Plotting Functions¶
This module defines MSA analysis functions.

showMSAOccupancy
(msa, occ='res', indices=None, count=False, **kwargs)[source]¶ Show a bar plot of occupancy calculated for
MSA
instance msa usingcalcMSAOccupancy()
. occ may be'res'
or'col'
, or a a precalculated occupancy array. If xaxis 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)[source]¶ 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 casecalcShannonEntropy()
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)[source]¶ Show a heatmap of mutual information array.
MSA
instances or Numpy character arrays storing sequence alignment are also accepted as mutinfo argument, in which casebuildMutinfoMatrix()
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)[source]¶ Show a heatmap of direct information array.
MSA
instances or Numpy character arrays storing sequence alignment are also accepted as dirinfo argument, in which casebuildDirectInfoMatrix()
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)[source]¶ Show a heatmap of SCA (statistical coupling analysis) array.
MSA
instances. blahor 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.