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 | sequence of str) – One or several views to show in the figure. The options are: 'lateral', 'medial', 'ventral', 'dorsal', 'rostral', 'parietal', 'frontal', 'caudal'.

  • 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 (scalar) – Layout parameters (figure width/height, subplot width/height).

  • h (scalar) – Layout parameters (figure width/height, subplot width/height).

  • axw (scalar) – Layout parameters (figure width/height, subplot width/height).

  • 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 – PySurfer Brain instance containing the plot.

Return type

surfer.Brain

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)