@@ -21,8 +21,6 @@ Imports:

   GenomeInfoDb,

   Biostrings,

   DT,

-  scales,

-  viridis,

   HDF5Array (>= 1.7.5)

 Suggests:

   BSgenome.Mmusculus.UCSC.mm10,

@@ -28,10 +28,8 @@ importFrom(annotatr,build_annotations)

 importFrom(annotatr,builtin_genomes)

 importFrom(annotatr,summarize_annotations)

 importFrom(bsseq,getCoverage)

-importFrom(scales,comma)

 importFrom(stats,aggregate)

 importFrom(stats,dbinom)

 importFrom(stats,sd)

 importFrom(utils,read.csv)

 importFrom(utils,read.table)

-importFrom(viridis,scale_fill_viridis)

@@ -25,8 +25,6 @@

 #'mbiasDirectory=system.file("extdata",package='scmeth')

 #'outDir <- system.file(package='scmeth')

 #'report(bs,outDir,Hsapiens,'hg38',mbiasDir=mbiasDirectory,small=TRUE)

-#'@importFrom scales comma

-#'@importFrom viridis scale_fill_viridis

 #'@importFrom HDF5Array loadHDF5SummarizedExperiment

 #'@import knitr

 #'@import DT

@@ -259,12 +259,11 @@ g

 methylDistMatrix <- scmeth::methylationDist(bs,subSample=params$nCpGs,offset=params$offset,coverageVec=covVec)

 g <- ggplot2::ggplot(methylDistMatrix, ggplot2::aes_string(x='Var2',

-                                                        y='Var1',fill='value'))

-g <- g + ggplot2::geom_tile(color="white", size=0.1)

-g <- g + viridis::scale_fill_viridis(name="Fraction of \n CpGs observed", label=scales::comma)

+                                                        y='value',group='Var1'))

+g <- g + ggplot2::geom_point()

+g <- g + ggplot2::geom_line()

 #g <- g + ggplot2::coord_equal() # Adds same aspect ratio

 g <- g + ggplot2::labs(x=NULL, y=NULL, title="Methylation Distribution")

-g <- g + ggthemes::theme_tufte(base_family="Helvetica")

 g <- g + ggplot2::theme(plot.title=ggplot2::element_text(hjust=0))

 g <- g + ggplot2::theme(axis.text.y=ggplot2::element_blank())

 # get rid of tick marks

@@ -70,7 +70,6 @@ Code chunk below shows how it can be loaded.

 </p>

 ```{r, eval=FALSE}

-# Works in devtools::check but not in bioconductor

 directory <- system.file("extdata","bismark_data",package='scmeth')

 bsObject <- HDF5Array::loadHDF5SummarizedExperiment(directory)

 ```