itpseq.Replicate.logo

Replicate.logo(logo_kwargs=None, ax=None, fMet=False, type='information', **kwargs)

Generates a sequence logo based on the aligned inverse-toeprints, using the logomaker library.

Parameters:

• logo_kwargs (dict, optional) – Additional keyword arguments passed to logomaker.Logo for customizing the sequence logo. Defaults to {‘color_scheme’: ‘NajafabadiEtAl2017’}.

• ax (matplotlib.axes.Axes, optional) – Pre-existing matplotlib Axes to draw the logo on. A new Axes is created if not provided.

• fMet (bool, optional) – If False, removes m (formyl-methionine / start codon) from the alignment when building the logo. Defaults to False.

• type (str, optional) – The transformation type applied to the counts matrix. Possible values include: - ‘information’ for information content. - ‘probability’ for probabilities. Defaults to ‘information’.

• **kwargs (dict) – Additional keyword arguments passed to filter the input data (e.g., pos, min_peptide, max_peptide…).

Returns:

A logomaker.Logo object representing the sequence logo.

Return type:

logomaker.Logo

Notes

• Sequence alignment data is first converted to a counts matrix via the logomaker.alignment_to_matrix method.

• The ribosomal site corresponding to each position is annotated on the x-axis.

• Transformation of the counts matrix (e.g., counts to information) is performed using logomaker.transform_matrix.

Examples

Simple logo plot with default settings

>>> logo = obj.logo()

Logo plot with min_peptide filtering

>>> logo = obj.logo(min_peptide=3)

Logo plot with custom transformation type and filtering

>>> logo = obj.logo(type='probability', min_peptides=2, fMet=True)