Module `plottools.significance`

Indicating statsitical significance.

Axes member functions

significance_bar(): horizontal bar with asterisks indicating significance level.

Install/uninstall significance functions

You usually do not need to call these functions. Upon loading the significance module, install_significance() is called automatically.

install_significance(): install functions of the significance module in matplotlib.
uninstall_significance(): uninstall all code of the significance module from matplotlib.

Expand source code

"""
Indicating statsitical significance.

## Axes member functions

- `significance_bar()`: horizontal bar with asterisks indicating significance level.


## Install/uninstall significance functions

You usually do not need to call these functions. Upon loading the significance
module, `install_significance()` is called automatically.

- `install_significance()`: install functions of the significance module in matplotlib.
- `uninstall_significance()`: uninstall all code of the significance module from matplotlib.
"""

import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt


def significance_bar(ax, p, x0, x1, y, **kwargs):
    """
    A horizontal bar with asterisks indicating significance level.
    
    Plot a horizontal bar from x0 to x1 at height y
    for indicating significance. On top of the bar plot
    asterisks according to the significance value p are drawn.
    If p > 0.05 nothing is plotted.
    p<0.001: '***', p<0.01: '**', p<0.05: '*'.

    Note: call this function AFTER ylim has been set!

    Parameters
    ----------
    ax: matplotlib axes
        Axes to which the inset is added.
    p: float
        Significance level.
    x0: float
        x-coordinate of starting point of significance bar in data units.
    x1: float
        x-coordinate of ending point of significance bar in data units.
    y: float
        y-coordinate of significance bar in data units.
    kwargs: key-word arguments
        Passed on to `ax.text()` used to print the asterisks.
    """
    # set label:
    if p < 0.001:
        ps = '***'
    elif p < 0.01:
        ps = '**'
    elif p < 0.05:
        ps = '*'
    else:
        return
    # ax dimensions:
    pixely = np.abs(np.diff(ax.get_window_extent().get_points()[:,1]))[0]
    unity = np.abs(np.diff(ax.get_ylim()))[0]
    dyu = unity/pixely
    fs = mpl.rcParams['font.size']
    if 'fontsize' in kwargs and isinstance(kwargs['fontsize'], (float, int)):
        fs = kwargs['fontsize']
    dy = 0.3*fs*dyu
    lw = 1.0
    lh = ax.plot([x0, x0, x1, x1], [y-dy, y, y, y-dy], color='black', lw=lw,
                 solid_capstyle='butt', solid_joinstyle='miter', clip_on=False)
    # get y position of line in figure pixel coordinates:
    ly = np.array(lh[0].get_window_extent(ax.get_figure().canvas.get_renderer()))[1,1]
    th = ax.text(0.5*(x0+x1), y, ps, ha='center', va='bottom', **kwargs)
    ty = np.array(th.get_window_extent(ax.get_figure().canvas.get_renderer()))[0,1]
    dty = ly+0.5*lw -0.4*fs - ty
    th.set_position((0.5*(x0+x1), y+dty*dyu))


def install_significance():
    """ Install significance functions on matplotlib axes.

    This function is also called automatically upon importing the module.

    See also
    --------
    uninstall_significance()
    """
    if not hasattr(mpl.axes.Axes, 'significance_bar'):
        mpl.axes.Axes.significance_bar = significance_bar

        
def uninstall_significance():
    """ Uninstall significance functions from matplotlib axes.

    Call this function to disable anything that was installed by `install_significance()`.

    See also
    --------
    install_significance()
    """
    if hasattr(mpl.axes.Axes, 'significance_bar'):
        delattr(mpl.axes.Axes, 'significance_bar')

        
install_significance()


def demo():
    """ Run a demonstration of the significance module.
    """
    fig, ax = plt.subplots()
    fig.suptitle('plottools.significance')
    x1 = 1.0+0.3*np.random.randn(50)
    x2 = 4.0+0.5*np.random.randn(50)
    ax.boxplot([x1, x2])
    ax.set_xlim(0.5, 2.5)
    ax.set_ylim(0.0, 8)
    ax.significance_bar(0.002, 1, 2, 6)
    plt.show()
    

if __name__ == "__main__":
    demo()

Functions

def significance_bar(ax, p, x0, x1, y, **kwargs)

A horizontal bar with asterisks indicating significance level.

Plot a horizontal bar from x0 to x1 at height y for indicating significance. On top of the bar plot asterisks according to the significance value p are drawn. If p > 0.05 nothing is plotted. p<0.001: '', p<0.01: '', p<0.05: ''.

Note: call this function AFTER ylim has been set!

Parameters

ax : matplotlib axes: Axes to which the inset is added.
p : float: Significance level.
x0 : float: x-coordinate of starting point of significance bar in data units.
x1 : float: x-coordinate of ending point of significance bar in data units.
y : float: y-coordinate of significance bar in data units.
kwargs : key-word arguments: Passed on to ax.text() used to print the asterisks.

Expand source code

def significance_bar(ax, p, x0, x1, y, **kwargs):
    """
    A horizontal bar with asterisks indicating significance level.
    
    Plot a horizontal bar from x0 to x1 at height y
    for indicating significance. On top of the bar plot
    asterisks according to the significance value p are drawn.
    If p > 0.05 nothing is plotted.
    p<0.001: '***', p<0.01: '**', p<0.05: '*'.

    Note: call this function AFTER ylim has been set!

    Parameters
    ----------
    ax: matplotlib axes
        Axes to which the inset is added.
    p: float
        Significance level.
    x0: float
        x-coordinate of starting point of significance bar in data units.
    x1: float
        x-coordinate of ending point of significance bar in data units.
    y: float
        y-coordinate of significance bar in data units.
    kwargs: key-word arguments
        Passed on to `ax.text()` used to print the asterisks.
    """
    # set label:
    if p < 0.001:
        ps = '***'
    elif p < 0.01:
        ps = '**'
    elif p < 0.05:
        ps = '*'
    else:
        return
    # ax dimensions:
    pixely = np.abs(np.diff(ax.get_window_extent().get_points()[:,1]))[0]
    unity = np.abs(np.diff(ax.get_ylim()))[0]
    dyu = unity/pixely
    fs = mpl.rcParams['font.size']
    if 'fontsize' in kwargs and isinstance(kwargs['fontsize'], (float, int)):
        fs = kwargs['fontsize']
    dy = 0.3*fs*dyu
    lw = 1.0
    lh = ax.plot([x0, x0, x1, x1], [y-dy, y, y, y-dy], color='black', lw=lw,
                 solid_capstyle='butt', solid_joinstyle='miter', clip_on=False)
    # get y position of line in figure pixel coordinates:
    ly = np.array(lh[0].get_window_extent(ax.get_figure().canvas.get_renderer()))[1,1]
    th = ax.text(0.5*(x0+x1), y, ps, ha='center', va='bottom', **kwargs)
    ty = np.array(th.get_window_extent(ax.get_figure().canvas.get_renderer()))[0,1]
    dty = ly+0.5*lw -0.4*fs - ty
    th.set_position((0.5*(x0+x1), y+dty*dyu))

def install_significance()

Install significance functions on matplotlib axes.

This function is also called automatically upon importing the module.