg image
-               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((numBinsToDisplay*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() * binWidth + labelBump) + " " + toString((numBinsToDisplay*binHeight + 120))  + "\">\n";
                outsvg << "<g>\n";
                
                //white backround
-               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((numBinsToDisplay*5 + 120))  + "\"/>"; 
+               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * binWidth+labelBump) + "\" height=\"" + toString((numBinsToDisplay*binHeight + 120))  + "\"/>";
                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\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n"; 
-               }
-
+               for (int h = 0; h < lookup.size()+1; h++) {
+            if (h == 0) {
+                string tempLabel = "OTU";
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(labelBump-labelBump/2+1) + "\" y=\"50\">" + tempLabel + "</text>\n";
+            }else {
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((binWidth * h) - 150) - ((int)lookup[h-1]->getGroup().length() / 2)+labelBump/2) + "\" y=\"50\">" + lookup[h-1]->getGroup() + "</text>\n";
+            }
+               }
+        
                //output legend and color labels
                string color;
                int x = 0;
-               int y = 103 + (numBinsToDisplay*5);
+               int y = 103 + (numBinsToDisplay*binHeight);
                printLegend(y, superMaxRelAbund);
                
                y = 70;
                for (int i = 0; i < numBinsToDisplay; i++) {
+            outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + sortedLabels[i] + "</text>\n";
+            x += labelBump;
                        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 << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"" + toString(binWidth) +  "\" height=\"" + toString(binHeight) +  "\"/>\n";
+                               x += binWidth;
                        }
                        x = 0;
-                       y += 5;
+                       y += binHeight;
                }
                
                outsvg << "</g>\n</svg>\n";
@@ -499,12 +525,14 @@ string HeatMap::getPic(vector<SharedRAbundFloatVector*> lookup) {
        }
 }
 //**********************************************************************************************************************
-int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
+vector<string> HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
        try {
                                
                vector<SharedRAbundFloatVector*> 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;
+        
+        vector<string> sortedLabels = m->currentSharedBinLabels;
                
                /****************** find order of otus **********************/
                if (sorted == "shared") {
@@ -513,7 +541,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
                        place = orderTopOtu(lookup);    
                }else if (sorted == "topgroup") {
                        place = orderTopGroup(lookup);  
-               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return 1; }
+               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return sortedLabels; }
                                
                
                /******************* create copy of lookup *********************/
@@ -536,6 +564,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
                        for (int j = 0; j < looktemp.size(); j++) {                                                                                                             // 3 -> 2
                                float newAbund = looktemp[j]->getAbundance(i);                                                                                          // 1 -> 3
                                lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
+                sortedLabels[place[i]] = m->currentSharedBinLabels[i];
                        }
                }
                
@@ -544,7 +573,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
 //                     delete looktemp[j];
                }
                
-               return 0;
+               return sortedLabels;
                
        }
        catch(exception& e) {