Created
December 5, 2013 20:49
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Visualize a list of sequences (of same length, assuming DNA encoding) as a color coded matrix
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| import pylab | |
| import numpy | |
| def show_seqs(seqs): | |
| """ | |
| plot color coded training sequences | |
| """ | |
| pylab.figure() | |
| num_seqs = len(seqs) | |
| len_seqs = len(seqs[0]) | |
| color_matrix = numpy.zeros((num_seqs, len_seqs)) | |
| base_map= {"A": 0, "T": 1, "G": 2, "C": 3} | |
| for i, seq in enumerate(seqs): | |
| for j, nucl in enumerate(seq): | |
| color_matrix[i,j] = base_map[nucl] | |
| pylab.imshow(color_matrix) | |
| # add a 'best fit' line | |
| #y = mlab.normpdf( bins, mu, sigma) | |
| #l = pylab.plot(bins, y, 'r--', linewidth=1) | |
| pylab.title("seqs distribution") | |
| pylab.xlabel("seq pos") | |
| pylab.ylabel("seq") | |
| pylab.show() |
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