## ---- eval=FALSE--------------------------------------------------------- # # try http:// if https:// URLs are not supported # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("cellscape") ## ---- eval=FALSE--------------------------------------------------------- # example("cellscape") ## ---- echo=FALSE--------------------------------------------------------- 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) ## ---- eval=FALSE--------------------------------------------------------- # ?cellscape ## ---- eval=FALSE--------------------------------------------------------- # browseVignettes("cellscape")