itpseq.Sample.codon_violin

Sample.codon_violin(pos, *, motif=None, query=None, col='log2FoldChange', sort_by='median', line_color='k', line_width=0.625, ax=None, violin_kwargs=None, **kwargs)

Plots violin plots for each amino acid motif, with one line per combination of codons.

Parameters:

• pos (str) – Position to use to compute the DE (in amino-acid positions).

• motif (str) – Regex used to filter the data by protein motif. This parameter is strongly recommended for motifs of more than one amino-acid.

• query (str or callable, optional) – Query string or callable used to filter the rows of the input. If a callable, should return a boolean Series/array to filter the rows.

• col (str, optional) – Column from the output of DE to use as the Y-axis.

• sort_by (str, optional) – Method to use to sort the violin plots. Defaults to ‘median’.

• line_color (str, optional) – Color of the inner lines in the violin plot.

• line_width (float, optional) – Width of the inner lines in the violin plot.

• ax (matplotlib.Axes, optional) – If passed, will plot on this Axes.

• violin_kwargs (dict, optional) – Parameters passed to violinplot.

• kwargs (dict, optional) – Parameters passed to DE.

Notes

This method should be used with a filter to avoid producing extremely large graphs.

Examples

Create violin plots for -2:P positions with Q/K fixed in the E/P sites.

>>> sample.codon_violin(pos='-2:P', motif='.QK')