aaanalysis.AAlogoPlot

class aaanalysis.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.

Supports single and stacked multiple sequence logo visualizations with automatic TMD/JMD part annotations. 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, target_p1_site, ...])	Plot multiple sequence logos stacked vertically for group comparison.
`single_logo`([df_logo, df_logo_info, ...])	Plot a single sequence logo with optional bit-score bar and TMD/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 JMD-N region (>=0). Used together with jmd_c_len to derive the 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.