AnimalPlotter

class neurodent.visualization.AnimalPlotter(war: WindowAnalysisResult, save_fig: bool = False, save_path: Path | None = None)

Bases: AnimalFeatureParser

Class for plotting results from an AnimalOrganizer/WindowAnalysisResult.

Parameters:

• war (WindowAnalysisResult) – The analysis results to plot.

• save_fig (bool, optional) – Whether to save figures to disk. Defaults to False.

• save_path (Path, optional) – Directory where figures will be saved. Defaults to None.

Variables:

• window_result (WindowAnalysisResult) – The analysis results being plotted.

• genotype (str) – Genotype of the animal.

• channel_names (list[str]) – List of channel names.

• n_channels (int) – Number of channels.

• channel_abbrevs (list[str]) – Abbreviated channel names for plotting.

• save_fig (bool) – Whether to save figures to disk.

• save_path (Path) – Directory where figures will be saved.

__init__(war: WindowAnalysisResult, save_fig: bool = False, save_path: Path | None = None) → None

plot_coherecorr_matrix(groupby='animalday', bands=None, figsize=None, cmap='viridis', **kwargs)

plot_coherecorr_diff(groupby='isday', bands=None, figsize=None, cmap='bwr', **kwargs)

plot_linear_temporal(multiindex=['animalday', 'animal', 'genotype'], features: list[str] | None = None, channels: list[int] | None = None, figsize=None, score_type='z', show_endfile=False, **kwargs)

plot_coherecorr_spectral(multiindex=['animalday', 'animal', 'genotype'], features: list[str] | None = None, figsize=None, score_type='z', cmap='bwr', triag=True, show_endfile=False, duration_name='duration', endfile_name='endfile', **kwargs)

plot_psd_histogram(groupby='animalday', figsize=None, avg_channels=False, plot_type='loglog', plot_slope=True, xlim=None, **kwargs)

plot_psd_spectrogram(multiindex=['animalday', 'animal', 'genotype'], freq_range=(1, 50), center_stat='mean', mode='z', figsize=None, cmap='magma', **kwargs)

plot_temporal_heatmap(features: list[str] | str | None = None, figsize=None, cmap='viridis', score_type=None, norm=None, **kwargs)

Create temporal heatmap showing feature patterns over time.

Creates a heatmap where: - X-axis: Time of day (timestamp mod 24h) - Y-axis: Days - Color: Feature values (flattened across channels)

Parameters

featureslist[str], optional

List of features to plot. If None, uses non-band linear features.

figsizetuple, optional

Figure size (width, height)

cmapstr, optional

Colormap for the heatmap

score_typestr, optional

Standardization method for feature values

normmatplotlib.colors.Normalize, optional

Normalization object for the colormap. If None, uses default normalization. Common options: - matplotlib.colors.Normalize(vmin=0, vmax=1) # Fixed range - matplotlib.colors.CenteredNorm(vcenter=0) # Auto-detect range around 0 - matplotlib.colors.LogNorm() # Logarithmic scale

**kwargs

Additional arguments passed to matplotlib