Global-Sigma.r
In destiny: Creates diffusion maps

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))