## ----------------------------------------------------------------------------- set.seed(1) ## ----------------------------------------------------------------------------- library(destiny) # load destiny… data(guo) # …and sample data library(gridExtra) # Also we need grid.arrange ## ----------------------------------------------------------------------------- par(mar = rep(0, 4)) graph <- igraph::graph_from_literal( data -+ 'transition probabilities' -+ DiffusionMap, 'transition probabilities' -+ DPT) plot( graph, layout = igraph::layout_as_tree, vertex.size = 50, vertex.color = 'transparent', vertex.frame.color = 'transparent', vertex.label.color = 'black') ## ----------------------------------------------------------------------------- dm <- DiffusionMap(guo) dpt <- DPT(dm) ## ----------------------------------------------------------------------------- set.seed(4) dpt_random <- DPT(dm, tips = sample(ncol(guo), 3L)) ## ----------------------------------------------------------------------------- grid.arrange(plot(dpt), plot(dpt_random), ncol = 2) ## ----------------------------------------------------------------------------- grid.arrange( plot(dpt, col_by = 'DPT3'), plot(dpt, col_by = 'Gata4', pal = viridis::magma), ncol = 2 ) ## ----------------------------------------------------------------------------- plot(dpt, root = 2, paths_to = c(1,3), col_by = 'branch') ## ----------------------------------------------------------------------------- plot(dpt, col_by = 'branch', divide = 3, dcs = c(-1,-3,2), pch = 20)