def make_the_gene_with_exon_and_map(chr,
gene_name,
ax,
exon_lib,
x,
y,
locus,
frequency,
width=30.0,
height=5.0,
scale=1.0):
genome = EnsemblRelease(75)
genes = genome.genes_by_name(gene_name)
gene = genes[0]
gene_start = gene.start
gene_end = gene.end
gene_length = float(gene_end - gene_start)
# draw the gene
ax.add_patch(
patches.Rectangle(
(x, y - height / 2),
width,
height,
alpha=0.5,
color="dodgerblue",
linewidth=0,
))
# find the exon ids
exon_id = genome.exon_ids_of_gene_name(gene_name)
# plot the gene with exons
for i in exon_id:
position = exon_lib[i]
exon_start = int(position[0])
exon_end = int(position[1])
exon_length = exon_end - exon_start
plot_length = exon_length / gene_length * width
plot_x = (exon_start - gene_start) / gene_length * width
ax.add_patch(
patches.Rectangle(
(x + plot_x, y - height / 2 - 0.5 * scale),
plot_length,
height + 1 * scale,
color="black",
alpha=0.4,
linewidth=0,
))
# map the read to the plot
for i in range(len(locus)):
plot_x = (locus[0] - gene_start) / gene_length * width
if frequency[i] < 0.0001:
bar_length = 1
else:
bar_length = abs(math.log(frequency[i] / 0.01) * 2)
ax.plot(
(x + plot_x, x + plot_x),
(y + height / 2 + scale * 0.5,
y + height / 2 + scale * 0.5 + bar_length),
color="darkblue",
alpha=0.5,
linewidth=2,
)
# gene name at the left
ax.text(x - 0.5,
y,
gene_name + '\n' + chr,
horizontalalignment='right',
verticalalignment='center',
fontsize=25,
fontweight="bold")
# gene start
ax.text(
x,
y - height / 2 - 0.8 * scale,
gene_start,
horizontalalignment='center',
verticalalignment='top',
fontsize=12,
)
# gene end
ax.text(
x + width,
y - height / 2 - 0.8 * scale,
gene_end,
horizontalalignment='center',
verticalalignment='top',
fontsize=12,
)
