## ----------------------------------------------------------------------------- library("LACE") data(longitudinal_sc_variants) names(longitudinal_sc_variants) ## ----------------------------------------------------------------------------- lik_weights = c(0.2308772,0.2554386,0.2701754,0.2435088) ## ----------------------------------------------------------------------------- alpha = list() alpha[[1]] = c(0.02,0.01,0.01,0.01) alpha[[2]] = c(0.10,0.05,0.05,0.05) beta = list() beta[[1]] = c(0.10,0.05,0.05,0.05) beta[[2]] = c(0.10,0.05,0.05,0.05) head(alpha) head(beta) ## ----------------------------------------------------------------------------- inference = LACE(D = longitudinal_sc_variants, lik_w = lik_weights, alpha = alpha, beta = beta, keep_equivalent = TRUE, num_rs = 5, num_iter = 10, n_try_bs = 5, num_processes = NA, seed = 12345, verbose = FALSE) ## ----------------------------------------------------------------------------- data(inference) print(names(inference)) ## ----fig.width=12, fig.height=8, warning=FALSE, fig.cap="Inferred model"------ clone_labels = c("ARPC2","PRAME","HNRNPC","COL1A2","RPL5","CCT8") longitudinal.tree = longitudinal.tree.plot(inference = inference, labels_show = "clones", clone_labels = clone_labels, legend_position = "topright")