Following code extracts demographic history from population table, and draws the right panel of Fig. 5.
library(ggplot2)
library(tumopp)
.alt = list(k = c(1, 8, 2 ** 30))
.const = list(D = 3L, C = "hex", N = 16384L, L = "const")
args_table = tumopp::make_args(alt = .alt, const = .const, each = 1L)
results = tumopp::tumopp(args_table)
df = results |>
dplyr::mutate(demography = purrr::map(population, \(x) {
tumopp::extract_history(x) |> tumopp::summarize_demography()
})) |>
dplyr::select(shape, demography) |>
tidyr::unnest("demography")
.breaks = .alt[["k"]]
.labels = ifelse(.breaks < 1e6, .breaks, expression(infinity))
.values = setNames(grey(c(0.666, 0.4, 0)), .breaks)
labels_log10 = function(breaks) {
parse(text = paste0("10^", log10(breaks)))
}
fig5b = ggplot(df) +
aes(time, size, group = shape) +
geom_line(aes(color = as.factor(shape)), linewidth = 1, alpha = 0.8) +
scale_y_log10(breaks = 10 ** seq_len(4L), labels = labels_log10) +
scale_color_manual(
name = expression(italic(k)),
labels = .labels, values = .values,
guide = guide_legend(reverse = TRUE, override.aes = list(size = 3))
) +
labs(x = expression(Time ~ (italic(t))), y = "# of tumor cells") +
theme_bw() +
theme(
panel.grid = element_blank(),
axis.ticks = element_blank(),
legend.key.height = unit(0.7, "lines"),
legend.position = c(0.98, 0.02), legend.justification = c(1, 0)
)
# ggsave("fig5b.png", fig5b, width = 3, height = 3)