Plot distributions of substitution rates (Ka, Ks, or Ka/Ks) per species

Usage

plot_rates_by_species(
  kaks_list,
  rate_column = "Ks",
  bytype = FALSE,
  range = c(0, 2),
  fill = "deepskyblue3",
  color = "deepskyblue4"
)

kaks_list: A list of data frames with substitution rates per gene pair in each species as returned by pairs2kaks().
rate_column: Character indicating the name of the column to plot. Default: "Ks".
bytype: Logical indicating whether or not to show distributions by type of duplication. Default: FALSE.
range: Numeric vector of length 2 indicating the minimum and maximum values to plot. Default: c(0, 2).
fill: Character with color to use for the fill aesthetic. Ignored if bytype = TRUE. Default: "deepskyblue3".
color: Character with color to use for the color aesthetic. Ignored if bytype = FALSE. Default: "deepskyblue4".

A ggplot object.

Data will be plotted using the species order of the list. To change the order of the species to plot, reorder the list elements in kaks_list.

data(fungi_kaks)

# Plot rates
plot_rates_by_species(fungi_kaks, rate_column = "Ka_Ks")