metaseq.minibrowser.GeneModelMiniBrowser

class metaseq.minibrowser.GeneModelMiniBrowser(genomic_signal_objs, db, **kwargs)

Bases: metaseq.minibrowser.SignalMiniBrowser

Mini-browser to show a signal panel on top and gene models on the bottom.

Parameters:

• genomic_signal_objs – a list of genomic_signals objects
• db – a gffutils.FeatureDB

Methods

close_all()	Close all figures spawned by this class.
example_panel(ax, feature)	A example panel that just prints the text of the feature.
gene_panel(ax, feature)	Plots gene models on an Axes.
make_fig()	Figure constructor, called before self.plot()
panels()	Add 2 panels to the figure, top for signal and bottom for gene models
plot(feature)	Spawns a new figure showing data for feature.
signal_panel(ax, feature)	Plots each genomic signal as a line using the corresponding

Methods

__init__(genomic_signal_objs, db, \*\*kwargs)	Mini-browser to show a signal panel on top and gene models on the bottom.
close_all()	Close all figures spawned by this class.
example_panel(ax, feature)	A example panel that just prints the text of the feature.
gene_panel(ax, feature)	Plots gene models on an Axes.
make_fig()	Figure constructor, called before self.plot()
panels()	Add 2 panels to the figure, top for signal and bottom for gene models
plot(feature)	Spawns a new figure showing data for feature.
signal_panel(ax, feature)	Plots each genomic signal as a line using the corresponding

__init__(genomic_signal_objs, db, **kwargs)

Mini-browser to show a signal panel on top and gene models on the bottom.

Parameters:

• genomic_signal_objs – a list of genomic_signals objects
• db – a gffutils.FeatureDB

close_all()

Close all figures spawned by this class.

example_panel(ax, feature)

A example panel that just prints the text of the feature.

gene_panel(ax, feature)

Plots gene models on an Axes.

Queries the database

Parameters:

• ax – matplotlib.Axes object
• feature – pybedtools.Interval

make_fig()

Figure constructor, called before self.plot()

panels()

Add 2 panels to the figure, top for signal and bottom for gene models

plot(feature)

Spawns a new figure showing data for feature.

Parameters:feature – A pybedtools.Interval object

Using the pybedtools.Interval feature, creates figure specified in BaseMiniBrowser.make_fig() and plots data on panels according to self.panels().

signal_panel(ax, feature)

Plots each genomic signal as a line using the corresponding plotting_kwargs