Including ggplot2 Plots in Python Notebooks
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For an article on A/B testing that I am preparing, I asked my partner Dr. Nina Zumel if she could do me a favor and write some code to produce the diagrams. She prepared an excellent parameterized diagram generator. However being the author of the book Practical Data Science with R, she built it in R using ggplot2. This would be great, except the A/B testing article is being developed in Python, as it targets programmers familiar with Python.
As the production of the diagrams is not part of the proposed article, I decided to use the rpy2 package to integrate the R diagrams directly into the new worksheet. Alternatively, I could translate her code into Python using one of: Seaborn objects, plotnine, ggpy, or others. The large number of options is evidence of how influential Leland Wilkinson’s grammar of graphics (gg) is.
Let’s try the rpy2 approach.
For our example we import our modules, including a small adaptor I wrote called r_tools.
# import our modules
import numpy as np
from IPython.display import Code, display, Image
from rpy2 import robjects
from r_tools import get_ggplot_fn_by_name
import pandas as pd
Now all we have to do use her code is:
1) Source her .R file to load the function.
2) Get a reference to the diagram producing function.
This is done as follows.
# read the .R file into the R interpreter environment
robjects.r("source('significance_power_visuals.R')")
# get a Python reference to the sig_pow_visuals R function
sig_pow_visuals = get_ggplot_fn_by_name("sig_pow_visuals")
Now we can use the diagram code. What the A/B testing diagram is and how to pick the arguments will be the content of our later article. The thing to notice now is: we generate the diagram from the R code, working in Python.
# make the example diagram
n = 557
r = 0.1
t = 0.061576
power = 0.9
significance = 0.02
display(sig_pow_visuals(
stdev=np.sqrt(0.5 / n),
effect_size=r,
threshold=t,
title=f"(correct) A/B test with size={n}, decision threshold = {t:.4f} (vertical line)",
subtitle=f"Notice, 1-power = {1-power:.2f} = green area, significance = {significance:.2f} = orange area"
))
For the above to work, one must have an installed R environment (with the appropriate packages) and a properly installed and configured rpy2.
The above example is a bit unusual, in that it is a plot that doesn’t take an incoming data frame as an argument. More often we are likely wanting to pass a Pandas data frame into R. This is also quite easy.
To see this, consider another .R file that defines the following R function.
# show the contents of a .R file
display(Code("plot_frame.R", language="R"))
library(ggplot2)
plt_frame <- function(d) {
ggplot(data = d, mapping = aes(x = x, y = y)) +
geom_point()
}
We can source this .R file and get a reference to the desired function as before.
robjects.r("source('plot_frame.R')")
plt_frame = get_ggplot_fn_by_name(
"plt_frame",
# ggplot2::ggsave() arguments
width=3,
height=2,
units="in",
)
With the function reference in hand, we can now plot.
display(plt_frame(
pd.DataFrame({
"x": [1.0, 2.0, 3.0],
"y": [1.0, -1.0, 2.0],
})))
The adapter also adds some minimal function help (source file name and names of arguments).
help(plt_frame)
Help on function plt_frame in module r_tools:
plt_frame(*args, **kwargs) -> IPython.core.display.Image
imported R function plt_frame() (assumed to return a ggplot)
wrapped fn returns IPython.display.Image
R source file: plot_frame.R
R definition environment: <environment: R_GlobalEnv>
R arguments:
$d
And that is one method to use R graphing in Python or mixed-language data science projects.
All of the code in this example can be found here.
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