@@ -31,8 +31,7 @@ Suggests:

     knitr,

     BiocStyle,

     testthat,

-    biomaRt,

-    ggbio

+    biomaRt

 License: Artistic-2.0

 LazyLoad: yes

 VignetteBuilder: knitr

@@ -313,27 +313,6 @@ plotHistogram <- function(model, state=NULL, chromosomes=NULL, start=NULL, end=N

 }

-#' Plot a karyogram with read counts and univariate peak calls

-#'

-#' Plot a karyogram with read counts and peak calls from a \code{\link{uniHMM}} object.

-#'

-#' @author Aaron Taudt

-#' @param model A \code{\link{uniHMM}} object or file that contains such an object.

-#' @return A \code{\link[ggplot2:ggplot]{ggplot}} object.

-plotKaryogram <- function(model) {

-

-    model <- suppressMessages( loadHmmsFromFiles(model, check.class=class.univariate.hmm)[[1]] )

-

-    # Plot the peaks

-    ggplt <- ggbio::autoplot(model$segments[model$segments$state=='modified'], layout='karyogram', color=getStateColors('modified'))

-

-    # Plot the read counts

-    ggplt <- ggplt + ggbio::layout_karyogram(model$bins, aes_string(x='start', y='counts'), ylim=c(10,40), geom='line', color=getStateColors('counts'))

-    ggplt <- ggplt + theme(axis.text.y=element_blank(), panel.background=element_blank())

-

-    return(ggplt)

-}

-

 #' @importFrom stats pnbinom qnorm dnorm

 plotNormalTransformation <- function(model, state='unmodified') {

deleted file mode 100644

@@ -1,20 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/plotting.R

-\name{plotKaryogram}

-\alias{plotKaryogram}

-\title{Plot a karyogram with read counts and univariate peak calls}

-\usage{

-plotKaryogram(model)

-}

-\arguments{

-\item{model}{A \code{\link{uniHMM}} object or file that contains such an object.}

-}

-\value{

-A \code{\link[ggplot2:ggplot]{ggplot}} object.

-}

-\description{

-Plot a karyogram with read counts and peak calls from a \code{\link{uniHMM}} object.

-}

-\author{

-Aaron Taudt

-}