Artists

class biaplotter.artists.Artist(ax: ~matplotlib.axes._axes.Axes | None = None, data: ~numpy.ndarray | None = None, categorical_colormap: ~matplotlib.colors.Colormap = <matplotlib.colors.LinearSegmentedColormap object>, color_indices: ~numpy.ndarray | None = None)

Bases: ABC

Abstract base class for artists in the BiAPlotter.

Parameters:

• ax (plt.Axes, optional) – axes to plot on, by default None

• data ((N, 2) np.ndarray) – data to be plotted

• categorical_colormap (Colormap, optional) – a colormap to use for the artist, by default cat10_mod_cmap from nap-plot-tools

• color_indices ((N,) np.ndarray, optional) – array of indices to map to the colormap, by default None

Properties Summary

data	Abstract property for the artist's data.
visible	Abstract property for the artist's visibility.
color_indices	Abstract property for the indices into the colormap.

Attributes Summary

ax	Stores axes to plot on
categorical_colormap	Stores the colormap to use for the artist

Methods Summary

draw()

Abstract method to draw or redraw the artist.

Properties Documentation

data

Abstract property for the artist’s data.

visible

Abstract property for the artist’s visibility.

color_indices

Abstract property for the indices into the colormap.

Attributes Documentation

ax: Axes

Stores axes to plot on

categorical_colormap: Colormap

Stores the colormap to use for the artist

Methods Documentation

abstract draw()

Abstract method to draw or redraw the artist.

class biaplotter.artists.Scatter(ax: ~matplotlib.axes._axes.Axes | None = None, data: ~numpy.ndarray | None = None, categorical_colormap: ~matplotlib.colors.Colormap = <matplotlib.colors.LinearSegmentedColormap object>, color_indices: ~numpy.ndarray | None = None)

Bases: Artist

Scatter plot artist for the BiAPlotter.

Inherits all parameters and attributes from abstract Artist. For parameter and attribute details, see the abstract Artist class documentation.

Parameters:

• ax (plt.Axes, optional) – axes to plot on, by default None

• data ((N, 2) np.ndarray) – data to be plotted

• categorical_colormap (Colormap, optional) – a colormap to use for the artist, by default cat10_mod_cmap from nap-plot-tools

• color_indices ((N,) np.ndarray[int] or int, optional) – array of indices to map to the colormap, by default None

Notes

Signals:

• data_changed_signal emitted when the data is changed.

• color_indices_changed_signal emitted when the color indices are changed.

Examples

>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>> from biaplotter.artists import Scatter
>>> data = np.random.rand(100, 2)
>>> fig, ax = plt.subplots()
>>> scatter = Scatter(ax)
>>> scatter.data = data
>>> scatter.visible = True
>>> scatter.color_indices = np.linspace(start=0, stop=5, num=100, endpoint=False, dtype=int)
>>> plt.show()

Properties Summary

data	Gets or sets the data associated with the scatter plot.
visible	Gets or sets the visibility of the scatter plot.
color_indices	Gets or sets the current color indices used for the scatter plot.
size	Gets or sets the size of the points in the scatter plot.

Attributes Summary

ax	Stores axes to plot on
categorical_colormap	Stores the colormap to use for the artist

Methods Summary

draw()

Draws or redraws the scatter plot.

Signals Summary

data_changed_signal	Signal emitted when the data is changed.
color_indices_changed_signal	Signal emitted when the color_indices are changed.

Properties Documentation

data

Gets or sets the data associated with the scatter plot.

Updates colors if color_indices are set. Triggers a draw idle command.

Returns:

data – data for the artist. Does not respond if set to None or empty array.

Return type:

(N, 2) np.ndarray

Notes

data_changed_signalSignal

Signal emitted when the data is changed.

visible

Gets or sets the visibility of the scatter plot.

Triggers a draw idle command.

Returns:

visible – visibility of the scatter plot.

Return type:

bool

color_indices

Gets or sets the current color indices used for the scatter plot.

Triggers a draw idle command.

Returns:

color_indices – indices to map to the categorical_colormap. Accepts a scalar or an array of integers.

Return type:

(N,) np.ndarray[int] or int

Notes

color_indices_changed_signalSignal

Signal emitted when the color indices are changed.

size

Gets or sets the size of the points in the scatter plot.

Triggers a draw idle command.

Returns:

size – size of the points in the scatter plot. Accepts a scalar or an array of floats.

Return type:

float or (N,) np.ndarray[float]

Attributes Documentation

ax: Axes

Stores axes to plot on

categorical_colormap: Colormap

Stores the colormap to use for the artist

Methods Documentation

draw()

Draws or redraws the scatter plot.

Signals Documentation

data_changed_signal: Signal

Signal emitted when the data is changed.

color_indices_changed_signal: Signal

Signal emitted when the color_indices are changed.

class biaplotter.artists.Histogram2D(ax: ~matplotlib.axes._axes.Axes | None = None, data: ~numpy.ndarray | None = None, categorical_colormap: ~matplotlib.colors.Colormap = <matplotlib.colors.LinearSegmentedColormap object>, color_indices: ~numpy.ndarray | None = None, bins=20, histogram_colormap: ~matplotlib.colors.Colormap = <matplotlib.colors.ListedColormap object>, cmin=0)

Bases: Artist

2D histogram artist for the BiAPlotter.

Inherits all parameters and attributes from abstract Artist. For parameter and attribute details, see the abstract Artist class documentation.

Parameters:

• ax (plt.Axes, optional) – axes to plot on, by default None

• data ((N, 2) np.ndarray) – data to be plotted

• categorical_colormap (Colormap, optional) – a colormap to use for the artist overlay, by default cat10_mod_cmap_first_transparent from nap-plot-tools (first color is transparent)

• color_indices ((N,) np.ndarray[int] or int, optional) – array of indices to map to the categorical_colormap, by default None

• bins (int, optional) – number of bins for the histogram, by default 20

• histogram_colormap (Colormap, optional) – colormap for the histogram, by default plt.cm.magma

Notes

Signals:

• data_changed_signal emitted when the data is changed.

• color_indices_changed_signal emitted when the color indices are changed.

Properties Summary

data	Gets or sets the data associated with the 2D histogram.
visible	Gets or sets the visibility of the 2D histogram.
color_indices	Gets or sets the current color indices used for the 2D histogram underlying data.
bins	Gets or sets the number of bins for the histogram.
histogram_colormap	Gets or sets the colormap for the histogram.
histogram	Returns the 2D histogram matplotlib object.

Attributes Summary

ax	Stores axes to plot on
categorical_colormap	Stores the colormap to use for the artist

Methods Summary

indices_in_above_threshold_patches(threshold)	Returns the indices of the points in that fall into the bins of the 2D histogram exceeding a specified threshold.
draw()	Draws or redraws the 2D histogram.

Signals Summary

data_changed_signal	Signal emitted when the data is changed.
color_indices_changed_signal	Signal emitted when the color_indices are changed.

Properties Documentation

data

Gets or sets the data associated with the 2D histogram.

Updates colors if color_indices are set. Triggers a draw idle command.

Returns:

data – data for the artist. Does not respond if set to None or empty array.

Return type:

(N, 2) np.ndarray

Notes

data_changed_signalSignal

Signal emitted when the data is changed.

visible

Gets or sets the visibility of the 2D histogram.

Triggers a draw idle command.

Returns:

visible – visibility of the 2D histogram.

Return type:

bool

color_indices

Gets or sets the current color indices used for the 2D histogram underlying data.

Triggers a draw idle command.

Returns:

color_indices – indices to map to the overlay colormap. Accepts a scalar or an array.

Return type:

(N,) np.ndarray[int] or int

Notes

color_indices_changed_signalSignal

Signal emitted when the color indices are changed.

bins

Gets or sets the number of bins for the histogram.

Returns:

bins – number of bins for the histogram.

Return type:

int

histogram_colormap

Gets or sets the colormap for the histogram.

Returns:

histogram_colormap – colormap for the histogram.

Return type:

Colormap

histogram

Returns the 2D histogram matplotlib object.

Returns:

histogram – 2D histogram matplotlib object.

Return type:

Tuple[np.ndarray, np.ndarray, np.ndarray, QuadMesh]

Attributes Documentation

ax: Axes

Stores axes to plot on

categorical_colormap: Colormap

Stores the colormap to use for the artist

Methods Documentation

indices_in_above_threshold_patches(threshold: int) → List[int]

Returns the indices of the points in that fall into the bins of the 2D histogram exceeding a specified threshold.

Parameters:

threshold (int) – The count threshold to exceed.

Returns:

indices – list of indices of points falling into the exceeding bins.

Return type:

List[int]

draw()

Draws or redraws the 2D histogram.

Signals Documentation

data_changed_signal: Signal

Signal emitted when the data is changed.

color_indices_changed_signal: Signal

Signal emitted when the color_indices are changed.