funnelplot 0.2.1

Simple funnel plots

Funnel plot

Simple funnel plots for visualising sub-group variance.

This package provides simple funnel plots in Python, using Matplotlib. This lets you quickly see whether sub-groups of a population are outliers compared to the full population.

Two methods are provided:

• parametric funnelplot which uses a standard distribution to estimate the intervals of the funnel (usually a normal distribution)
• bootstrap funnelplot which uses bootstrapped percentiles to estimate the intervals of the funnel

A utility function funnel() to make it easy to plot data by grouping Pandas DataFrames in a Seaborn-like API is provided.

Example

Data of test performance for California schools from pydataset/Caschool.

funnel(df=data("Caschool"), x="testscr", group="county")

Install

pip install funnelplot

Examples

Full caschool example

# load some example data
import pandas as pd
import matplotlib.pyplot as plt
from pydataset import data
from funnelplot.core import funnel

# create a suitable axis
fig,ax = plt.subplots(figsize=(4,6))
ax.set_frame_on(False)

# funnel plot, using 0.5% -> 99.5% interval
funnel(df=data("Caschool"), x="testscr", group="county", percentage=99.5, error_mode="data")

C:\Users\John\Dropbox\devel\funnelplot\funnelplot\core.py:14: RuntimeWarning: invalid value encountered in true_divide
  return band / np.sqrt(group_size)
C:\Users\John\Dropbox\devel\funnelplot\funnelplot\core.py:14: RuntimeWarning: divide by zero encountered in true_divide
  return band / np.sqrt(group_size)

# use bootstrap instead of normal fit
fig,ax = plt.subplots(figsize=(5,6))
ax.set_frame_on(False)
funnel(df=data("Caschool"), x='testscr', group="county", bootstrap_mode=True, error_mode="bootstrap")

Synthetic data example

## Synthetic data
import numpy as np
import random
random.seed(2020)
np.random.seed(2020)
groups = []
p_mean, p_std = 0, 1
# random groups, with different sizes, means and std. devs.
for i in range(25):
    n_group = np.random.randint(1, 80)
    g_std =  np.random.uniform(0.1, 4.5) 
    g_mean = np.random.uniform(-1.9, 0.5)
    groups.append(np.random.normal(p_mean + g_mean,
                                   p_std + g_std, 
                                   n_group))

ax, fig = plt.subplots(figsize=(9, 4))
funnel_plot(
    groups,
    labels=[random.choice("abcdefg") * 4 for i in range(len(groups))],
    percentage=95,
)

ax, fig = plt.subplots(figsize=(9, 4))
# bootstrap version, using medians instead of means
funnel_plot_bootstrap(
    groups,
    labels=[random.choice("abcdefg") * 4 for i in range(len(groups))],
    percentage=95,
    stat=np.median
)

API

• funnel(df, x, group, bootstrap_mode=False) show a DataFrame df as a funnel plot, rendering column x and grouping the data by group.

    Parameters:
        df: DataFrame
            The data to be shown.
        x:  string, column name
            The column of the frame to render as datapoints.
        group: string, column name
            The column to group the frame by
        bootstrap_mode: boolean, optional (default False)
            If True, uses the funnel_plot_bootstrap() function; otherwise
            use the parameteric funnel_plot() function
        **kwargs:
            passed to funnel_plot() / funnel_plot_bootstrap()
  

• funnel_plot(data_groups, ...) plot a list of arrays as a funnel plot.

    Parameters:
        data_groups: list of 1D arrays
            a list of 1D arrays the individual groups to be analysed.
        ax: axis, optional
            an Matplotlib axis to draw onto
        dist: distribution function, like scipy.stats.norm(0,1)
            function to use to get the ppf and cdf of for plotting
        percentage: float, 0.0 -> 100.0 (default 95)
            percentage  of interval enclosed (e.g. percentage=95 will enclose 2.5% to 97.5%)
        labels: list of strings, optional
            one label string per group, will be shown only for those groups that lie outside the funnel
        left_color: matplotlib color, optional (default C1)
            color to render points to the left of the funnel bounds (negative outliers)
        right_color: matplotlib color, optional (default C2)
            color to render points to the right of the funnel bounds (positive outliers)        
        error_mode: string, optional (default "data")
            For each outlier group, can show:
                "data": original data values for that group as a dot plot
                "none": no error bars
                "bootstrap": 95% bootstrap intervals, as lines
                "ci": 95% CI intervals, as lines
        show_rug: boolean, optional (default False):
            If True, show a rug plot at the bottom of the graph, for
            the whole group population
        show_contours: boolean optional (default True)
            true if additional contours shown
  

• funnel_plot_bootstrap(data_groups, ...) plot a list of arrays as a funnel plot, using bootstrapped intervals instead of a parametric distribution.

    Parameters:
        data_groups: list of 1D arrays
            a list of 1D arrays the individual groups to be analysed.
        ax: axis, optional
            an Matplotlib axis to draw onto
        percentage: float, 0.0 -> 100.0 (default 95)
            percentage  of interval enclosed (e.g. percentage=95 will enclose 2.5% to 97.5%)
        labels: list of strings, optional
            one label string per group, will be shown only for those groups that lie outside the funnel
        left_color: matplotlib color, optional (default C1)
            color to render points to the left of the funnel bounds (negative outliers)
        right_color: matplotlib color, optional (default C2)
            color to render points to the right of the funnel bounds (positive outliers)
        bootstrap_n: int, optional (default 1000)
            number of runs in the bootstrap
        error_mode: string, optional (default "data")
            For each outlier group, can show:
                "data": original data values for that group as a dot plot
                "none": no error bars
                "bootstrap": 95% bootstrap intervals, as lines
                "ci": 95% CI intervals, as lines
        show_rug: boolean, optional (default False):
            If True, show a rug plot at the bottom of the graph, for
            the whole group population            
        show_contours: boolean optional (default True)
            true if additional contours shown
        stat: function like np.mean, optional
            statistic to use when plotting the funnel plot