R/plot.factorSet.R

In davetgerrard/GenomicLayers: Simple, sequence-based simulation of epi-genomes.

# show the profile and modification specificities for a set of binding factors.
#' Plot to visualise a set of binding factor profiles and mod layers
#'
#' show the profile and modification specificities for a set of binding factors.
#'
#' @param factorSet the list of binding factors.
#' 
#' @seealso \code{\link{createBindingFactor.DNA_motif}} \code{\link{print.bfSet}}
#' 
#' @return NULL
#'
#' @examples
#' testFactor2 <- createBindingFactor.DNA_motif("test", patternString="ACTGGGCTA")
#' 
#' testFactor3 <- createBindingFactor.DNA_motif("test", patternString="ACTGGGCTA", profile.layers = c("LAYER.1", "LAYER.3"), profile.marks = c(0,0), 
#'                                              mod.layers = c("LAYER.2", "LAYER.4"), mod.marks=c(0,1))
#' 
#' # check that a profile looking for 1 will not find any.  N.B this WILL bind AFTER testFactor2
#' testFactor4 <- createBindingFactor.DNA_motif("test", patternString="ACTGGGCTA", profile.layers = c("LAYER.3", "LAYER.4"), profile.marks = c(0,1), 
#'                                              mod.layers = c("LAYER.1", "LAYER.2"), mod.marks=c(0,1))
#' 
#' testFactor5 <- createBindingFactor.layer_region("test5", patternLength = 150)
#' # now can match things genome wide. Need to run layerBinding and modification.
#' 
#' # need to have a factorSet, a list of bindingFactors
#' 
#' testFS <- list(testFactor2=testFactor2, testFactor3=testFactor3, testFactor4=testFactor4, testFactor5=testFactor5)
#' 
#' plot.factorSet(testFS)
#'
#' @export
plot.factorSet <- function(factorSet)  {

  layerMap <- data.frame()

  profileLayers <- character()
  modLayers <- character()

  for(i in 1:length(factorSet)) {
    profileLayers <- sort(union(profileLayers, names(factorSet[[i]]$profile)))
    modLayers <-  sort(union(modLayers, names(factorSet[[i]]$mods)))
  }
  # could just set modLayers <- profileLayers ?

  profile.layerMap <- matrix(NA, ncol=length(profileLayers), nrow=length(factorSet), dimnames=list(factor=1:length(factorSet), layer=profileLayers ))
  mod.layerMap <- matrix(NA, ncol=length(modLayers), nrow=length(factorSet), dimnames=list(factor=1:length(factorSet), layer=modLayers ))

  for(i in 1:length(factorSet)) {



    for(thisLayer in names(factorSet[[i]]$profile)) {
      if(thisLayer == "LAYER.0") {
        profile.layerMap[i,thisLayer] <- 1
      } else {
        profile.layerMap[i,thisLayer] <- factorSet[[i]]$profile[[thisLayer]]$pattern
      }

    }


    for(thisLayer in names(factorSet[[i]]$mods)) {
      #mod.layerMap[i,thisLayer] <- TRUE
      mod.layerMap[i,thisLayer] <- as.integer(factorSet[[i]]$mods[[thisLayer]]$state)

    }

  }

  par(mfrow=c(1,2))
  image(t(profile.layerMap), main="profile", axes=F, xlab="Layer") ; box()
  mtext(row.names(profile.layerMap), side=2, at=seq(0,1, length.out=nrow(profile.layerMap)), las=1)
  mtext(0:(ncol(profile.layerMap)-1), side=1, at=seq(0,1, length.out=ncol(profile.layerMap)), las=1)
  image(t(mod.layerMap), main="mods", axes=F, xlab="Layer"); box()
  mtext(row.names(mod.layerMap), side=2, at=seq(0,1, length.out=nrow(mod.layerMap)), las=1)
  mtext(1:ncol(mod.layerMap), side=1, at=seq(0,1, length.out=ncol(mod.layerMap)), las=1)
}
# plot.factorSet(factorSetRandom)
# plot.factorSet(testFS)