## ----eval=FALSE--------------------------------------------------------------- # # try http:// if https:// URLs are not supported # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("mapscape") ## ----eval=FALSE--------------------------------------------------------------- # example("mapscape") ## ----echo=FALSE--------------------------------------------------------------- library(mapscape) # EXAMPLE 1 - Patient A21, Gundem et al., 2015 # clonal prevalences clonal_prev <- read.csv(system.file("extdata", "A21_clonal_prev.csv", package = "mapscape")) # mutations mutations <- read.csv(system.file("extdata", "A21_mutations.csv", package = "mapscape")) # locations of each tumour sample on user-provided image sample_locations <- read.csv(system.file("extdata", "A21_sample_locations.csv", package = "mapscape")) # genotype tree edges tree_edges <- read.csv(system.file("extdata", "A21_tree.csv", package = "mapscape")) # image reference img_ref <- system.file("extdata", "A21_anatomical_image.png", package = "mapscape") # radial order of samples sample_ids <- c("H","F","J","D","A","I","C","E","G") # run mapscape mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, img_ref = img_ref, sample_ids = sample_ids, show_warnings=FALSE) ## ----echo=FALSE--------------------------------------------------------------- # run mapscape mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, img_ref = img_ref, show_warnings=FALSE) ## ----echo=FALSE--------------------------------------------------------------- sample_ids <- c("H","F","J","D","A","I","C","E","G") # run mapscape mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, img_ref = img_ref, sample_ids = sample_ids, show_warnings=FALSE) ## ----echo=FALSE--------------------------------------------------------------- # run mapscape mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, img_ref = img_ref, sample_ids = sample_ids, show_warnings=FALSE) ## ----echo=FALSE--------------------------------------------------------------- # run mapscape mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, img_ref = img_ref, sample_ids = sample_ids, show_warnings=FALSE, n_cells=300) ## ----echo=FALSE--------------------------------------------------------------- # run mapscape mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, img_ref = img_ref, sample_ids = sample_ids, show_warnings=FALSE, show_low_prev_gtypes = TRUE) ## ----echo=FALSE--------------------------------------------------------------- # run mapscape mapscape(clonal_prev = clonal_prev, tree_edges = tree_edges, sample_locations = sample_locations, img_ref = img_ref, sample_ids = sample_ids, show_warnings=FALSE) ## ----eval=FALSE--------------------------------------------------------------- # ?mapscape ## ----eval=FALSE--------------------------------------------------------------- # browseVignettes("mapscape")