Plotting Functions

This module defines MSA analysis functions.

showMSAOccupancy(msa, occ='res', indices=None, count=False, **kwargs)

Show a bar plot of occupancy calculated for MSA instance msa using calcMSAOccupancy(). occ may be 'res' or 'col', or a a pre-calculated occupancy array. If x-axis indices are not specified, they will be inferred from msa or given label that may correspond to a sequence in the msa.

Occupancy is plotted using bar() function.

showShannonEntropy(entropy, indices=None, **kwargs)

Show a bar plot of Shannon entropy array. MSA instances or Numpy character arrays storing sequence alignments are also accepted as entropy argument, in which case calcShannonEntropy() will be used for calculations. indices may be residue numbers, when not specified they will be inferred from msa or indices starting from 1 will be used.

Entropy is plotted using bar() function.

showMutinfoMatrix(mutinfo, *args, **kwargs)

Show a heatmap of mutual information array. MSA instances or Numpy character arrays storing sequence alignment are also accepted as mutinfo argument, in which case buildMutinfoMatrix() will be used for calculations. Note that x, y axes contain indices of the matrix starting from 1.

Mutual information is plotted using imshow() function. vmin and vmax values can be set by user to achieve better signals using this function.

showDirectInfoMatrix(dirinfo, *args, **kwargs)

Show a heatmap of direct information array. MSA instances or Numpy character arrays storing sequence alignment are also accepted as dirinfo argument, in which case buildDirectInfoMatrix() will be used for calculations. Note that x, y axes contain indices of the matrix starting from 1.

Direct information is plotted using imshow() function. vmin and vmax values can be set by user to achieve better signals using this function.

showSCAMatrix(scainfo, *args, **kwargs)

Show a heatmap of SCA (statistical coupling analysis) array. MSA instances. blah

or Numpy character arrays storing sequence alignment are also accepted as scainfo argument, in which case buildSCAMatrix() will be used for calculations. Note that x, y axes contain indices of the matrix starting from 1.

SCA information is plotted using imshow() function. vmin and vmax values can be set by user to achieve better signals using this function.