def MAF_comparison_boxplot(self):
long_format_mafs = self._generate_maf_long_df()
populations_to_plot = {
"superpopulation": ['AFR', 'EUR', 'AMR'],
"population": Dataset.used_populations(),
}
for population_level, long_df in long_format_mafs.items():
population_list = populations_to_plot[population_level]
mask = long_df["population"].isin(population_list)
long_df = long_df[mask]
fig_width = 13 if population_level == "population" else 7
fig = plt.figure(figsize=(fig_width, 4))
ax = fig.add_subplot(1, 1, 1)
panel_labels = long_df["panel"].unique()
colors = [v for k, v in panel_colors().items() if k in panel_labels]
sns.boxplot(data=long_df, x="population", y="MAF", hue="panel",
ax=ax, linewidth=0.3, showcaps=False, showfliers=False,
palette=sns.color_palette(colors), width=0.70)
self._boxplot_aesthetics(ax)
filename = "MAF_comparison__{}".format(population_level)
plt.savefig(join(self.PLOTS_DIR, filename), bbox_inches="tight")
plt.show()
def snp_distances_comparison_boxplot(self, panel_labels):
distances_long_format = self._generate_distances_long_format()
mask = distances_long_format["panel"].isin(panel_labels)
distances = distances_long_format[mask]
fig = plt.figure(figsize=(12, 3))
ax = fig.add_subplot(1, 1, 1)
panel_labels = distances["panel"].unique()
colors = [v for k, v in panel_colors().items() if k in panel_labels]
sns.boxplot(x="chromosome", y="value", hue="panel", data=distances,
ax=ax, linewidth=0.6, showcaps=False, showfliers=False,
palette=sns.color_palette(colors))
self._boxplot_aesthetics(ax)
plt.show()
