Create fancy (bokeh) gene locus plots from GenBank files
Project description
Gene Loci Comparison
Create fancy (bokeh) gene locus plots from GenBank files!
This repository extends the functionality of the excellent DnaFeaturesViewer
Setup
pip install git+https://github.com/MrTomRod/gene_loci_comparison.git
Examples
Bokeh
This library can also create interactive html/javascript-based plots. Open these files in your browser:
Single locus, specify colors
from gene_loci_comparison import Locus, Loci
import matplotlib
import matplotlib.pyplot as plt
matplotlib.rcParams['font.family'] = "PT Sans Narrow"
locus = Locus(gbk_file='/path/to/file.gbk', locus_tag='FAM3257_001019')
locus_to_color = dict(
FAM3257_001014='#1271c3',
FAM3257_001015='#3171c3',
FAM3257_001016='#5d71c3',
FAM3257_001017='#9371c3',
FAM3257_001018='#b171c3',
FAM3257_001019='#cb71c3',
FAM3257_001020='#ea71c3',
FAM3257_001021='#fd71c3',
# FAM3257_001021='#fd71c3' # last gene: white (default color)
)
locus.colorize(locus_to_color)
ax, _ = locus.plot(figure_width=12)
plt.show()
Multiple loci
from gene_loci_comparison import Loci
import matplotlib
matplotlib.rcParams['font.family'] = "PT Sans Narrow"
# Each locus is made from a gbk-file, a gene identifier and a title (optional)
loci_of_interest = [
dict(gbk='/path/to/file1.gbk', gene='FAM3257_00934', title='title1'),
dict(gbk='/path/to/file2.gbk', gene='FAM3257_000019', title='title2'),
dict(gbk='/path/to/file3.gbk', gene='FAM3257_001020', title='title3'),
]
# Highlight selected genes
locus_to_color_dict = {locus['gene']: '#1984ff' for locus in loci_of_interest}
# Generate loci object
loci = Loci.generate(
loci_of_interest,
locus_to_color_dict=locus_to_color_dict
)
plot = loci.plot(auto_reverse=False)
plot.show()
Multiple loci, autoreversed
To automatically reverse loci based on the direction of the selected genes. Simply set auto_reverse
to True
.
Multiple loci, with GC content
Change plotting method from plot_multiple
to plot_multiple_gc
.
plot = loci.plot_gc(
auto_reverse=True,
window_bp=200
)
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