@@ -1,7 +1,7 @@

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progresion with Epistasis 

-Version: 1.99.2

+Version: 1.99.3

 Date: 2015-06-19

 Author: Ramon Diaz-Uriarte. 

 Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>

@@ -23,4 +23,4 @@ Imports: Rcpp (>= 0.11.1), parallel, data.table, graph, Rgraphviz, gtools, igrap

 Suggests: BiocStyle, knitr, Oncotree, testthat

 LinkingTo: Rcpp

 VignetteBuilder: knitr

-SystemRequirements: C++11

+# SystemRequirements: C++11

@@ -723,15 +723,16 @@ fitnessEffectsToIgraph <- function(rT, epistasis, orderEffects) {

 plot.fitnessEffects <- function(x, type = "graphNEL",

-                               layout = NULL,

-                               expandModules = FALSE,

-                               ...) {

+                                layout = NULL,

+                                expandModules = FALSE,

+                                autofit = FALSE,

+                                return_g = FALSE,

+                                ...) {

     ## some other layouts I find OK

     ## layout.circle

     ## layout.reingold.tilford if really a tree

     ## o.w. it will use the default

     g <- x$graph

-

     if(type == "igraph") {

         if(expandModules && (!x$gMOneToOne)) {

@@ -739,7 +740,18 @@ plot.fitnessEffects <- function(x, type = "graphNEL",

             vlabels <- x$geneToModule[V(g)$name]

             V(g)$label <- vlabels

         }

-        plot.igraph(g, layout = layout)

+        if(autofit) {

+            plot(0, type = "n", axes = FALSE, ann = FALSE)

+            ## ideas from http://stackoverflow.com/questions/14472079/match-vertex-size-to-label-size-in-igraph

+            ## vsize <- (strwidth(V(g)$label) + strwidth("oo")) * 200

+            ## but this is a kludge.

+            vsize <- (nchar(V(g)$label) + 3) * 4.5

+            plot.igraph(g, vertex.size = vsize, vertex.shape = "rectangle",

+                        layout = layout)

+        } else {

+            plot.igraph(g, layout = layout)

+        }

+        if(return_g) return(g)

     }

     else if (type == "graphNEL") {

         g1 <- igraph.to.graphNEL(g)

@@ -758,9 +770,19 @@ plot.fitnessEffects <- function(x, type = "graphNEL",

             names(nnodes) <- nodes(g1)

             nAttrs$label <- nnodes

         }

-        plot(g1, edgeAttrs = list(arrowsize = a1, lty = s1, lwd = lwd,

-                     color = c1),

-             nodeAttrs = nAttrs)

+        if(autofit) {

+            nAttrs$width <- (nchar(nAttrs$label) + 1)/10

+            names(nAttrs$width) <- names(nAttrs$label)

+            plot(g1, edgeAttrs = list(arrowsize = a1, lty = s1, lwd = lwd,

+                         color = c1), attrs=list(node=list(shape = "rectangle")),

+                 nodeAttrs = nAttrs)

+            

+        } else {

+            plot(g1, edgeAttrs = list(arrowsize = a1, lty = s1, lwd = lwd,

+                         color = c1),

+                 nodeAttrs = nAttrs)

+        }

+        if(return_g) return(g1)

     } else {

         stop("plot type not recognized")

     }

@@ -1,3 +1,9 @@

+Changes in version 1.99.3 (2015-06-19):

+	- More examples to vignette

+	- Using Makevars

+	- More functionality to plot.fitnessEffects

+	- Will Windoze work now?

+

 Changes in version 1.99.2 (2015-06-19):

 	- Fixed typos and other minor in vignett.

@@ -10,7 +10,7 @@

 }

 \usage{

 \method{plot}{fitnessEffects}(x, type = "graphNEL", layout = NULL,

-expandModules = FALSE, ...)

+expandModules = FALSE, autofit = FALSE, return_g = FALSE, ...)

 %%plotFitnessEffects(fe, type = "graphNEL", layout = NULL, expandModules = FALSE)

 }

@@ -31,6 +31,12 @@ expandModules = FALSE, ...)

    If there are modules with multiple genes, if you set this to TRUE

   modules will be replaced by their genes.

 }

+

+\item{autofit}{If TRUE, we try to fit the edges to the labels. This is a

+  very experimental feature, likely to be not very robust.}

+

+\item{return_g}{It TRUE, the graph object (graphNEL or igrap) is returned.}

+

  \item{\dots}{

     Other arguments passed to \code{plot}. Not used for now.

   }

@@ -45,6 +51,8 @@ expandModules = FALSE, ...)

   type. Order relationships have an arrow from the earlier to the later

   event and have a different dotted line (lty 3).

+  If \code{return_g} is TRUE, you are returned also the graph object

+  (igraph or graphNEL) so that you can manipulate it further.

 }

 \author{

 Ramon Diaz-Uriarte

new file mode 100644

@@ -0,0 +1,3 @@

+## This is a C++11 package

+CXX_STD = CXX11

+  

new file mode 100644

@@ -0,0 +1,3 @@

+## This is a C++11 package

+CXX_STD = CXX11

+  

@@ -40,18 +40,19 @@ double prodFitness(std::vector<double> s) {

 		    [](double x, double y) {return (x * std::max(0.0, (1 + y)));});

 }

-// This is a better idea? If yes, change code in nr_fitness so that

-// birth 0 is not extinction.

-double prodFitnessNegInf(std::vector<double> s) {

-  double f = 1.0;

-  for(auto y : s) {

-    if( y == -std::numeric_limits<double>::infinity()) {

-      return -std::numeric_limits<double>::infinity();

-    } else {

-      f *= std::max(0.0, (1 + y));

-    }

-  }

-}

+// // This is a better idea? If yes, change code in nr_fitness so that

+// // birth 0 is not extinction.

+// double prodFitnessNegInf(std::vector<double> s) {

+//   double f = 1.0;

+//   for(auto y : s) {

+//     if( y == -std::numeric_limits<double>::infinity()) {

+//       return -std::numeric_limits<double>::infinity();

+//     } else {

+//       f *= std::max(0.0, (1 + y));

+//     }

+//   }

+//   return f;

+// }

 double prodDeathFitness(std::vector<double> s) {

   return accumulate(s.begin(), s.end(), 1.0,

@@ -239,10 +240,10 @@ std::vector<Poset_struct> rTable_to_Poset(Rcpp::List rt) {

     if(! is_sorted(Poset[i].parentsNumID.begin(), Poset[i].parentsNumID.end()) )

       throw std::logic_error("ParentsNumID not sorted");

-    if(isinf(Poset[i].s))

+    if(std::isinf(Poset[i].s))

       Rcpp::Rcout << "WARNING: at least one s is infinite" 

 		  << std::endl;

-    if(isinf(Poset[i].sh) && (Poset[i].sh > 0))

+    if(std::isinf(Poset[i].sh) && (Poset[i].sh > 0))

       Rcpp::Rcout << "WARNING: at least one sh is positive infinite" 

 		  << std::endl;

   }

@@ -938,9 +939,9 @@ void printPoset(const std::vector<Poset_struct>& Poset) {

       Rcpp::Rcout <<"\t\t typeDep = " << depToString(Poset[i].typeDep) << ' ' ;

       Rcpp::Rcout <<"\t s = " << Poset[i].s << " ";

       Rcpp::Rcout <<"\t sh = " << Poset[i].sh << std::endl;

-      if(isinf(Poset[i].sh))

+      if(std::isinf(Poset[i].sh))

 	++counterInfs;

-      if(isinf(Poset[i].sh) && (Poset[i].sh < 0))

+      if(std::isinf(Poset[i].sh) && (Poset[i].sh < 0))

 	++counterNegInfs;

       Rcpp::Rcout << "\t\t Number of parent modules or genes = " << 

 	Poset[i].parents.size() << std::endl;

@@ -1105,436 +1106,3 @@ double evalRGenotype(Rcpp::IntegerVector rG, Rcpp::List rFE,

 }

-

-// // [[Rcpp::export]]

-// void ovalRGenotype(Rcpp::IntegerVector rG, Rcpp::List rFE, bool verbose) {

-//   const Rcpp::List rF(rFE);

-//   fitnessEffectsAll F = convertFitnessEffects(rF);

-//   Genotype g = convertGenotypeFromR(rG, F);

-//   vector<double> s = evalGenotypeFitness(g, F);

-//   // if(verbose) {

-//   //   Rcpp::Rcout << "\n Individual s terms are :";

-//   //   for(auto i : s) Rcpp::Rcout << " " << i;

-//   //   Rcpp::Rcout << std::endl;

-//   // }

-// }

-

-// // [[Rcpp::export]]

-// void dummyconvertFitnessEffects(Rcpp::List rFE) {

-//   // Yes, some of the things below are data.frames in R, but for

-//   // us that is used just as a list.

-

-//   fitnessEffectsAll fe;

-  

-//   Rcpp::List rrt = rFE["long.rt"];

-//   Rcpp::List re = rFE["long.epistasis"];

-//   Rcpp::List ro = rFE["long.orderEffects"];

-//   Rcpp::List rgi = rFE["long.geneNoInt"];

-//   Rcpp::List rgm = rFE["geneModule"];

-//   bool rone = rFE["gMOneToOne"];

-  

-

-//   // if(rrt.size()) {

-//   //   fe.Poset = rTable_to_Poset(rrt);

-//   // } 

-//   // if(re.size()) {

-//   //   fe.Epistasis = convertEpiOrderEff(re);

-//   // } 

-//   // if(ro.size()) {

-//   //   fe.orderE = convertEpiOrderEff(ro);

-//   // } 

-//   if(rgi.size()) {

-//     fe.genesNoInt = convertNoInts(rgi);

-//   } else {

-//     fe.genesNoInt.shift = -9L;

-//   }

-//   // fe.Gene_Module_tabl = R_GeneModuleToGeneModule(rgm);

-//   // fe.allOrderG = sortedAllOrder(fe.orderE);

-//   // fe.allPosetG = sortedAllPoset(fe.Poset);

-//   // fe.gMOneToOne = rone;

-

-//   //return fe;

-// }

-

-

-

-// // [[Rcpp::export]]

-// void dummy(Rcpp::List rt) { 

-

-//   // The restriction table, or Poset, has a first element

-//   // with nothing, so that all references by mutated gene

-//   // are simply accessing the Poset[mutated gene] without

-//   // having to remember to add 1, etc.

-

-//   std::vector<Poset_struct> Poset;

-  

-//   Poset.resize(rt.size() + 1);

-//   Poset[0].child = "0"; //should this be Root?? I don't think so.

-//   Poset[0].childNumID = 0;

-//   Poset[0].typeDep = Dependency::NA;

-//   Poset[0].s = std::numeric_limits<double>::quiet_NaN();

-//   Poset[0].sh = std::numeric_limits<double>::quiet_NaN();

-//   Poset[0].parents.resize(0);

-//   Poset[0].parentsNumID.resize(0);

-

-//   Rcpp::List rt_element;

-//   // std::string tmpname;

-//   Rcpp::IntegerVector parentsid;

-//   Rcpp::CharacterVector parents;

-

-//   for(int i = 1; i != (rt.size() + 1); ++i) {

-//     rt_element = rt[i - 1];

-//     Poset[i].child = Rcpp::as<std::string>(rt_element["child"]);

-//     Poset[i].childNumID = as<int>(rt_element["childNumID"]);

-//     Poset[i].typeDep = stringToDep(as<std::string>(rt_element["typeDep"]));

-//     Poset[i].s = as<double>(rt_element["s"]);

-//     Poset[i].sh = as<double>(rt_element["sh"]);

-

-//     // if(i != Poset[i].childNumID) {

-//     // Nope: this assumes we only deal with posets.

-//     //   // Rcpp::Rcout << "\n childNumID, original = " << as<int>(rt_element["childNumID"]);

-//     //   // Rcpp::Rcout << "\n childNumID, Poset = " << Poset[i].childNumID;

-//     //   // Rcpp::Rcout << "\n i = " << i << std::endl;

-//     //   throw std::logic_error("childNumID != index");

-//     // }

-//     // Rcpp::IntegerVector parentsid = as<Rcpp::IntegerVector>(rt_element["parentsNumID"]);

-//     // Rcpp::CharacterVector parents = as<Rcpp::CharacterVector>(rt_element["parents"]);

-

-//     parentsid = as<Rcpp::IntegerVector>(rt_element["parentsNumID"]);

-//     parents = as<Rcpp::CharacterVector>(rt_element["parents"]);

-

-//     if( parentsid.size() != parents.size() ) {

-//       throw std::logic_error("parents size != parentsNumID size");

-//     }

-

-//     for(int j = 0; j != parentsid.size(); ++j) {

-//       Poset[i].parentsNumID.push_back(parentsid[j]);

-//       Poset[i].parents.push_back( (Rcpp::as< std::string >(parents[j])) );

-//       // tmpname = Rcpp::as< std::string >(parents[j]);

-//       // Poset[i].parents.push_back(tmpname);

-//     }

-

-//     // Should not be needed if R always does what is should. Disable later?

-//     if(! is_sorted(Poset[i].parentsNumID.begin(), Poset[i].parentsNumID.end()) )

-//       throw std::logic_error("ParentsNumID not sorted");

-    

-//     if(isinf(Poset[i].s))

-//       Rcpp::Rcout << "WARNING: at least one s is infinite" 

-// 		  << std::endl;

-//     if(isinf(Poset[i].sh) && (Poset[i].sh > 0))

-//       Rcpp::Rcout << "WARNING: at least one sh is positive infinite" 

-// 		  << std::endl;

-//   }

-// }

-

-// // [[Rcpp::export]]

-// void dummy2(Rcpp::List rFE) {

-//   // Yes, some of the things below are data.frames in R, but for

-//   // us that is used just as a list.

-

-//   fitnessEffectsAll fe;

-  

-//   Rcpp::List rrt = rFE["long.rt"];

-//   Rcpp::List re = rFE["long.epistasis"];

-//   Rcpp::List ro = rFE["long.orderEffects"];

-//   Rcpp::List rgi = rFE["long.geneNoInt"];

-//   Rcpp::List rgm = rFE["geneModule"];

-//   bool rone = rFE["gMOneToOne"];

-  

-

-//   if(rrt.size()) {

-//     fe.Poset = rTable_to_Poset(rrt);

-//   } 

-//   if(re.size()) {

-//     fe.Epistasis = convertEpiOrderEff(re);

-//   } 

-//   if(ro.size()) {

-//     fe.orderE = convertEpiOrderEff(ro);

-//   } 

-//   // if(rgi.size()) {

-//   //   fe.genesNoInt = convertNoInts(rgi);

-//   // } else {

-//   //   fe.genesNoInt.shift = -9L;

-//   // }

-  

-//   // fe.Gene_Module_tabl = R_GeneModuleToGeneModule(rgm);

-//   // fe.allOrderG = sortedAllOrder(fe.orderE);

-//   // fe.allPosetG = sortedAllPoset(fe.Poset);

-//   fe.gMOneToOne = rone;

-// }

-

-

-// // [[Rcpp::export]]

-// void wrap_test_rt(Rcpp::List rtR, Rcpp::DataFrame rGM) {

-//   std::vector<Poset_struct> Poset;

-//   std::vector<geneToModule> geneModules;

-//   std::vector<geneToModuleLong> geneModules;

-

-//   R_GeneModuleToGeneModule(rGM, geneModules, geneModules);

-//   printGeneToModule(geneModules);

-

-//   rTable_to_Poset(rtR, Poset);

-//   printPoset(Poset);

-// }

-

-// // stretching vector of mutatedDrv unlikely to speed up;

-// // access (seeing if a module gene in there) is O(1) but I do

-// // that for every gene and then sum over the vector (linear in

-// // number of positions?)

-

-// // Could be made much faster if we could assume lower numbered

-// // positions cannot depend on higher numbered ones. Nope, not that much.

-

-// SEXP wrap_test_checkRestriction(Rcpp::List rtR, 

-// 				Rcpp::DataFrame rGM,

-// 				Rcpp::IntegerVector genotype) {

-

-

-// Turn the following into a function called from R naturally.  Allows for

-// testing AND allows users to understand the consequences of an rt and a

-// genotype. The R function is evalGenotype

-

-

-// // [[Rcpp::export]]

-// SEXP eval_Genotype(Rcpp::List rtR, 

-// 		   Rcpp::DataFrame rGM,

-// 		   Rcpp::IntegerVector genotype) {

-

-  

-//   // std::vector<geneToModule> geneModules;

-//   std::vector<geneToModuleLong> geneModules;

-

-//   std::vector<int> Genotype;

-//   std::vector<double> s_vector;

-//   std::vector<double> sh_vector;

-

-//   std::vector<Poset_struct> Poset = rTable_to_Poset(rtR);

-//   geneModules = R_GeneModuleToGeneModule(rGM, geneModules, geneModules);

-

-

-//   Genotype = Rcpp::as< std::vector<int> >(genotype);

-

-//   evalPosetConstraints(Genotype, Poset, geneModules,  s_vector, sh_vector);

-

-//   // Rcpp::Rcout << "s_vector:\n ";

-//   // for (auto c : s_vector)

-//   //   Rcpp::Rcout << c << ' ';

-//   // Rcpp::Rcout << std::endl;

-//   // Rcpp::Rcout << "sh_vector:\n ";

-//   // for (auto c : sh_vector)

-//   //   Rcpp::Rcout << c << ' ';

-//   // Rcpp::Rcout << std::endl;

-

-//   return

-//     List::create(Named("s_vector") = s_vector,

-// 		 Named("sh_vector") = sh_vector);

-// }

-

-

-// when mutation happens, if a passenger, insert in mutatedPass and give p_vector.

-  // if(mutatedPos >= numDrivers) { //the new mutation is a passenger

-  //   // do something: iterate through the passenger part of genotype

-  //   // keeping the rest of the parent stuff.

-  //   return;

-  // } else {

-

-

-// if driver, insert in Drv.

-// and check restrictions

-

-

-// static void printOrderEffects(const std::vector<epistasis>& orderE) {

-//   // do something

-// }

-

-

-

-

-

-

-

-

-// // [[Rcpp::export]]

-// void wrap_FitnessEffects(Rcpp::List rtR,

-// 			Rcpp::List longEpistasis,

-// 			Rcpp::List longOrderE,

-// 			Rcpp::DataFrame rGM,

-// 			Rcpp::DataFrame geneNoInt,

-// 			Rcpp::IntegerVector gMOneToOne) {

-

-   

-//   std::vector<Poset_struct> Poset;

-//   std::vector<geneToModule> geneModules;

-//   std::vector<geneToModuleLong> geneModules;

-

-//   convertFitnessEffects(rtR, longEpistasis, longOrderE,

-// 			rGM, geneNoInt, gMOneToOne,

-// 			Poset, geneModules, geneModules);

-//   printGeneToModule(geneModules);

-//   printPoset(Poset);

-// }

-

-

-

-// void readFitnessEffects(Rcpp::List rtR,

-// 			       Rcpp::List longEpistasis,

-// 			       Rcpp::List longOrderE,

-// 			       Rcpp::DataFrame rGM,

-// 			       Rcpp::DataFrame geneNoInt,

-// 			       Rcpp::IntegerVector gMOneToOne,

-// 			       std::vector<Poset_struct>&  Poset,

-// 			       std::vector<geneToModule>& geneModules,

-// 			       std::vector<geneToModuleLong>& geneModules

-// 			       // return objects

-// 			       // something else

-// 			       ) {

-//    rTable_to_Poset(rtR, Poset);

-//    R_GeneModuleToGeneModule(rGM, geneModules, geneModules);

- 

-// }

-

-

-// epistasis and order can also be of modules, as we map modules to genes

-// for that.

-

-

-

-// How we store a given genotype and how we store the restrictions need to

-// have a 1-to-1 mapping.

-

-

-// checkEpistasis: for every epistatic set, check if there?

-

-// checkOrderEffects: we find each member in the vector, but the indices

-// must be correlative.

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-// static void evalPosetConstraints(const std::vector<int>& Drv,

-// 			     const std::vector<Poset_struct>& Poset,

-// 			     const std::vector<geneToModule>& geneToModules,

-// 			     std::vector<double>& s_vector,

-// 			     std::vector<double>& sh_vector) {

-//   size_t numDeps;

-//   size_t sumDepsMet = 0;

-//   int parent_module_mutated = 0;

-//   std::vector<int> mutatedModules;

-  

-

-//   // Map mutated genes to modules (mutatedModules) and then examine, for

-//   // each mutatedModule, if its dependencies (in terms of modules) are met.

-

-//   mutatedModules = DrvToModule(Drv, geneToModules);

-

-//   for(auto it_mutatedModule = mutatedModules.begin();

-//       it_mutatedModule != mutatedModules.end(); ++it_mutatedModule) {

-//     if( (Poset[(*it_mutatedModule)].parentsNumID.size() == 1) &&

-// 	(Poset[(*it_mutatedModule)].parentsNumID[0] == 0) ) { //Depends only on root.

-//       // FIXME: isn't it enough to check the second condition?

-//       s_vector.push_back(Poset[(*it_mutatedModule)].s);

-//     } else {

-//       sumDepsMet = 0;

-//       numDeps = Poset[(*it_mutatedModule)].parentsNumID.size();

-//       for(auto it_Parents = Poset[(*it_mutatedModule)].parentsNumID.begin();

-// 	  it_Parents != Poset[(*it_mutatedModule)].parentsNumID.end();

-// 	  ++it_Parents) {

-// 	// if sorted, could use binary search

-// 	// FIXME: try a set or sort mutatedModules?

-

-// 	//parent_module_mutated =

-// 	//std::binary_search(mutatedModules.begin(), mutatedModules.end(),

-// 	//(*it_Parents))

-

-// 	parent_module_mutated = 

-// 	  (std::find(mutatedModules.begin(), 

-// 		     mutatedModules.end(), 

-// 		     (*it_Parents)) != mutatedModules.end());

-// 	if(parent_module_mutated)  {

-// 	  ++sumDepsMet;

-// 	  if( Poset[(*it_mutatedModule)].typeDep == Dependency::semimonotone)

-// 	    break;

-// 	}

-//       }

-//       if( ((Poset[(*it_mutatedModule)].typeDep == Dependency::semimonotone) && 

-// 	   (sumDepsMet)) ||

-// 	  ((Poset[(*it_mutatedModule)].typeDep == Dependency::monotone) && 

-// 	   (sumDepsMet == numDeps)) ) {

-// 	s_vector.push_back(Poset[(*it_mutatedModule)].s);

-//       } else {

-// 	sh_vector.push_back(Poset[(*it_mutatedModule)].sh);

-//       }

-//     }

-//   }

-  

-// }

-

-

-

-// std::vector<double> evalPosetConstraints0(const std::vector<int>& mutatedModules,

-// 					 const std::vector<Poset_struct>& Poset) {

-

-//   size_t numDeps;

-//   size_t sumDepsMet = 0;

-//   int parent_module_mutated = 0;

-//   // std::vector<int> mutatedModules;

-  

-//   std::vector<double> s;

-  

-//   // Map mutated genes to modules (mutatedModules) and then examine, for

-//   // each mutatedModule, if its dependencies (in terms of modules) are met.

-

-  

-

-//   for(auto it_mutatedModule = mutatedModules.begin();

-//       it_mutatedModule != mutatedModules.end(); ++it_mutatedModule) {

-//     if( (Poset[(*it_mutatedModule)].parentsNumID.size() == 1) &&

-// 	(Poset[(*it_mutatedModule)].parentsNumID[0] == 0) ) { //Depends only on root.

-//       // FIXME: isn't it enough to check the second condition?

-//       s.push_back(Poset[(*it_mutatedModule)].s);

-//     } else {

-//       sumDepsMet = 0;

-//       numDeps = Poset[(*it_mutatedModule)].parentsNumID.size();

-//       for(auto it_Parents = Poset[(*it_mutatedModule)].parentsNumID.begin();

-// 	  it_Parents != Poset[(*it_mutatedModule)].parentsNumID.end();

-// 	  ++it_Parents) {

-

-// 	parent_module_mutated = binary_search(mutatedModules.begin(), 

-// 					      mutatedModules.end(),

-// 					      (*it_Parents));

-// 	  // (std::find(mutatedModules.begin(), 

-// 	  // 	     mutatedModules.end(), 

-// 	  // 	     (*it_Parents)) != mutatedModules.end());

-// 	if(parent_module_mutated)  {

-// 	  ++sumDepsMet;

-// 	  if( Poset[(*it_mutatedModule)].typeDep == Dependency::semimonotone)

-// 	    break;

-// 	}

-//       }

-//       if( ((Poset[(*it_mutatedModule)].typeDep == Dependency::semimonotone) && 

-// 	   (sumDepsMet)) ||

-// 	  ((Poset[(*it_mutatedModule)].typeDep == Dependency::monotone) && 

-// 	   (sumDepsMet == numDeps)) ) {

-// 	s.push_back(Poset[(*it_mutatedModule)].s);

-//       } else {

-// 	s.push_back(Poset[(*it_mutatedModule)].sh);

-//       }

-//     }

-//   }

-//   return s;

-// }

@@ -242,7 +242,7 @@ Before anything else, let us load the package. We also explicitly load

 \Biocpkg{graph} and \CRANpkg{igraph} for the vignette to work (you do not

 need that for your usual interactive work).

-<<echo=FALSE>>=

+<<results="hide">>=

 library(OncoSimulR)

 library(graph)

 library(igraph)

@@ -2314,6 +2314,53 @@ plot(pancr)

 Of course the ``s'' and ``sh'' are set arbitrarily here.

+\subsection{Raphael and Vandin's modules}\label{raphael-ex}

+

+In \cite{Raphael2014a}, Raphael and Vandin show several progression models

+in terms of modules. The extended poset for the colorectal cancer model in

+their Figure 4.a is (s and sh are arbitrary):

+

+

+<<fig.height = 4>>=

+rv1 <- allFitnessEffects(data.frame(parent = c("Root", "A", "KRAS"),

+                                    child = c("A", "KRAS", "FBXW7"),

+                                    s = 0.1,

+                                    sh = -0.01,

+                                    typeDep = "MN"),

+                         geneToModule = c("Root" = "Root",

+                             "A" = "EVC2, PIK3CA, TP53",

+                             "KRAS" = "KRAS",

+                             "FBXW7" = "FBXW7"))

+

+plot(rv1, expandModules = TRUE, autofit = TRUE)

+

+@ 

+

+We use the (experimental) \Rcode{autofit} option to fit the labels to the

+edges.

+

+

+Their Figure 5b is

+

+<<fig.height=12>>=

+

+rv2 <- allFitnessEffects(data.frame(parent = c("Root", "1", "2", "3", "4"),

+                                    child = c("1", "2", "3", "4", "ELF3"),

+                                    s = 0.1,

+                                    sh = -0.01,

+                                    typeDep = "MN"),

+                         geneToModule = c("Root" = "Root",

+                             "1" = "APC, FBXW7",

+                             "2" = "ATM, FAM123B, PIK3CA, TP53",

+                             "3" = "BRAF, KRAS, NRAS",

+                             "4" = "SMAD2, SMAD4, SOX9",

+                             "ELF3" = "ELF3"))

+plot(rv2, "igraph", expandModules = TRUE, 

+     layout = layout.reingold.tilford,

+     autofit = TRUE)

+

+@ 

+

 \section{Running the simulations}\label{simul}

@@ -2629,7 +2676,7 @@ Often, you will want to simulate multiple runs of the same scenario, and

 do something with them. Conceptually, the first step is running multiple

 simulations and, then, sampling them.

-We will use the ``pancreas'' example, above \section{pancreas}

+We will use the ``pancreas'' example, above section \ref{pancreas}.

 <<>>=

@@ -1,15 +1,15 @@

 \usepackage[%

-		shash={4d8bb43},

-		lhash={4d8bb439bd91e1f2a877322a8d59485a34678e58},

-		authname={ramon diaz-uriarte (at Bufo)},

+		shash={1db4b3a},

+		lhash={1db4b3a4511805f1d9914d24b269f5e10f4753a1},

+		authname={Ramon Diaz-Uriarte (at Coleonyx)},

 		authemail={rdiaz02@gmail.com},

 		authsdate={2015-06-19},

-		authidate={2015-06-19 14:00:52 +0200},

-		authudate={1434715252},

-		commname={ramon diaz-uriarte (at Bufo)},

+		authidate={2015-06-19 22:51:22 +0200},

+		authudate={1434747082},

+		commname={Ramon Diaz-Uriarte (at Coleonyx)},

 		commemail={rdiaz02@gmail.com},

 		commsdate={2015-06-19},

-		commidate={2015-06-19 14:00:52 +0200},

-		commudate={1434715252},

-		refnames={ (HEAD, master)}

+		commidate={2015-06-19 22:51:22 +0200},

+		commudate={1434747082},

+		refnames={ (HEAD, origin/master, origin/HEAD, master)}

 	]{gitsetinfo}

\ No newline at end of file