eelbrain.plot.brain.p_map¶

eelbrain.plot.brain.p_map(p_map, param_map=None, p0=0.05, p1=0.01, p0alpha=0.5, *args, **kwargs)¶

Plot a map of p-values in source space.

Parameters:

p_map : NDVar | NDTest: Map of p values, or test result.
param_map : NDVar: Statistical parameter covering the same data points as p_map. Only the sign is used, for incorporating the directionality of the effect into the plot.
p0 : scalar: Highest p-value that is visible.
p1 : scalar: P-value where the colormap changes from ramping alpha to ramping color.
p0alpha : 1 >= float >= 0: Alpha at p0. Set to 0 for a smooth transition, or a larger value to clearly delineate significant regions (default 0.5).
surf : ‘inflated’ | ‘pial’ | ‘smoothwm’ | ‘sphere’ | ‘white’: Freesurfer surface to use as brain geometry.
views : str | iterator of str: View or views to show in the figure. Options are: ‘rostral’, ‘parietal’, ‘frontal’, ‘ventral’, ‘lateral’, ‘caudal’, ‘medial’, ‘dorsal’.
hemi : ‘lh’ | ‘rh’ | ‘both’ | ‘split’: Which hemispheres to plot (default based on data).
colorbar : bool: Add a colorbar to the figure (use .plot_colorbar() to plot a colorbar separately).
time_label : str: Label to show time point. Use 'ms' or 's' to display time in milliseconds or in seconds, or supply a custom format string to format time values (in seconds; default is 'ms').
w, h, axw, axh : scalar: Layout parameters (figure width/height, subplot width/height).
foreground : mayavi color: Figure foreground color (i.e., the text color).
background : mayavi color: Figure background color.
parallel : bool: Set views to parallel projection (default True).
cortex : str | tuple | dict: Mark gyri and sulci on the cortex. Presets: 'classic' (default), 'high_contrast', 'low_contrast', 'bone'. Can also be a single color (e.g. 'red', (0.1, 0.4, 1.)) or a tuple of two colors for gyri and sulci (e.g. ['red', 'blue'] or [(1, 0, 0), (0, 0, 1)]). For all options see the PySurfer documentation.
title : str: title for the window (default is the subject name).
smoothing_steps : None | int: Number of smoothing steps if data is spatially undersampled (pysurfer Brain.add_data() argument).
mask : bool | matplotlib color: Shade areas that are not in p_map. Can be matplotlib color, including alpha (e.g., (1, 1, 1, 0.5) for semi-transparent white).
subjects_dir : None | str: Override the subjects_dir associated with the source space dimension.
name : str: Equivalent to title, for consistency with other plotting functions.

Returns:

brain : surfer.Brain: PySurfer Brain instance containing the plot.

Notes

In order to make economical use of the color lookup table, p-values are remapped for display. P-values larger than p0 are mapped to 0, p-values for positive effects to [step, p0 + step] and p-values for negative effects to [-step, -(p0 + step)].

Due to this, in order to plot a colorbar only including positive differences yse:

>>> brain.plot_colorbar(clipmin=0)

and to include only negative effects:

>>> brain.plot_colorbar(clipmax=0)