cvmplot is a data visualization python package for SZQ lab used in TransposonSequencing/cgMLST/wgMLST data analysis based on matplotlib.
Python 3.9 or later is required for installation.
Install PyPI package:
pip3 install cvmplot
Jupyter notebooks containing code examples below is available here.
import random
from cvmplot.cvmplot import cvmplot as cvmplot
# prepare cds data
gene_data = [
{"start": 11120, "end": 13800, "strand": 1, "name": "gene1", 'color':'red'},
{"start": 14231, "end": 15286, "strand": -1, "name": "gene2", 'color':'lightblue'},
{"start": 16868, "end": 18212, "strand": 1, "name": "gene3", 'color':'green'},
{"start": 18500, "end": 19863, "strand": -1, "name": "gene4", 'color':'blue'},
{"start": 20123, "end": 24632, "strand": 1, "name": "gene5", 'color':'#d1af3f'},
{"start": 25159, "end": 27000, "strand": -1, "name": "gene6", 'color':'cyan'},
{"start": 27360, "end": 29888, "strand": 1, "name": "gene7", 'color':'#f9d9d9'},
]
bar_positions = np.random.randint(10000, 30000, size=1000) # Bar x-axis positions
bar_data = np.random.randint(50,100, size=1000) # Bar plot values
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=True, cds_labelsize=7, cds_labrotation=45, track_start=10000, cds_color='lightblue'
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('general_plot.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=True, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs'
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('tracklabel_plot.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=True, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_labelsize=8
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('tracklabelsize_plot.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=True, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_labelsize=8, track_height=0.3,
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('trackheight_plot.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=True, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_labelsize=8, track_height=0.3, bax_bottompos=2
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('bax_bottompos.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=False, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_labelsize=8, track_height=0.3, bax_bottompos=2
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('cds_label.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=False, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_height=0.3, bax_bottompos=2, track_labelsize=15
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('tracklabelsize.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=False, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_height=0.3, bax_bottompos=2.2, track_labelsize=8, track_sublabelpos='top-right'
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('track_sublabelpos_plot.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=False, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_height=0.3, bax_bottompos=2.2, track_labelsize=8, track_sublabelpos='top-right',
bar_color='lightblue'
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('barcolor_plot.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=False, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_height=0.3, bax_bottompos=2.2, track_labelsize=8, track_sublabelpos='top-right',
bar_color='lightblue', bax_height=7
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('bax_height_plot.png', bbox_inches='tight')
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_length=20000,
cds_label=False, cds_labelsize=7, cds_labrotation=45, track_start=10000, track_label='GENEs',
track_height=0.3, bax_bottompos=2.2, track_labelsize=8, track_sublabelpos='top-right',
bar_color='lightblue', bax_height=4, cds_arrowshaftratio=1
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('cds_arrowshaftratio_plot.png', bbox_inches='tight')
gb2cds('GENEBANKE_FILE.gb') function will return a dict with contigs name as key and a list as value including the CDS 'start, end, strand, name, color' used in tnseqplot funtion
cds_data = cvmplot.gb2cds('HA3S26.gbff')
gene_data = cds_data['NODE_1_length_1210584_cov_117.87540']
# Simulate the insertion data in the range of 1-20000
bar_positions = np.random.randint(1, 20000, size=500) # Bar x-axis positions
bar_data = np.random.randint(50,100, size=500) # Bar plot values
fig, cds_ax, bar_ax = cvmplot.tnseqplot(inspos=bar_positions, inscount=bar_data, cds=gene_data, track_start=1,
track_length=20000, cds_label=False, track_height=0.3, bax_bottompos=2
)
bar_ax.set_ylabel('Insert frequency')
plt.show()
fig.savefig('genbank_plot.png', bbox_inches='tight')
