Skip to content

added doane bin calculation and logmodulus in x-axis #236

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: dev
Choose a base branch
from
Open

added doane bin calculation and logmodulus in x-axis #236

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 25 additions & 13 deletions bin/plot_svlendist.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,20 @@
import gzip
import csv

def log_modulus(x):
y=np.sign(x)*np.log10(np.abs(x))
return y

def log_modulus_inv(x):
y=np.sign(x)*( 10**np.abs(x) )
return y

def get_sample_name(vcf_file):
base_name = os.path.basename(vcf_file)
return base_name.split('.')[0]

def format_bp_label(value, pos):
value = abs(value)
value = abs(log_modulus_inv(value))
if value >= 1e6:
return f'{value / 1e6:.1f} Mbp'
elif value >= 1e3:
Expand Down Expand Up @@ -194,21 +202,21 @@ def plot_svlen_distributions(svlen_data, max_svlen, output_file, plot_title):
colors = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b']
line_styles = ['-', '--', ':', '-.']

num_bins = 50
bins = np.linspace(-max_svlen, max_svlen, num_bins * 2)


for i, (file_name, lengths_dict) in enumerate(svlen_data.items()):
current_color = colors[i % len(colors)]
current_linestyle = line_styles[i % len(line_styles)]

all_lengths = lengths_dict['positive'] + lengths_dict['negative']

if all_lengths:
counts, bin_edges = np.histogram(all_lengths, bins=bins)
if all_lengths:
counts, bin_edges = np.histogram(all_lengths, bins="doane")
bin_centers = (bin_edges[:-1] + bin_edges[1:]) / 2

plt.plot(bin_centers, counts, label=file_name,
color=current_color, linestyle=current_linestyle, linewidth=3)
bin_centers=log_modulus(bin_centers)
plt.bar(bin_centers, counts, label=file_name,
color=current_color,edgecolor="black",alpha=0.6,
width=0.1
)

plt.yscale('log')

Expand All @@ -217,14 +225,18 @@ def plot_svlen_distributions(svlen_data, max_svlen, output_file, plot_title):
plt.title(plot_title, fontsize=18, fontweight='bold', pad=20)

legend = plt.legend(title="Tool", title_fontsize=16, fontsize=14)
for handle in legend.legendHandles:
handle.set_linewidth(4.0)
try:
for handle in legend.legendHandles:
handle.set_linewidth(4.0)
except:
pass

plt.grid(True, which="both", linestyle='--', alpha=0.7)

plt.xlim(-max_svlen, max_svlen)
plt.xlim(log_modulus(-max_svlen), log_modulus(max_svlen) )

plt.gca().xaxis.set_major_formatter( plt.FuncFormatter(format_bp_label) )

plt.gca().xaxis.set_major_formatter(plt.FuncFormatter(format_bp_label))

plt.tight_layout()

Expand Down
Loading