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 plot(self, filename, panel_list, ancestries_df):
dataset_label, _ = self._unique_dataset_and_K_check(ancestries_df)
dataset = Dataset(dataset_label)
population_order = Dataset.used_populations()
rows, cols = 1, len(panel_list)
width, height = self.PLOT_SIZE
fig = plt.figure(figsize=(cols * width, rows * height), dpi=30)
fig.set_size_inches((cols*width), (rows*height))
ax_ids = (np.arange(rows * cols) + 1).tolist()[::-1]
# One subplot per panel
for panel in panel_list:
df_lite = ancestries_df.xs(panel.label, level="panel")
df_lite = df_lite.reset_index(drop=True).set_index("population")
plot_title = "Dataset: {}\n{}".format(dataset.name, panel.name)
ax = fig.add_subplot(rows, cols, ax_ids.pop())
fig, tax = ternary.figure(scale=1, ax=ax)
df_lite = df_lite.loc[population_order]
df_lite = df_lite[["EUR", "AFR", "AMR"]].dropna()
df_grouped = df_lite.groupby(level="population", sort=False)
for population, df_pop_group in df_grouped:
tax.scatter(
df_pop_group.values, label=population, s=45,
alpha=0.75, color=population_colors(population),
marker=population_markers(population)
)
self._ternary_plot_aesthetics(tax, plot_title, df_lite)
makedirs(self.PLOTS_DIR, exist_ok=True)
plt.savefig(join(self.PLOTS_DIR, filename), bbox_inches="tight")
