Export MIDs for all labeled ions

dweindl · Feb 6, 2017 · db1cbbc · db1cbbc
1 parent bd462a7
commit db1cbbc
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Showing 5 changed files with 132 additions and 21 deletions.
diff --git a/gui/miamainwindow.cpp b/gui/miamainwindow.cpp
@@ -674,7 +674,7 @@ void MIAMainWindow::exportMIDs()
     QFile f(filename);
     f.open(QIODevice::WriteOnly);
     QTextStream out(&f);
-    networkSet->exportMIDs(out);
+    networkSet->exportAllMIDs(out);
 }
 
 void MIAMainWindow::updateCompoundList()

diff --git a/src/labelingnetworkset.cpp b/src/labelingnetworkset.cpp
@@ -42,26 +42,28 @@ LabelingNetworkSet::~LabelingNetworkSet()
     }
 }
 
-void LabelingNetworkSet::exportMIDs(QTextStream &qout)
+void LabelingNetworkSet::exportSelectedMIDs(QTextStream &qout)
 {
     std::stringstream out;
     std::string sep = ",";
     std::string quote = "\"";
 
     // header
     out<<"Metabolite"<<sep<<"RI"<<sep<<"Ions (M0)"<<sep<<"M";
+    // header abundances
     for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
         std::string t = datasets[ds]->getSettings().experiment;
         out <<sep<<quote<<t<<quote;
     }
-    for(int ds = 0; ds < datasets.size(); ++ds) { // confidence intervals
+    // header confidence intervals
+    for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
         std::string t = "CI " + datasets[ds]->getSettings().experiment;
         out <<sep<<quote<<t<<quote;
     }
     out<<std::endl;
 
     // data
-    for(int n = 0; n < nodes.size(); ++n) {
+    for(int n = 0; n < nodes.size(); ++n) { // foreach compound
         NodeCompound *nc = nodes[n];
 
        // determine max. MID length for this compound
@@ -73,22 +75,11 @@ void LabelingNetworkSet::exportMIDs(QTextStream &qout)
             }
         }
 
-        // ri
-        double ri = 0;
-        double riCount = 0;
-        for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
-            std::string t = datasets[ds]->getSettings().experiment;
-            if(nc->hasDataForExperiment(t)) {
-                ri += nc->getLabeledCompound(t)->getRetentionIndex();
-                ++riCount;
-            }
-        }
-
-        ri /= riCount;
+        double ri = nc->getAverageRetentionIndex();
 
 
+        // list of selected ions m/z
         std::stringstream ions;
-
         for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
             std::string t = datasets[ds]->getSettings().experiment;
             double ion = 0;
@@ -99,7 +90,8 @@ void LabelingNetworkSet::exportMIDs(QTextStream &qout)
             ions << ion << " ";
         }
 
-        for(int i = 0; i < midLen; ++i) {
+        // abundances and confidence interval
+        for(int i = 0; i < midLen; ++i) { // for each M+x
             out<<quote<<nc->getCompoundName()<<quote<<sep<<ri<<sep<<ions.str()<<sep<<i;
 
             // abundance
@@ -125,15 +117,112 @@ void LabelingNetworkSet::exportMIDs(QTextStream &qout)
                 out << sep;
                 out << (ci.size() > i ? ci[i] : 0);
             }
-
-//            out<<sep<<nc->getANOVAPvalueForMassIsotopomer(i);
             out<<std::endl;
         }
     }
 
     qout<<out.str().c_str();
 }
 
+void LabelingNetworkSet::exportAllMIDs(QTextStream &qout)
+{
+    std::stringstream out;
+    std::string sep = ",";
+    std::string quote = "\"";
+
+    // header
+    out<<"Metabolite"<<sep<<"RI"<<sep<<"Ions (M0)"<<sep<<"M";
+    // header abundances
+    for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
+        std::string t = datasets[ds]->getSettings().experiment;
+        out <<sep<<quote<<t<<quote;
+    }
+    // header confidence intervals
+    for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
+        std::string t = "CI " + datasets[ds]->getSettings().experiment;
+        out <<sep<<quote<<t<<quote;
+    }
+    out<<std::endl;
+
+    // data
+    for(int n = 0; n < nodes.size(); ++n) { // foreach compound
+        NodeCompound *nc = nodes[n];
+
+        std::set<int> lions = nc->getAllLabeledIons();
+        for(std::set<int>::iterator it = lions.begin(); it != lions.end(); ++it) {
+            int ion = *it;
+
+            // determine max. MID length for this ion
+            int midLen = 0;
+            for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
+                std::string t = datasets[ds]->getSettings().experiment;
+                if(nc->hasDataForExperiment(t)) {
+                    // index of ion
+                    const std::vector<float> tmpIons = nc->getLabeledCompound(t)->getLabeledIons();
+                    for(int i = 0; i < tmpIons.size(); ++i) {
+                        if((int)tmpIons[i] == ion) {
+                            midLen = std::max(midLen, (int) (nc->getLabeledCompound(t)->getIsotopomers()[i].size()));
+                            break;
+                        }
+                    }
+                }
+            }
+            double ri = nc->getAverageRetentionIndex();
+
+            // abundances and confidence interval
+            for(int i = 0; i < midLen; ++i) { // for each M+x
+                out<<quote<<nc->getCompoundName()<<quote<<sep<<ri<<sep<<ion<<sep<<i;
+
+                // abundance
+                for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
+                    std::string t = datasets[ds]->getSettings().experiment;
+                    std::vector<double> mid;
+
+                    if(nc->hasDataForExperiment(t)) {
+                        // index of ion
+                        const std::vector<float> tmpIons = nc->getLabeledCompound(t)->getLabeledIons();
+
+                        for(int j = 0; j < tmpIons.size(); ++j) {
+
+                            if((int)tmpIons[j] == ion) {
+                                mid = nc->getLabeledCompound(t)->getIsotopomers()[j];
+                                break;
+                            }
+                        }
+                    }
+
+                    out << sep;
+                    out << (mid.size() > i ? mid[i] : 0);
+                }
+
+                // confidence interval
+                for(int ds = 0; ds < datasets.size(); ++ds) { // each experiment
+                    std::string t = datasets[ds]->getSettings().experiment;
+                    std::vector<double> ci;
+
+                    if(nc->hasDataForExperiment(t)) {
+                        // index of ion
+                        const std::vector<float> tmpIons = nc->getLabeledCompound(t)->getLabeledIons();
+                        for(int j = 0; j < tmpIons.size(); ++j) {
+                            if((int)tmpIons[j] == ion) {
+                                ci = nc->getLabeledCompound(t)->getConfidenceIntervals()[j];
+                                break;
+                            }
+                        }
+                    }
+
+                    out << sep;
+                    out << (ci.size() > i ? ci[i] : 0);
+                }
+                out<<std::endl;
+            }
+        }
+    }
+
+    qout<<out.str().c_str();
+}
+
+
 bool LabelingNetworkSet::nodeHasEdges(int n)
 {
     bool connected = false;

diff --git a/src/labelingnetworkset.h b/src/labelingnetworkset.h
@@ -56,7 +56,9 @@ class LabelingNetworkSet : public QObject
     LabelingNetworkSet();
     ~LabelingNetworkSet();
 
-    void exportMIDs(QTextStream &qout);
+    void exportSelectedMIDs(QTextStream &qout);
+
+    void exportAllMIDs(QTextStream &qout);
 
     bool nodeHasEdges(int n);
 

diff --git a/src/nodecompound.cpp b/src/nodecompound.cpp
@@ -74,6 +74,12 @@ labid::LabeledCompound *NodeCompound::getLabeledCompound(std::string experiment)
     return lcs[idx];
 }
 
+labid::LabeledCompound *NodeCompound::getLabeledCompound(QString experiment)
+{
+    int idx = experimentsLab.indexOf(experiment);
+    return lcs[idx];
+}
+
 void NodeCompound::removeLabeledCompound(labid::LabeledCompound *lc)
 {
     int idx = lcs.indexOf(lc);
@@ -410,6 +416,18 @@ double NodeCompound::getANOVAPvalue(std::vector<double> means, std::vector<doubl
     return p;
 }
 
+double NodeCompound::getAverageRetentionIndex()
+{
+    double ri = 0;
+    double riCount = 0;
+    foreach(QString key, experimentsLab){
+        ri += getLabeledCompound(key)->getRetentionIndex();
+        ++riCount;
+    }
+
+    return ri /= riCount;
+}
+
 std::vector<std::string> NodeCompound::getExperiments()
 {
     std::vector<std::string> v;

diff --git a/src/nodecompound.h b/src/nodecompound.h
@@ -48,6 +48,7 @@ class NodeCompound
 
     void addLabeledCompound(std::string experiment, labid::LabeledCompound *lc);
     labid::LabeledCompound *getLabeledCompound(std::string experiment);
+    labid::LabeledCompound *getLabeledCompound(QString experiment);
     void removeLabeledCompound(labid::LabeledCompound *);
     void addUnlabeledCompound(std::string experiment, labid::LISpectrum *ls);
     labid::LISpectrum* getUnlabeledCompound(std::string experiment);
@@ -64,6 +65,7 @@ class NodeCompound
     double getMinANOVAPvalue();
     double getANOVAPvalueForMassIsotopomer(int m);
     double getANOVAPvalue(std::vector<double> means, std::vector<double> sds, int n);
+    double getAverageRetentionIndex();
 
     std::vector<std::string> getExperiments(); // The different tracer names // unique!
     bool hasDataForExperiment(std::string);