AAlogoPlot

class AAlogoPlot(logo_type='probability', jmd_n_len=10, jmd_c_len=10, verbose=True)[source]

Bases: object

Amino Acid logo Plot (AAlogoPlot) class for visualizing sequence logos.

Every plotting method returns a (fig, ax) pair (a thin tuple subclass): unpack as fig, ax = .... For backward compatibility, the returned object also forwards attribute access to ax, so legacy ax = ...; ax.set_title(...) keeps working.

Renders single and stacked multiple sequence logos (via the logomaker [Tareen20] package) with automatic target middle domain (TMD) / juxta middle domain (JMD) part annotations. jmd_n_len and jmd_c_len are set at initialization and used by all plot methods to derive the TMD region length from the logo DataFrame. The logo_type set at initialization controls only the y-axis label; the logo data itself is provided as a pre-computed df_logo from AAlogo.

Added in version 1.0.3.

Parameters:

logo_type (Literal[‘probability’, ‘weight’, ‘counts’, ‘information’])
jmd_n_len (int)
jmd_c_len (int)
verbose (bool)

Methods

`multi_logo`([list_df_logo, ...])	Plot multiple sequence logos stacked vertically for group comparison, each with an optional bit-score bar on top.
`single_logo`([df_logo, df_logo_info, ...])	Plot a single sequence logo with optional bit-score bar and target middle domain (TMD) / juxta middle domain (JMD) annotations.

__init__(logo_type='probability', jmd_n_len=10, jmd_c_len=10, verbose=True)[source]

Parameters:

logo_type ({'probability', 'weight', 'counts', 'information'}, default='probability') –
Type of sequence logo encoding, used to set the y-axis label:
- 'probability': y-axis label is 'Probability [%]'.
- 'weight': y-axis label is 'Weight'.
- 'counts': y-axis label is 'Counts'.
- 'information': y-axis label is 'Bits'.
jmd_n_len (int, default=10) – Length of the juxta middle domain (JMD)-N region (>=0). Used together with jmd_c_len to derive the target middle domain (TMD) length from the logo DataFrame for part annotations.
jmd_c_len (int, default=10) – Length of the JMD-C region (>=0).
verbose (bool, default=True) – If True, verbose outputs are enabled.