## ----eval=FALSE--------------------------------------------------------------- # # try http:// if https:// URLs are not supported # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("timescape") ## ----eval=FALSE--------------------------------------------------------------- # example("timescape") ## ----echo=FALSE--------------------------------------------------------------- library(timescape) ## ----echo=FALSE--------------------------------------------------------------- # EXAMPLE 1 - Acute myeloid leukemia patient, Ding et al., 2012 # genotype tree edges tree_edges <- read.csv(system.file("extdata", "AML_tree_edges.csv", package = "timescape")) # clonal prevalences clonal_prev <- read.csv(system.file("extdata", "AML_clonal_prev.csv", package = "timescape")) # targeted mutations mutations <- read.csv(system.file("extdata", "AML_mutations.csv", package = "timescape")) # perturbations perturbations <- data.frame( pert_name = c("Chemotherapy"), prev_tp = c("Diagnosis")) # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, perturbations = perturbations, height=260) ## ----echo=FALSE--------------------------------------------------------------- # EXAMPLE 2 - Patient 7, McPherson and Roth et al., 2016 # genotype tree edges tree_edges <- read.csv(system.file("extdata", "px7_tree_edges.csv", package = "timescape")) # clonal prevalences clonal_prev <- read.csv(system.file("extdata", "px7_clonal_prev.csv", package = "timescape")) # clone colours clone_colours <- data.frame(clone_id = c("A","B","C","D","E"), colour = c("d0ced0", "2CD0AB", "FFD94B", "FD8EE5", "F8766D")) # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, clone_colours = clone_colours, height=260, alpha=15) ## ----echo=FALSE--------------------------------------------------------------- # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260, alpha=15) ## ----echo=FALSE--------------------------------------------------------------- # clone colours clone_colours <- data.frame(clone_id = c("A","B","C","D","E"), colour = c("#e41a1c", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00")) # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, clone_colours = clone_colours, height=260, alpha=15) ## ----echo=FALSE--------------------------------------------------------------- # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260, alpha=10) ## ----echo=FALSE--------------------------------------------------------------- # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260, alpha=90) ## ----echo=FALSE--------------------------------------------------------------- # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260, alpha=15, xaxis_title="My X Axis", yaxis_title="My Y Axis", phylogeny_title="My Phylogeny") ## ----echo=FALSE--------------------------------------------------------------- # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260, alpha=15, genotype_position="stack") ## ----echo=FALSE--------------------------------------------------------------- # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260, alpha=15, genotype_position="space") ## ----echo=FALSE--------------------------------------------------------------- # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260, alpha=15, genotype_position="centre") ## ----echo=FALSE--------------------------------------------------------------- # EXAMPLE 1 - Acute myeloid leukemia patient, Ding et al., 2012 # genotype tree edges tree_edges <- read.csv(system.file("extdata", "AML_tree_edges.csv", package = "timescape")) # clonal prevalences clonal_prev <- read.csv(system.file("extdata", "AML_clonal_prev.csv", package = "timescape")) # targeted mutations mutations <- read.csv(system.file("extdata", "AML_mutations.csv", package = "timescape")) # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, height=260) ## ----echo=FALSE--------------------------------------------------------------- # perturbations perturbations <- data.frame( pert_name = c("Chemotherapy"), prev_tp = c("Diagnosis")) # run timescape timescape(clonal_prev = clonal_prev, tree_edges = tree_edges, perturbations = perturbations, height=260) ## ----eval=FALSE--------------------------------------------------------------- # ?timescape ## ----eval=FALSE--------------------------------------------------------------- # browseVignettes("timescape")