In [1]:

import matplotlib.pyplot as plt
from msaplot import msaplot

In [2]:

%load_ext autoreload
%autoreload 2

In [12]:

seq1="CAGGTGCACCTGCAGGAGTCGGGCCCCGGACTAGTGAAGTCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGACTCCATCAGACGTGATACTTACTACTGGAGCTGGATCCGGCAGACTCCGGGGAAGGGACTGGAGTGGCTTGGATATGTCTTTAAAAGTGGGAGCACAAAGTACAACCCCTCCTTCAAGCGTCGAGTCGACATATCAGTAGACACGTCCAAGGAGCAGTTCTCCCTGACATTGACGTCTGTGACCACTGCGGACACGGCCGTATACTTCTGTGCGAGAGAGTGGTACTATGGTTCGGGGGCCCCCCACAACTGGCTCGACTCCTGGAGCCAGGGAACCCTGGTCACCGTCTCCTCAG"
seq2="CAGGTGCACCTGCAGGAGTCGGGCCCCGGACTAGTGAAGTCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGACTCCATCAGACGTGATACTTACTACTGGAGCTGGATCCGGCAGACTCCGGGGAAGGGACTGGAGTGGCTTGGATATGTCTTTAAAAGTGGGAGCACAAAGTACAACCCCTCCTTCAAGCGTCGAGTCGACATATCAGTAGACACGTCCAAGGAGCAGTTCTCCCTGACATTGACGTCTGTGACCACTGCGGACACGGCCGTATACTTCTGTGCGAGAGAGTGGTACTATGGTTCGGGGGCCCCCCACAACTGGCTCGACTCCTGGAGCCAGGGAACCCTGGTCACCGTCTCCTCAG"
germline="CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAG------TAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTGGTACTATGGTTCGGGGGCCCCCCACAACTGGTTCGACTCCTGGGGCCAAGGAACCCTGGTCACCGTCTCCTCAG"

In [52]:

msaplot.DrawComplexMSA(msa=[seq1,seq2, germline], wrap=50, 
               seq_names = ['seq1', 'seq2', 'germline'],
               color_map = msaplot.GetColorMap("dna"),
               panels=[msaplot.DrawAnnotation, msaplot.DrawSeqLogo, msaplot.DrawMSA, msaplot.DrawConsensusHisto], 
               panel_params = [{"annotations":[["CDR1",75,104], ["CDR2",156,176], 
                                               ["CDR3",288,344]]}, 
                               {}, {"show_char":True}, {}], figsize=[12,24])
               #panel_height_ratios=[0.4, 1, 0.25])
#plt.tight_layout()
plt.show()

In [53]:

msaplot.DrawComplexMSA(msa=["AC-GAT", "A-CGT-"],
               panels=[msaplot.DrawSeqLogo, msaplot.DrawMSA, msaplot.DrawConsensusHisto])

Out[53]:

array([<Axes: >, <Axes: >, <Axes: >], dtype=object)

In [4]:

#ax = plt.gca()
#ax.set(xlim=[-20,20], ylim=[-20, 20])
ax, color_map=msaplot.DrawMSA(msa=["AC-GAT", "A-CGT-"], seq_names = ["r1", "r2"],
           start = 1, end = 4)

In [5]:

#ax = plt.gca()
#ax.set(xlim=[-20,20], ylim=[-20, 20])
msaplot.DrawSeqLogo(["AC-G-T", "ACCGT-", "ACGAGT", "ACGAGT"], color_map, 4, start = 1, end = 3)

In [6]:

msaplot.DrawConsensusHisto(msa=["AC-G-T", "A-CGT-", "ACGAGT"], color=[0,105/255,62/255])

In [28]:

msaplot.DrawAnnotation(msa=["AC-G-T", "A-CGT-", "ACGAGT"], annotations=[['x',1,3], ['y', 4,5]],
                      start=2, end=3)

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