Artists

Artists#

class biaplotter.artists.Artist(ax: ~matplotlib.axes._axes.Axes | None = None, data: ~numpy.ndarray | None = None, overlay_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
overlay_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

`color_indices`	Gets or sets the current color indices used for the artist.
`data`	Gets or sets the data associated with the artist.
`ids`	Gets or sets the IDs associated with the data.
`overlay_colormap`	Gets or sets the overlay colormap for the artist.
`visible`	Gets or sets the visibility of the artist.
`x_label_text`	Gets or sets the x-axis label.
`x_label_color`	Gets or sets the x-axis label color.
`y_label_text`	Gets or sets the y-axis label.
`y_label_color`	Gets or sets the y-axis label color.

Attributes Summary

`ax`	Stores axes to plot on

Methods Summary

draw()

Draws or redraws the artist.

Properties Documentation

color_indices#

Gets or sets the current color indices used for the artist.

Triggers a draw idle command.

Returns:: color_indices – indices to map to the overlay_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.

data#

Gets or sets the data associated with the artist.

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 are changed.

ids#

Gets or sets the IDs associated with the data.

Returns:: ids – Array of IDs corresponding to the data points.
Return type:: (N,) np.ndarray[int]

overlay_colormap#

Gets or sets the overlay colormap for the artist.

Returns:: overlay_colormap – colormap for the artist with a categorical attribute.
Return type:: BiaColormap

visible#

Gets or sets the visibility of the artist.

Triggers a draw idle command.

Returns:: visible – visibility of the artist.
Return type:: bool

x_label_text#: Gets or sets the x-axis label.

x_label_color#: Gets or sets the x-axis label color.

y_label_text#: Gets or sets the y-axis label.

y_label_color#: Gets or sets the y-axis label color.

Attributes Documentation

ax: Axes#: Stores axes to plot on

Methods Documentation

draw()#: Draws or redraws the artist.

class biaplotter.artists.Scatter(ax: ~matplotlib.axes._axes.Axes | None = None, data: ~numpy.ndarray | None = None, overlay_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
overlay_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 are 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 artist.
`visible`	Gets or sets the visibility of the artist.
`color_indices`	Gets or sets the current color indices used for the artist.
`alpha`	Gets or sets the alpha value of the scatter plot.
`size`	Gets or sets the size of the points in the scatter plot.
`overlay_colormap`	Gets or sets the overlay colormap for the artist.
`overlay_visible`
`color_normalization_method`	Gets or sets the normalization method for the color indices.

Attributes Summary

`ax`	Stores axes to plot on

Methods Summary

draw()

Draws or redraws the artist.

Signals Summary

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

Properties Documentation

data#

Gets or sets the data associated with the artist.

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 are changed.

visible#

Gets or sets the visibility of the artist.

Triggers a draw idle command.

Returns:: visible – visibility of the artist.
Return type:: bool

color_indices#

Gets or sets the current color indices used for the artist.

Triggers a draw idle command.

Returns:: color_indices – indices to map to the overlay_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]

alpha#

Gets or sets the alpha value of the scatter plot.

Returns:: alpha – alpha value of the scatter plot.
Return type:: float

overlay_colormap#

Gets or sets the overlay colormap for the artist.

Returns:: overlay_colormap – colormap for the artist with a categorical attribute.
Return type:: BiaColormap

overlay_visible#

color_normalization_method#

Gets or sets the normalization method for the color indices.

Returns:: color_normalization_method – the normalization method for the color indices.
Return type:: str

Attributes Documentation

ax: plt.Axes#: Stores axes to plot on

Methods Documentation

draw()#: Draws or redraws the artist.

Signals Documentation

data_changed_signal: Signal#: Signal emitted when the data are 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, overlay_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
overlay_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 overlay_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
cmin (int, optional) – minimum count for the histogram, by default 0 Values below cmin are set to NaN (to be transparent).

Notes

Signals:

data_changed_signal emitted when the data are changed.

color_indices_changed_signal emitted when the color indices are changed.

Properties Summary

`data`	Gets or sets the data associated with the artist.
`visible`	Gets or sets the visibility of the artist.
`color_indices`	Gets or sets the current color indices used for the artist.
`bins`	Gets or sets the number of bins for the histogram.
`cmin`	Gets or sets the minimum count for the histogram.
`histogram`	Returns the 2D histogram array and edges.
`histogram_colormap`	Gets or sets the colormap for the histogram.
`histogram_interpolation`	Gets or sets the interpolation method for the histogram.
`histogram_color_normalization_method`	Gets or sets the normalization method for the histogram.
`overlay_colormap`	Gets or sets the overlay colormap for the artist.
`overlay_interpolation`	Gets or sets the interpolation method for the overlay histogram.
`overlay_color_normalization_method`	Gets or sets the normalization method for the overlay histogram.
`overlay_opacity`	Gets or sets the opacity of the overlay histogram.
`overlay_visible`	Gets or sets the visibility of the overlay histogram.

Attributes Summary

`ax`	Stores axes to plot on

Methods Summary

`indices_in_patches_above_threshold`(threshold)	Returns the indices of the points that fall into the bins of the 2D histogram exceeding a specified threshold counts value.
`draw`()	Draws or redraws the artist.

Signals Summary

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

Properties Documentation

data#

Gets or sets the data associated with the artist.

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 are changed.

visible#

Gets or sets the visibility of the artist.

Triggers a draw idle command.

Returns:: visible – visibility of the artist.
Return type:: bool

color_indices#

Gets or sets the current color indices used for the artist.

Triggers a draw idle command.

Returns:: color_indices – indices to map to the overlay_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.

bins#

Gets or sets the number of bins for the histogram.

Returns:: bins – number of bins for the histogram.
Return type:: int

cmin#

Gets or sets the minimum count for the histogram.

Values below cmin are set to NaN (to be transparent).

Returns:: cmin – minimum count for the histogram.
Return type:: int

histogram#

Returns the 2D histogram array and edges.

Returns:: histogram – 2D histogram, x edges, and y edges.
Return type:: Tuple[np.ndarray, np.ndarray, np.ndarray]

histogram_colormap#

Gets or sets the colormap for the histogram.

Returns:: histogram_colormap – colormap for the histogram.
Return type:: Colormap

histogram_interpolation#

Gets or sets the interpolation method for the histogram.

Returns:: histogram_interpolation – interpolation method for the histogram.
Return type:: str

histogram_color_normalization_method#

Gets or sets the normalization method for the histogram.

Returns:: color_normalization_method – the normalization method for the histogram.
Return type:: str

overlay_colormap#

Gets or sets the overlay colormap for the artist.

Returns:: overlay_colormap – colormap for the artist with a categorical attribute.
Return type:: BiaColormap

overlay_interpolation#

Gets or sets the interpolation method for the overlay histogram.

Returns:: overlay_interpolation – interpolation method for the overlay histogram.
Return type:: str

overlay_color_normalization_method#

Gets or sets the normalization method for the overlay histogram.

Returns:: overlay_color_normalization_method – the normalization method for the overlay color indices.
Return type:: str

overlay_opacity#

Gets or sets the opacity of the overlay histogram.

Triggers a draw idle command.

Returns:: overlay_opacity – opacity of the overlay histogram.
Return type:: float

overlay_visible#

Gets or sets the visibility of the overlay histogram.

Triggers a draw idle command.

Returns:: overlay_visible – visibility of the overlay histogram.
Return type:: bool

Attributes Documentation

ax: plt.Axes#: Stores axes to plot on

Methods Documentation

indices_in_patches_above_threshold(threshold: int) → List[int]#

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

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 artist.

Signals Documentation

data_changed_signal: Signal#: Signal emitted when the data are changed.

color_indices_changed_signal: Signal#: Signal emitted when the color_indices are changed.

Artists

Contents

Artists#