def chromosomes_with_SNPs_plot(self, panel, xlabels_on=True):
genome = Genome.regions()
fig, ax = plt.subplots()
chrom_linewidth = 0.75
chrom_color = "Grey"
# p arm ends where centromere starts ;)
for chrom, centromere_start in genome["centromere_start"].iteritems():
ax.plot([chrom, chrom], [0, centromere_start], color=chrom_color,
lw=chrom_linewidth)
q_arms = genome[["centromere_end", "chr_length"]]
for chrom, (q_start, chrom_end) in q_arms.iterrows():
ax.plot([chrom, chrom], [q_start, chrom_end], color=chrom_color,
lw=chrom_linewidth)
# SNPs
panel.snps.plot(ax=ax, kind="scatter", x="chr", y="position", lw=1,
s=120, color="black", marker="_")
ax = self._chromosomes_plot_aesthetics(ax, genome)
if not xlabels_on:
ax.set_xticklabels([])
ax.set_xlabel("")
filename = "chromosomes_with_SNPs__{}".format(panel.label)
filepath = join(PLOTS_DIR, filename)
print(filepath)
plt.savefig(filepath, bbox_inches="tight")
return ax
def _generate_distances_long_format(self):
genome = Genome.regions()
panel_analyser = PanelAnalyser()
frames = [panel_analyser.snp_distances_per_chromosome(panel, genome)
for panel in Panel.all_panels()]
distances = pd.concat(frames).T
return pd.melt(distances)