\name{allFitnessEffects}
\alias{allFitnessEffects}
\alias{allMutatorEffects}

\title{Create fitness and mutation effects specification from
  restrictions, epistasis, and order effects.  }

\description{
  Given one or more of a set of poset restrictions, epistatic
  interactions, order effects, and genes without interactions, as well
  as, optionally, a mapping of genes to modules, return the complete
  fitness specification.

  For mutator effects, given one or more of a set of epistatic
  interactions and genes without interactions, as well as, optionally, a
  mapping of genes to modules, return the complete specification of how
  mutations affect the mutation rate.
  
  The output of these functions is not intended for user consumption,
  but as a way of preparing data to be sent to the C++ code.  }


\usage{

allFitnessEffects(rT = NULL, epistasis = NULL, orderEffects = NULL,
  noIntGenes = NULL, geneToModule = NULL, drvNames = NULL,
  genotFitness = NULL,  keepInput = TRUE)

allMutatorEffects(epistasis = NULL, noIntGenes = NULL,
                   geneToModule = NULL,
                  keepInput =  TRUE)
}




\arguments{
  \item{rT}{A restriction table that is an extended version of a poset 
    (see \code{\link{poset}} ).
    A restriction table is a data frame where each row shows one edge
    between a parent and a child. A restriction table contains exactly these
    columns, in this order:
    \describe{
    \item{parent}{The identifiers of the parent nodes, in a
      parent-child relationship. There must be at least on entry with the
      name "Root".}
    \item{child}{The identifiers of the child nodes.}
    \item{s}{A numeric vector with the fitness effect that applies
      if the relationship is satisfied.}
    \item{sh}{A numeric vector with the fitness effect that applies if
      the relationship is not satisfied. This provides a way of
      explicitly modeling deviatons from the restrictions in the graph,
      and is discussed in Diaz-Uriarte, 2015. }
    \item{typeDep}{The type of dependency. Three possible types of
      relationship exist:
      \describe{
	\item{AND, monotonic, or CMPN}{Like in the CBN model, all parent nodes
	  must be present for a relationship to be satisfied. Specify it
	  as "AND" or "MN" or "monotone".}
	\item{OR, semimonotonic, or DMPN}{A single parent node is enough
	  for a relationship to be satisfied. Specify it as "OR" or
	  "SM" or "semimonotone".}
	\item{XOR or XMPN}{Exactly one parent node must be mutated for a
	  relationship to be satisfied. Specify it as "XOR" or "xmpn" or
	  "XMPN".}
      }
      In addition, for the nodes that depend only on the root node, you
      can use "--" or "-" if you want (though using any of the other
      three would have the same effects if a node that connects to root
      only connects to root).}
  }
  }
  \item{epistasis}{
    A named numeric vector. The names identify the relationship, and the
    numeric value is the fitness (or mutator) effect. For the names, each of the
    genes or modules involved is separated by a ":". A negative sign
    denotes the absence of that term.
  }
  \item{orderEffects}{
    A named numeric vector, as for \code{epistasis}. A ">" separates the
  names of the genes of modules of a relationship, so that "U > Z" means
  that the relationship is satisfied when mutation U has happened before
  mutation Z.
}
\item{noIntGenes}{
  A numeric vector (optionally named) with the fitness coefficients (or
      mutator multiplier factor) of genes
  (only genes, not modules) that show no interactions. These genes
  cannot be part of modules. But you can specify modules that have
  no epistatic interactions. See examples and vignette.

  Of course, avoid using potentially confusing characters in the
  names. In particular, "," and ">" are not allowed as gene names.
}

\item{geneToModule}{
      
  A named character vector that allows to match genes and modules. The
  names are the modules, and each of the values is a character vector
  with the gene names, separated by a comma, that correspond to a
  module. Note that modules cannot share genes. There is no need for
  modules to contain more than one gene.  If you specify a geneToModule
  argument, and you used a restriction table, the \code{geneToModule} 
  must necessarily contain, in the first position, "Root" (since the
  restriction table contains a node named "Root"). See examples below.
}
    

\item{drvNames}{The names of genes that are considered drivers. This is
  only used for: a) deciding when to stop the simulations, in case you
  use number of drivers as a simulation stopping criterion (see
  \code{\link{oncoSimulIndiv}}); b) for summarization purposes (e.g.,
  how many drivers are mutated); c) in figures. But you need not
  specifiy anything if you do not want to, and you can pass an empty
  vector (as \code{character(0)}). The default has changed with respect
  to v.2.1.3 and previous: it used to be to assume that all
  genes that were not in the \code{noIntGenes} were drivers. The default
  now is to assume nothing: if you want \code{drvNames} you have
  to specify them.

}

\item{genotFitness}{A matrix or data frame that contains explicitly the
  mapping of genotypes to fitness. For now, we only allow epistasis-like
  relations between genes (so you cannot code order effects this way).

  Genotypes can be specified in two ways:
  \itemize{
    
    \item As a matrix (or data frame) with g + 1 columns (where g >
    1). Each of the first g columns contains a 1 or a 0 indicating that
    the gene of that column is mutated or not. Column g+ 1 contains the
    fitness values. This is, for instance, the output you will get from
    \code{\link{rfitness}}. If the matrix has all columns named, those
    will be used for the names of the genes. Of course, except for
    column or row names, all entries in this matrix or data frame must
    be numeric.
    
    \item As a two column data frame. The second column is fitness, and
    the first column are genotypes, given as a character vector. For
    instance, a row "A, B" would mean the genotype with both A and B mutated.
  }
  In all cases, fitness must be \code{>= 0}. If any possible genotype is
  missing, its fitness is assumed to be 0, except for WT (if WT is
    missing, its fitness is assumed to be 1 ---see examples).
}


\item{keepInput}{
  If TRUE, whether to keep the original input. This is only useful for
  human consumption of the output. It is useful because it is easier to
  decode, say, the restriction table from the data frame than from the
  internal representation. But if you want, you can set it to FALSE and
  the object will be a little bit smaller.}
}

\details{
  \code{allFitnessEffects} is used for extremely flexible specification of fitness
  and mutator effects, including posets, XOR relationships, synthetic mortality and
  synthetic viability, arbitrary forms of epistatis, arbitrary forms of
  order effects, etc. Please, see the vignette for detailed and
  commented examples.

  \code{allMutatorEffects} provide the same flexibility, but without
  order and posets (this might be included in the future, but I have
  seen no empirical or theoretical argument for their existence or
  relevance as of now, so I do not add them to minimize unneeded complexity).

  If you use both for simulations in the same call to, say,
  \code{\link{oncoSimulIndiv}}, all the genes specified in
  \code{allMutatorEffects} MUST be included in the
  \code{allFitnessEffects} object. If you want to have genes that have
  no direct effect on fitness, but that affect mutation rate, you MUST
  specify them in the call to \code{allFitnessEffects}, for instance as
  \code{noIntGenes} with an effect of 0.


  If you use \code{genotFitness} then you cannot pass modules,
  noIntgenes, epistasis, or rT. This makes sense, because using
  \code{genotFitness} is saying
  "this is the mapping of genotypes to fitness. Period", so we should
  not allow further modifications from other terms.

  If you use \code{genotFitness} you need to be careful when you use
  Bozic's model (as you get a death rate of 0).


  If you use \code{genotFitness} note that we force the WT (wildtype) to
  always be 1 so fitnesses are rescaled. 


}


\value{
  
  An object of class "fitnessEffects" or "mutatorEffects". This is just
  a list, but it is not intended for human consumption.  The components
  are:

  \item{long.rt}{The restriction table in "long format", so as to be
    easy to parse by the C++ code.}

  \item{long.epistasis}{Ditto, but for the epistasis specification.}

  \item{long.orderEffects}{Ditto for the order effects.}

  \item{long.geneNoInt}{Ditto for the non-interaction genes.}

  \item{geneModule}{Similar, for the gene-module correspondence.}

  \item{graph}{An \code{igraph} object that shows the restrictions,
    epistasis and order effects, and is useful for plotting.}
  
  \item{drv}{The numeric identifiers of the drivers. The numbers
    correspond to the internal numeric coding of the genes.}

  \item{rT}{If \code{keepInput} is TRUE, the original restriction
    table.}

  \item{epistasis}{If \code{keepInput} is TRUE, the original epistasis
  vector.}

  \item{orderEffects}{If \code{keepInput} is TRUE, the original order
  effects vector.}

  \item{noIntGenes}{If \code{keepInput} is TRUE, the original 
    noIntGenes.}
}
\references{
    Diaz-Uriarte, R. (2015). Identifying restrictions in the order of
  accumulation of mutations during tumor progression: effects of
  passengers, evolutionary models, and sampling
  \url{http://www.biomedcentral.com/1471-2105/16/41/abstract}

    McFarland, C.~D. et al. (2013). Impact of deleterious passenger
  mutations on cancer progression.  \emph{Proceedings of the National
  Academy of Sciences of the United States of America\/}, \bold{110}(8),
  2910--5.


}

\note{
  Please, note that the meaning of the fitness effects in the
  McFarland model is not the same as in the original paper; the fitness
  coefficients are transformed to allow for a simpler fitness function
  as a product of terms. This differs with respect to v.1. See the
  vignette for details.

  The names of the genes and modules can be fairly arbitrary. But if you
  try hard you can confuse the parser. For instance, using gene or
  module names that contain "," or ":", or ">" is likely to get you into
  trouble. Of course, you know you should not try to use those
  characters because you know those characters have special meanings to
  separate names or indicate epistasis or order relationships.  Right
  now, using those characters as names is caught (and result in
  stopping) if passed as names for noIntGenes.  }




\author{ Ramon Diaz-Uriarte
}

\seealso{
  
  \code{\link{evalGenotype}}, \code{\link{oncoSimulIndiv}},
  \code{\link{plot.fitnessEffects}},
  \code{\link{evalGenotypeFitAndMut}},
  \code{\link{rfitness}},
  \code{\link{plotFitnessLandscape}}

}
\examples{
## A simple poset or CBN-like example

cs <-  data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
                 child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
                 s = 0.1,
                 sh = -0.9,
                 typeDep = "MN")

cbn1 <- allFitnessEffects(cs)

plot(cbn1)


## A more complex example, that includes a restriction table
## order effects, epistasis, genes without interactions, and moduels
p4 <- data.frame(parent = c(rep("Root", 4), "A", "B", "D", "E", "C", "F"),
                 child = c("A", "B", "D", "E", "C", "C", "F", "F", "G", "G"),
                 s = c(0.01, 0.02, 0.03, 0.04, 0.1, 0.1, 0.2, 0.2, 0.3, 0.3),
                 sh = c(rep(0, 4), c(-.9, -.9), c(-.95, -.95), c(-.99, -.99)),
                 typeDep = c(rep("--", 4), 
                     "XMPN", "XMPN", "MN", "MN", "SM", "SM"))

oe <- c("C > F" = -0.1, "H > I" = 0.12)
sm <- c("I:J"  = -1)
sv <- c("-K:M" = -.5, "K:-M" = -.5)
epist <- c(sm, sv)

modules <- c("Root" = "Root", "A" = "a1",
             "B" = "b1, b2", "C" = "c1",
             "D" = "d1, d2", "E" = "e1",
             "F" = "f1, f2", "G" = "g1",
             "H" = "h1, h2", "I" = "i1",
             "J" = "j1, j2", "K" = "k1, k2", "M" = "m1")

set.seed(1) ## for repeatability
noint <- rexp(5, 10)
names(noint) <- paste0("n", 1:5)

fea <- allFitnessEffects(rT = p4, epistasis = epist, orderEffects = oe,
                         noIntGenes = noint, geneToModule = modules)

plot(fea)


## Modules that show, between them,
## no epistasis (so multiplicative effects).
## We specify the individual terms, but no value for the ":".

fnme <- allFitnessEffects(epistasis = c("A" = 0.1,
                                        "B" = 0.2),
                          geneToModule = c("A" = "a1, a2",
                                           "B" = "b1"))

evalAllGenotypes(fnme, order = FALSE, addwt = TRUE)


## Epistasis for fitness and simple mutator effects

fe <- allFitnessEffects(epistasis = c("a : b" = 0.3,
                                          "b : c" = 0.5),
                            noIntGenes = c("e" = 0.1))

fm <- allMutatorEffects(noIntGenes = c("a" = 10,
                                       "c" = 5))

evalAllGenotypesFitAndMut(fe, fm, order = FALSE)


## Simple fitness effects (noIntGenes) and modules
## for mutators

fe2 <- allFitnessEffects(noIntGenes =
                         c(a1 = 0.1, a2 = 0.2,
                           b1 = 0.01, b2 = 0.3, b3 = 0.2,
                           c1 = 0.3, c2 = -0.2))

fm2 <- allMutatorEffects(epistasis = c("A" = 5,
                                       "B" = 10,
                                       "C" = 3),
                         geneToModule = c("A" = "a1, a2",
                                          "B" = "b1, b2, b3",
                                          "C" = "c1, c2"))

evalAllGenotypesFitAndMut(fe2, fm2, order = FALSE)



## Passing fitness directly, a complete fitness specification
## with a two column data frame with genotypes as character vectors

(m4 <- data.frame(G = c("A, B", "A", "WT", "B"), F = c(3, 2, 1, 4)))
fem4 <- allFitnessEffects(genotFitness = m4)

## Verify it interprets what it should: m4 is the same as the evaluation
## of the fitness effects (note row reordering)
evalAllGenotypes(fem4, addwt = TRUE, order = FALSE)


## Passing fitness directly, a complete fitness specification
## that uses a three column matrix

m5 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), c(1, 2, 3, 5.5))
fem5 <- allFitnessEffects(genotFitness = m5)

## Verify it interprets what it should: m5 is the same as the evaluation
## of the fitness effects 
evalAllGenotypes(fem5, addwt = TRUE, order = FALSE)


## Passing fitness directly, an incomplete fitness specification
## that uses a three column matrix

m6 <- cbind(c(1, 1), c(1, 0), c(2, 3))
fem6 <- allFitnessEffects(genotFitness = m6)
evalAllGenotypes(fem6, addwt = TRUE, order = FALSE)



## Plotting a fitness landscape

fe2 <- allFitnessEffects(noIntGenes =
                         c(a1 = 0.1, 
                           b1 = 0.01,
                           c1 = 0.3))

plot(evalAllGenotypes(fe2, order = FALSE))

## same as
plotFitnessLandscape(evalAllGenotypes(fe2, order = FALSE))

## same as
plotFitnessLandscape(fe2)


###### Defaults for missing genotypes

## As a two-column data frame

(m8 <- data.frame(G = c("A, B, C", "B"), F = c(3, 2)))
evalAllGenotypes(allFitnessEffects(genotFitness = m8), addwt = TRUE)

## As a matrix 

(m9 <- rbind(c(0, 1, 0, 1, 4), c(1, 0, 1, 0, 1.5)))
evalAllGenotypes(allFitnessEffects(genotFitness = m9), addwt = TRUE)


## Reinitialize the seed
set.seed(NULL)
}

\keyword{ manip }
\keyword{ list }