## ---- eval=FALSE---------------------------------------------------------
#  # try http:// if https:// URLs are not supported
#  source("https://bioconductor.org/biocLite.R")
#  biocLite("cellscape")

## ---- eval=FALSE---------------------------------------------------------
#  example("cellscape")

## ---- echo=FALSE---------------------------------------------------------
library(devtools)  
source("https://bioconductor.org/biocLite.R")
biocLite("cellscape")
library(cellscape) 
#' # single cell tree edges
tree_edges <- read.csv(system.file("extdata", "targeted_tree_edges.csv", package = "cellscape"))
#' # targeted mutations
targeted_data <- read.csv(system.file("extdata", "targeted_muts.csv", package = "cellscape"))
#' # genotype tree edges
gtype_tree_edges <- data.frame("source"=c("Ancestral", "Ancestral", "B","C", "D"), "target"=c("A", "B", "C", "D", "E"))
#' # annotations
sc_annot <- read.csv(system.file("extdata", "targeted_annots.csv", package = "cellscape"))
#' # mutation order
mut_order <- scan(system.file("extdata", "targeted_mut_order.txt", package = "cellscape"), what=character())
#' # run cellscape
cellscape(mut_data=targeted_data, tree_edges=tree_edges, sc_annot = sc_annot, gtype_tree_edges=gtype_tree_edges, mut_order=mut_order)

## ---- eval=FALSE---------------------------------------------------------
#  ?cellscape

## ---- eval=FALSE---------------------------------------------------------
#  browseVignettes("cellscape")

