## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # BiocManager::install("cellscape") ## ----eval=FALSE--------------------------------------------------------------- # example("cellscape") ## ----echo=FALSE--------------------------------------------------------------- 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")