bx.motif.logo package

Module contents

bx.motif.logo.eps_logo(matrix, base_width, height, colors={'A': '0.00 1.00 0.00', 'C': '0.00 0.00 1.00', 'G': '1.00 0.65 0.00', 'T': '1.00 0.00 0.00'})

Return an EPS document containing a sequence logo for matrix where each bases is shown as a column of base_width points and the total logo height is height points. If colors is provided it is a mapping from characters to rgb color strings.

bx.motif.logo.freqs_to_heights(matrix)

Calculate logo height using the method of:

Schneider TD, Stephens RM. “Sequence logos: a new way to display consensus sequences.” Nucleic Acids Res. 1990 Oct 25;18(20):6097-100.