import matplotlib.patches as patches
import matplotlib.pyplot as plt
[docs]
class Ideogram:
"""
from sequana import FastA
f = FastA("assembly.fa")
N = len(f)
L = [ f.get_lengths_as_dict()[str(x)] for x in range(1,N+1)]
#
import pandas as pd
centromeres = pd.read_csv("centromeres.csv", sep=",")
C = [centromeres.query('chrom==@x')['hic_position'].values[0] for x in range(1,N+1)]
telomeres = pd.read_csv("telomeres//sequana.telomark.telomark.csv")
X1 = telomeres['5to3_LHS_position'].values
X2 = telomeres['3to5_RHS_position'].values
X2 = L - X2
"""
def __init__(self, df, gaps={}):
self.df = df.copy()
self.gaps = gaps
self.chrom_width = 0.6
self.spacing = 1.0
self.tri_height = 10000 # how far triangles extend
[docs]
def plot(self, figsize=(10, 12)):
N = len(self.df)
fig, ax = plt.subplots(figsize=figsize)
C = self.df["centromere"].values
L = self.df["length"].values
X1 = self.df["LHS_telomere"].values
X2 = self.df["RHS_telomere"].values
for i in range(N):
xpos = i * self.spacing
length = float(L[i])
centromere = float(C[i])
x1 = float(X1[i])
x2 = float(X2[i])
# Bottom chromosome segment (up to centromere)
chrom_bottom = patches.Rectangle(
(xpos, 0), self.chrom_width, centromere - self.tri_height, edgecolor="black", facecolor="lightgrey"
)
ax.add_patch(chrom_bottom)
# Top chromosome segment (after centromere)
chrom_top = patches.Rectangle(
(xpos, centromere + self.tri_height),
self.chrom_width,
length - centromere - self.tri_height,
edgecolor="black",
facecolor="lightgrey",
)
ax.add_patch(chrom_top)
# Bottom (inverted) triangle - centromere
triangle_bottom = patches.Polygon(
[
(xpos, centromere - self.tri_height),
(xpos + self.chrom_width / 2, centromere),
(xpos + self.chrom_width, centromere - self.tri_height),
],
closed=True,
color="red",
)
ax.add_patch(triangle_bottom)
# Top triangle - centromere
triangle_top = patches.Polygon(
[
(xpos, centromere + self.tri_height),
(xpos + self.chrom_width / 2, centromere),
(xpos + self.chrom_width, centromere + self.tri_height),
],
closed=True,
color="red",
)
ax.add_patch(triangle_top)
# Telomeres
tel_left = patches.Rectangle((xpos, 0), self.chrom_width, x1, facecolor="green")
ax.add_patch(tel_left)
tel_right = patches.Rectangle((xpos, x2), self.chrom_width, length - x2, facecolor="green")
ax.add_patch(tel_right)
if self.gaps and str(i + 1) in self.gaps.keys():
for position in self.gaps[str(i + 1)][1:]:
gap = patches.Rectangle((xpos, position), self.chrom_width, 20000, facecolor="blue", zorder=20)
ax.add_patch(gap)
# Aesthetics
ax.set_xlim(-0.5, self.spacing * N)
ax.set_ylim(0, max(L) + 20000)
ax.set_xticks([i * self.spacing + self.chrom_width / 2 for i in range(N)])
ax.set_xticklabels([str(i + 1) for i in range(N)], rotation="vertical", fontsize=16)
ax.set_ylabel("Position (bp)", fontsize=16)
ax.set_xlabel("Chromosome", fontsize=16)
ax.set_title("Chromosome Ideogram")
