Plot a phylogeny of the clones.
  Plot a phylogeny of the clones, controlling which clones are displayed,
  and whether to shown number of times of appearance, and time of first
  appearance of a clone.
plotClonePhylog(x, N = 1, t ="last", timeEvents = FALSE,
                 keepEvents = FALSE, fixOverlap = TRUE,
                 returnGraph = FALSE, ...)


  \item{x}{ The output from a simulation, as obtained from
  \code{oncoSimulIndiv}, \code{oncoSimulPop}, or \code{oncoSimulSample}
  (see \code{\link{oncoSimulIndiv}}). This must be from v.2 and forward
  (no phylogenetic information is stored for earlier objects).

\item{N}{ Show in the plot all clones that have a population size of at
  least N at time \code{time} and the parents of those clones (parents
  are shown regardless of population size ---i.e., you can see extinct
  parents).  If you want to show everything that ever appeared, set N = 0.}

\item{t}{ The time at which \code{N} should be satisfied. This can
  either be the string "last", meaning the last time of the simulation,
  or a range of two values. In the second case, all clones with
  population size of at least \code{N} in at least one time point
  between time[1] and time[2] will be shown (togheter with their parents).}

\item{timeEvents}{If TRUE, the vertical position of the nodes in the
  plot will be proportional to their time of first appearance. }

\item{keepEvents}{If TRUE, the graph will show all the birth
  events. Thus, the number of arrows shows the number of times a clone
  give rise to another. For large graphs with many events, this slows
  the graph considerably.}

\item{fixOverlap}{When using \code{timeEvents = TRUE} nodes can overlap
  (as we modify their vertical location after igraph has done the
  initial layout). This attempts to fix that problem by randomly
  relocating, along the X axis, the nodes that have the same X value.}

\item{returnGraph}{If TRUE, the igraph object is returned. You can use
  this to plot the object however you want or obtain the adjacency matrix.}
\item{\dots}{ Additional arguments. Currently not used.}.

\note{ If you want to obtain the adjacency matrix, this is trivial: just
  set \code{returnGraph = TRUE} and use \code{\link{get.adjacency}}. See
  an example below.  
  A plot is produced. If \code{returnGraph} the igraph object is returned.
  Ramon Diaz-Uriarte



tmp <-  oncoSimulIndiv(examplesFitnessEffects[["o3"]],
                       model = "McFL", 
                       mu = 5e-5,
                       detectionSize = 1e8, 
                       detectionDrivers = 3,
                       sampleEvery = 0.025,
                       max.num.tries = 10,
                       keepEvery = 5,
                       initSize = 2000,
                       finalTime = 3000,
                       onlyCancer = FALSE,
                       keepPhylog = TRUE)

## Show only those with N > 10 at end
plotClonePhylog(tmp, N = 10)

## Show only those with N > 1 between times 5 and 1000
plotClonePhylog(tmp, N = 1, t = c(5, 1000))

## Show everything, even if teminal nodes are extinct
plotClonePhylog(tmp, N = 0)

## Show time when first appeared
plotClonePhylog(tmp, N = 10, timeEvents = TRUE)

## Show each event
## This can take a few seconds
plotClonePhylog(tmp, N = 10, keepEvents = TRUE)

## Adjacency matrix
get.adjacency(plotClonePhylog(tmp, N = 10, returnGraph = TRUE))


\keyword{ hplot }