inst/doc/cellscape_vignette.R

In cellscape: Explores single cell copy number profiles in the context of a single cell tree

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#  # try http:// if https:// URLs are not supported
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("cellscape")

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#  example("cellscape")

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library(devtools)  
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("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)

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#  ?cellscape

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#  browseVignettes("cellscape")