added log10 and log2 scalers for heatmap

diff --git a/globaldata.cpp b/globaldata.cpp
index 2c02ca9ad560f73ecea8277420fb569b04844d82..6ab20f3ced51bc003f6beb0760753023e2cdc76f 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -305,7 +305,7 @@ void GlobalData::clear() {
        step                    =       "0.01";
        form                    =       "integral";
        sorted                  =       "1";  //0 means don't sort, 1 means sort.
-       scaler                  =       "log2";
+       scaler                  =       "log10";
 }
 
 //*******************************************************/

diff --git a/heatmap.cpp b/heatmap.cpp
index 75a2b873f917dfc872d443f73bb17e7d21dbb2db..d75f6f6410d8a6f9cc97a40a959c17caf1b6e0e5 100644 (file)
--- a/heatmap.cpp
+++ b/heatmap.cpp
@@ -95,35 +95,39 @@ void HeatMap::getPic(SharedOrderVector* sharedorder) {
                //get users scaling method
                scaler = globaldata->getScaler();
                
-               int maxbin = 0;
+               float maxbin = 0.0;
                for (int i = 0; i < lookup.size(); i++) {
                        for (int j = 0; j < lookup[i]->size(); j++) {
-                               //if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
-                                       //if (scaler == "log10") {
-                                       //      colorScale[-log((log10(lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()))] = "";  
+                               if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
+                                       if (scaler == "log10") {
+                                               colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";  
+                                               if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
        //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << (lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) << '\t';
-       //cout << -log((log10(lookup[i]->getAbundance(j)) / lookup[i]->getNumSeqs())) << endl;
-                                       //}else if (scaler == "log2") {
-                                               //colorScale[-log((log2(lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()))] = "";  //cout << (int)log2(lookup[i]->getAbundance(j)) << endl;
+       //cout << (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)) << endl;
+                                       }else if (scaler == "log2") {
+                                               colorScale[(log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";  
+                                               if (maxbin < (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
        //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs() << '\t';
-       //cout << -log((log2(lookup[i]->getAbundance(j)) / lookup[i]->getNumSeqs())) << endl;
-                               //      }else if (scaler == "linear") {
+       //cout << (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)) << endl;
+                                       }else if (scaler == "linear") {
                                                colorScale[lookup[i]->getAbundance(j)] = "";
                                                if (maxbin < lookup[i]->getAbundance(j)) { maxbin = lookup[i]->getAbundance(j); }
-       //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs() << '\t';
-       //cout << lookup[i]->getAbundance(j) /(float) lookup[i]->getNumSeqs() << endl;
-                                       //}else {  //if user enters invalid scaler option.
-                                       //      cout << scaler << " is not a valid scaler option. I will use log10." << endl;
-                                       //      colorScale[-log(log10(lookup[i]->getAbundance(j) / lookup[i]->getNumSeqs()))] = "";   
-                                       //} 
-                               //}else { colorScale[0] = "00";  }
+       //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) << '\t';
+       //cout << lookup[i]->getAbundance(j) << endl;
+                                       }else {  //if user enters invalid scaler option.
+                                               cout << scaler << " is not a valid scaler option. I will use log10." << endl;
+                                               colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = ""; 
+                                               if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()) * 100); }  
+                                       } 
+                               }else { colorScale[0] = "00";  }
                                
                        }
                }
-               
+//cout << "maxbin = "  << maxbin << endl;      
                //get scaler
                float scalers = 255 / (float) maxbin;
                
+               
                //go through map and give each score a color value
                for (it = colorScale.begin(); it != colorScale.end(); it++) {
                        it->second = toHex(int(float(it->first) * scalers));
@@ -155,8 +159,23 @@ void HeatMap::getPic(SharedOrderVector* sharedorder) {
                int y = 90 + (lookup[0]->getNumBins()*5);
                for (it = colorScale.begin(); it != colorScale.end(); it++) {
                        color = it->second;     
+                       float value = it->first;
+                       
+                       //convert it->first to relative abundance again
+                       if (scaler == "log10") {
+                               value = pow(10, value) / 100;
+                       }else if (scaler == "log2") {
+                               value = pow(2, value) / 100;
+                       }else {  value = pow(10, value) / 100;  } 
+                       
+                       string itprec = toString(value);
+                       
+                       //set precision of relative abundance to 2
+                       int pos = itprec.find_first_of('.');
+                       itprec = itprec.substr(0,pos+3);
+
                        outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"25\" height=\"10\"/>\n";
-                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + toString(it->first) + "</text>\n";
+                       outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + itprec + "</text>\n";
                        x += 25;
                }
                
@@ -167,15 +186,15 @@ void HeatMap::getPic(SharedOrderVector* sharedorder) {
                for (int i = 1; i <= lookup[0]->getNumBins(); i++) {
                        for (int j = 0; j < lookup.size(); j++) {
                                
-                               //if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
-                                       //if (scaler == "log10") {
-                                       //      color = colorScale[(int)log10(lookup[j]->getAbundance(i))];  
-                                       //}else if (scaler == "log2") {
-                                       //      color = colorScale[(int)log2(lookup[j]->getAbundance(i))];  
-                               //      }else if (scaler == "linear") {
+                               if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
+                                       if (scaler == "log10") {
+                                               color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];  
+                                       }else if (scaler == "log2") {
+                                               color = colorScale[(log2((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];  
+                                       }else if (scaler == "linear") {
                                                color = colorScale[lookup[j]->getAbundance(i)]; 
-                                       //}else {  color = colorScale[(int)log10(lookup[j]->getAbundance(i))];  } 
-                               //}else { color = "OO";  }
+                                       }else {  color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];      } 
+                               }else { color = "OO";  }
 
                                
                                outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
@@ -185,11 +204,9 @@ void HeatMap::getPic(SharedOrderVector* sharedorder) {
                        y += 5;
                }
                
-               outsvg << "</g>\n</svg>\n";
                
+               outsvg << "</g>\n</svg>\n";
                outsvg.close();
-
-               
                
        }
        catch(exception& e) {

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 7ac616feb6cc82be610c73a7e853d50a17693998..9e85590bc2854aae88d46ce711a9f080ab5b04a6 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -203,7 +203,7 @@ int HelpCommand::execute(){
                cout << "Example heatmap(groups=A-B-C, line=1-3-5, sorted=0, scaler=log10)." << "\n";
                cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
                cout << "The default value for sorted is 1 meaning you want the shared otus on top, you may change it to 0 meaning the exact representation of your input file." << "\n";
-               cout << "The default value for scaler is log2; your other options are log10 and linear." << "\n";
+               cout << "The default value for scaler is log10; your other options are log2 and linear." << "\n";
                cout << "The heatmap command outputs a .svg file for each line or label you specify." << "\n";
                cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "venn") {