def _chromosomes_plot_aesthetics(self, ax, genome):
plt.gcf().set_size_inches(self.FIGSIZE)
max_len = genome["chr_length"].max()
hide_spines_and_ticks(ax)
ax.title.set_fontsize(16)
ax.title.set_fontweight("bold")
ax.set_xlabel("Autosoma")
ax.set_xlim([0, 23])
ax.set_xticks(genome.index)
ax.set_xticklabels(genome.index, rotation=0, fontsize=14)
ax.yaxis.labelpad = 15
ax.xaxis.labelpad = 15
ax.set_ylim([0, max_len * 1.05])
ax.set_ylabel("Posición (Mb)", )
yinterval = 10**7
yticks = np.arange(0, max_len + yinterval, yinterval) // 1
yticks = [t for t in yticks if t % (50*10**6) == 0]
ax.set_yticks(yticks)
yticklabels = np.arange(0, max_len + yinterval, yinterval) // 10**6
ax.set_yticklabels([l for l in yticklabels if l % 50 == 0])
ax.legend(loc="best", scatterpoints=1)
return ax
def _pca_plot_aesthetics(self, ax):
plot_helpers.hide_spines_and_ticks(ax, spines="all")
ax.tick_params(axis="x", bottom="off", top="off", labelbottom="off")
ax.tick_params(axis="y", left="off", right="off", labelleft="off")
grey_spines(ax)
return ax
def _ternary_plot_aesthetics(self, tax, title, df):
hide_spines_and_ticks(tax.get_axes(), spines="all")
tax.boundary(linewidth=0.25)
tax.clear_matplotlib_ticks()
tax.set_title(title, position=(0.5, 1.15))
tax.legend(frameon=False, scatterpoints=1, bbox_to_anchor=(0.975, 1.125))
tax.bottom_axis_label(df.columns[0], position=(1, 0, 0), rotation=0)
tax.right_axis_label(df.columns[1], position=(-0.1, 1.2, -0.1), rotation=0)
tax.left_axis_label(df.columns[2], position=(0, 0, 1), rotation=0)
return tax
def _boxplot_aesthetics(self, ax, legend_on=False):
title = "\n".join(["MAF promedio por población"])
ax.set_title(title, y=1.08, fontweight="bold")
ax.set_ylabel("Frecuencia del alelo menor")
ax.set_xlabel("")
ax.yaxis.labelpad = ax.xaxis.labelpad = 15
ax.legend(loc="upper left", bbox_to_anchor=(0.8, 1.29),
frameon=True)
ax.legend_.get_frame().set_facecolor("white")
ax.yaxis.grid(linestyle="dotted")
hide_spines_and_ticks(ax)
def _boxplot_aesthetics(self, ax):
ax.set_title("Distancia media entre AIMs", y=1.08, fontweight="bold")
ax.set_ylabel("Distancia (Mpb)")
ax.set_xlabel("Cromosoma")
y_range = np.array(ax.get_yticks())
ax.set_yticklabels([int(y) for y in y_range // 10**6])
ax.yaxis.labelpad = ax.xaxis.labelpad = 15
ax.yaxis.grid(linestyle="dotted")
hide_spines_and_ticks(ax)
