alphagenome.visualization.plot_components.VariantAnnotation

class alphagenome.visualization.plot_components.VariantAnnotation(variants, colors='orange', alpha=0.8, labels=None, use_default_labels=True, label_angle=15, label_position='left')

Visualizes variants as thin line-like rectangles across plot components.

Attributes

Table

VariantAnnotation.has_labels

Returns True if the annotation has labels.

VariantAnnotation.is_variant

Returns True if the annotation is a variant annotation.

Methods

Table

add_label(ax, label_x_position, label, ...)	Adds a single angled label to an axis.
plot_ax(ax, interval[, hspace])	Adds a variant annotation to an individual axis.
plot_labels(ax, interval, label_height_factor)	Adds variant labels to an axis.

VariantAnnotation.add_label(ax, label_x_position, label, angle, label_height_factor, label_position='left')

Adds a single angled label to an axis.

Parameters:

• ax (Axes) – The matplotlib axis to add the label to.

• label_x_position (float) – The x position of the label.

• label (str) – The label text.

• angle (float) – The angle of the label.

• label_height_factor (float) – A scaling factor for the label height.

• label_position (str (default: 'left')) – The (horizontal) placement of the label, relative to the x position. Can be any position string accepted by the horizontalalignment argument of matplotlib.axes.Axes.text.

VariantAnnotation.plot_ax(ax, interval, hspace=0.0)

Adds a variant annotation to an individual axis.

Parameters:

• ax (Axes) – The matplotlib axis to add the annotation to.

• interval (Interval) – The genomic interval to plot.

• hspace (float (default: 0.0)) – The vertical space between subplots.

VariantAnnotation.plot_labels(ax, interval, label_height_factor)

Adds variant labels to an axis.

Parameters:

• ax (Axes) – The matplotlib axis to add the labels to.

• interval (Interval) – The genomic interval to plot.

• label_height_factor (float) – A scaling factor for the label height.