options(repr.plot.width = 7, repr.plot.height = 6) options(jupyter.plot_mimetypes = c('application/pdf', 'image/png')) library(destiny) data(guo_norm) sigmas <- find_sigmas(guo_norm, verbose = FALSE) optimal_sigma(sigmas) palette(cube_helix(6)) plots <- lapply( list('local', 5, round(optimal_sigma(sigmas), 2), 100), function(sigma) plot( DiffusionMap(guo_norm, sigma), 1:2, main = paste('σ =', sigma), col_by = 'num_cells', draw_legend = FALSE)) do.call(gridExtra::grid.arrange, c(plots, ncol = 2))