metaseq.minibrowser.GeneModelMiniBrowser

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

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)[source]

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)[source]

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()[source]

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

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