itpseq.Sample.itp_len_plot

Sample.itp_len_plot(ax=None, min_codon=0, max_codon=10, limit=100, norm=True, kind='line', row=None, col=None, plt_kwargs={'aspect': 3, 'height': 2}, **kwargs)

Generates a plot of inverse-toeprint (ITP) counts per length.

This method uses the output of itp_len to create a plot showing the counts of inverse-toeprints across lengths for each replicate. Optionally, counts can be normalized (per million reads), and the plotted lengths can be limited.

Parameters:

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

• min_codon (int, optional) – The minimum codon position to annotate on the plot. Defaults to 0.

• max_codon (int, optional) – The maximum codon position to annotate on the plot. Defaults to 10.

• limit (int, optional) – The maximum length to include in the plot. Defaults to 100.

• norm (bool, optional) – Whether to normalize counts to reads per million. Defaults to True.

• kind (str) – Type of plot to use. Defaults to ‘line’.

• row (str, optional) – attribute to use as rows in the FacetGrid

• col (str, optional) – attribute to use as columns in the FacetGrid

• plt_kwargs – parameters used in the FacetGrid if col/row is used.

• kwargs (optional) – Additional parameters to pass to the seaborn plotting function.

Return type:

matplotlib.axes.Axes or seaborn.axisgrid.FacetGrid

See also

DataSet.itp_len_plot

Notes

• The x-axis represents the distance from the 3’ end of the inverse-toeprint in nucleotides.

• The y-axis shows the counts of inverse-toeprints, either absolute or normalized per million reads.

• Each replicate is plotted independently and distinguished by the hue attribute in the plot.

Examples

Create a line plot with all replicates:

>>> sample.itp_len_plot(norm=False)

Create a bar plot per replicate:

>>> sample.itp_len_plot(kind='bar', row='replicate')