Alex Averbuch Alex Averbuch - 2 months ago 23
Python Question

Is it possible to draw a matplotlib boxplot given the percentile values instead of the original inputs?

From what I can see,

boxplot()
method expects a sequence of raw values (numbers) as input, from which it then computes percentiles to draw the boxplot(s).

I would like to have a method by which I could pass in the percentiles and get the corresponding
boxplot
.

For example:

Assume that I have run several benchmarks and for each benchmark I've measured latencies ( floating point values ). Now additionally, I have precomputed the percentiles for these values.

Hence for each benchmark, I have the 25th, 50th, 75th percentile along with the min and max.

Now given these data, I would like to draw the box plots for the benchmarks.

Answer

To draw the box plot using just the percentile values and the outliers ( if any ) I made a customized_box_plot function that basically modifies attributes in a basic box plot ( generated from a tiny sample data ) to make it fit according to your percentile values.

The customized_box_plot function

def customized_box_plot(percentiles, axes, redraw = True, *args, **kwargs):
    """
    Generates a customized boxplot based on the given percentile values
    """

    box_plot = axes.boxplot([[-9, -4, 2, 4, 9],]*n_box, *args, **kwargs) 
    # Creates len(percentiles) no of box plots

    min_y, max_y = float('inf'), -float('inf')

    for box_no, (q1_start, 
                 q2_start,
                 q3_start,
                 q4_start,
                 q4_end,
                 fliers_xy) in enumerate(percentiles):

        # Lower cap
        box_plot['caps'][2*box_no].set_ydata([q1_start, q1_start])
        # xdata is determined by the width of the box plot

        # Lower whiskers
        box_plot['whiskers'][2*box_no].set_ydata([q1_start, q2_start])

        # Higher cap
        box_plot['caps'][2*box_no + 1].set_ydata([q4_end, q4_end])

        # Higher whiskers
        box_plot['whiskers'][2*box_no + 1].set_ydata([q4_start, q4_end])

        # Box
        box_plot['boxes'][box_no].set_ydata([q2_start, 
                                             q2_start, 
                                             q4_start,
                                             q4_start,
                                             q2_start])

        # Median
        box_plot['medians'][box_no].set_ydata([q3_start, q3_start])

        # Outliers
        if fliers_xy is not None and len(fliers_xy[0]) != 0:
            # If outliers exist
            box_plot['fliers'][box_no].set(xdata = fliers_xy[0],
                                           ydata = fliers_xy[1])

            min_y = min(q1_start, min_y, fliers_xy[1].min())
            max_y = max(q4_end, max_y, fliers_xy[1].max())

        else:
            min_y = min(q1_start, min_y)
            max_y = max(q4_end, max_y)

        # The y axis is rescaled to fit the new box plot completely with 10% 
        # of the maximum value at both ends
        axes.set_ylim([min_y*1.1, max_y*1.1])

    # If redraw is set to true, the canvas is updated.
    if redraw:
        ax.figure.canvas.draw()

    return box_plot

USAGE

Using inverse logic ( code at the very end ) I extracted the percentile values from this example

>>> percentiles
(-1.0597368367634488, 0.3977683984966961, 1.0298955252405229, 1.6693981537742526, 3.4951447843464449)
(-0.90494930553559483, 0.36916539612108634, 1.0303658700697103, 1.6874542731392828, 3.4951447843464449)
(0.13744105279440233, 1.3300645202649739, 2.6131540656339483, 4.8763411136047647, 9.5751914834437937)
(0.22786243898199182, 1.4120860286080519, 2.637650402506837, 4.9067126578493259, 9.4660357513550899)
(0.0064696168078617741, 0.30586770128093388, 0.70774153557312702, 1.5241965711101928, 3.3092932063051976)
(0.007009744579241136, 0.28627373934008982, 0.66039691869500572, 1.4772725266672091, 3.221716765477217)
(-2.2621660374110544, 5.1901313713883352, 7.7178532139979357, 11.277744848353247, 20.155971739152388)
(-2.2621660374110544, 5.1884411864079532, 7.3357079047721054, 10.792299385806913, 18.842012119715388)
(2.5417888074435702, 5.885996170695587, 7.7271286220368598, 8.9207423361593179, 10.846938621419374)
(2.5971767318505856, 5.753551925927133, 7.6569980004033464, 8.8161056254143233, 10.846938621419374)

Note that to keep this short I haven't shown the outliers vectors which will be the 6th element of each of the percentile array.

Also note that all usual additional kwargs / args can be used since they are simply passed to the boxplot method inside it :

>>> fig, ax = plt.subplots()
>>> b = customized_box_plot(percentiles, ax, redraw=True, notch=0, sym='+', vert=1, whis=1.5)
>>> plt.show()

Box Plot using Percentile values

EXPLANATION

The boxplot method returns a dictionary mapping the components of the boxplot to the individual matplotlib.lines.Line2D instances that were created.

Quoting from the matplotlib.pyplot.boxplot documentation :

That dictionary has the following keys (assuming vertical boxplots):

boxes: the main body of the boxplot showing the quartiles and the median’s confidence intervals if enabled.

medians: horizonal lines at the median of each box.

whiskers: the vertical lines extending to the most extreme, n-outlier data points. caps: the horizontal lines at the ends of the whiskers.

fliers: points representing data that extend beyond the whiskers (outliers).

means: points or lines representing the means.

For example observe the boxplot of a tiny sample data of [-9, -4, 2, 4, 9]

>>> b = ax.boxplot([[-9, -4, 2, 4, 9],])
>>> b
{'boxes': [<matplotlib.lines.Line2D at 0x7fe1f5b21350>],
'caps': [<matplotlib.lines.Line2D at 0x7fe1f54d4e50>,
<matplotlib.lines.Line2D at 0x7fe1f54d0e50>],
'fliers': [<matplotlib.lines.Line2D at 0x7fe1f5b317d0>],
'means': [],
'medians': [<matplotlib.lines.Line2D at 0x7fe1f63549d0>],
'whiskers': [<matplotlib.lines.Line2D at 0x7fe1f5b22e10>,
             <matplotlib.lines.Line2D at 0x7fe20c54a510>]} 

>>> plt.show()

A Sample box plot

The matplotlib.lines.Line2D objects have two methods that I'll be using in my function extensively. set_xdata ( or set_ydata ) and get_xdata ( or get_ydata ).

Using these methods we can alter the position of the constituent lines of the base box plot to conform to your percentile values ( which is what the customized_box_plot function does ). After altering the constituent lines' position, you can redraw the canvas using figure.canvas.draw()

Summarizing the mappings from percentile to the coordinates of the various Line2D objects.

The Y Coordinates :

  • The max ( q4_end - end of 4th quartile ) corresponds to the top most cap Line2D object.
  • The min ( q1_start - start of the 1st quartile ) corresponds to the lowermost most cap Line2D object.
  • The median corresponds to the ( q3_start ) median Line2D object.
  • The 2 whiskers lie between the ends of the boxes and extreme caps ( q1_start and q2_start - lower whisker; q4_start and q4_end - upper whisker )
  • The box is actually an interesting n shaped line bounded by a cap at the lower portion. The extremes of the n shaped line correspond to the q2_start and the q4_start.

The X Coordinates :

  • The Central x coordinates ( for multiple box plots are usually 1, 2, 3... )
  • The library automatically calculates the bounding x coordinates based on the width specified.

INVERSE FUNCTION TO RETRIEVE THE PERCENTILES FROM THE boxplot DICT:

def get_percentiles_from_box_plots(bp):
    percentiles = []
    for i in range(len(bp['boxes'])):
        percentiles.append((bp['caps'][2*i].get_ydata()[0],
                           bp['boxes'][i].get_ydata()[0],
                           bp['medians'][i].get_ydata()[0],
                           bp['boxes'][i].get_ydata()[2],
                           bp['caps'][2*i + 1].get_ydata()[0],
                           (bp['fliers'][i].get_xdata(),
                            bp['fliers'][i].get_ydata())))
    return percentiles

NOTE: The reason why I did not make a completely custom boxplot method is because, there are many features offered by the inbuilt box plot that cannot be fully reproduced.

Also excuse me if I may have unnecessarily explained something that may have been too obvious.

Comments