itpseq.Sample.itoeprint

Sample.itoeprint(plot='bands', norm='mean', norm_range=(21, 51), exposure=1, limit=(0, 100), show_range=False, ax=None, interactive=False)

Plots a virtual inverse-toeprint gel.

Parameters:

• plot (str, optional) – Type of representation. “bands” will display lines with a width proportional to the number of reads. “shades” will display a fixed-height line with a varying shade.

• norm (str, optional) – Type of normalization for each lane (possible values are None, ‘mean’, ‘median’, ‘max’, ‘std’)

• norm_range (tuple, optional) – Range of lengths considered to perform the normalization. Defaults to 21-51, which corresponds to the first 10 codons after the start.

• exposure (int, optional) – Modulates the global intensity of the bands in the “bands” type of plot.

• limit (tuple, optional) – Limits the visible range of lengths.

• show_range (bool, optional) – Shows the regions excluded from the normalization in light red.

• ax (matplotlib.axes.Axes, optional) – ax to use for plotting, otherwise create a new figure.

• interactive (bool, optional) – If True, creates an interactive display to test all parameters. Requires to run in a notebook with ipywidgets.

Return type:

matplotlib.axes.Axes

Examples

Create a virtual inverse-toeprint with bands.

>>> sample.itoeprint(exposure=3)

Create a virtual inverse-toeprint with shades:

>>> sample.itoeprint(plot='shades')

Create an interactive visualization (requires running in a notebook with ipywidgets):

>>> sample.itoeprint(interactive=True)