You can use Python with examiner, thanks to the support
for Python in RStudio and library(knitr) via
library(reticulate). Just load reticulate and
start Python chunks with ```{python} instead of the usual
```{r}.
This article assumes you have managed to install and use Python as
described in the reticulate documentation.
You may need an R wrapper to display some kinds of rich content. Below we illustrate a few.
To test this on your system, make an examiner
project and create a question Rmd from the template
New File > R Markdown > From Template > demo_python.
Making Python available to reticulate
Read the reticulate docs on how to make this
work. Replace the use_condaenv() call with
whatever works for you. Here I use an env with packages for graphics,
tables, and animated images.
library(reticulate)
if (!("examiner" %in% conda_list()$name)) {
conda_create("examiner", c("pandas", "matplotlib", "ffmpeg", "tabulate"))
}
use_condaenv("examiner")Plain text Python output
The following chunk begins with ```{python}, so it will be run with the python engine.
## {'This': 4, 'is': 2, 'a': 1, 'test': 4}Matplotlib graphics
Figures will display automatically if they are open when the chunk
ends, even if you don’t call the usual plt.show().
Python figures cannot be sized via knitr chunk options. Instead,
plt.figure(figsize = ..., dpi = ...) or
fig.set_size_inches() or fig.set_dpi(), see
below.
Pandas data frames
The default plain text display works as expected.
import pandas as pd
data = {
'Column 1': ['Row1-Col1', 'Row2-Col1'],
'Column 2': ['Row1-Col2', 'Row2-Col2'],
'Column 3': ['Row1-Col3', 'Row2-Col3']
}
table = pd.DataFrame(data, index=['Row 1', 'Row 2'])
table## Column 1 Column 2 Column 3
## Row 1 Row1-Col1 Row1-Col2 Row1-Col3
## Row 2 Row2-Col1 Row2-Col2 Row2-Col3For Pandas’ HTML format (ugly) or Markdown (slightly prettier), store
the generated markup in a Python string, which you then display from an
R chunk using htmltools::HTML(). (Printing from the Python
chunk will wrap the output in <pre><code> tags
so the markup doesn’t render.)
Python chunk:
R chunks:
htmltools::HTML(py$table_html)| Column 1 | Column 2 | Column 3 | |
|---|---|---|---|
| Row 1 | Row1-Col1 | Row1-Col2 | Row1-Col3 |
| Row 2 | Row2-Col1 | Row2-Col2 | Row2-Col3 |
To output generated markdown, use the chunk option
results="asis".
cat(py$table_md)| Column 1 | Column 2 | Column 3 | |
|---|---|---|---|
| Row 1 | Row1-Col1 | Row1-Col2 | Row1-Col3 |
| Row 2 | Row2-Col1 | Row2-Col2 | Row2-Col3 |
Matplotlib animations
Canvas has a 16 kB limit on question size, and WISEflow does not
allow inline images. Hence, animated gifs or mp4 videos must be saved by
your code and then included with Markdown or
knitr::include_graphics(). With this workaround, animation
in Matplotlib works well.
import matplotlib.pyplot as plt
import numpy as np
import matplotlib.animation as animation
fig, ax = plt.subplots()
fig.set_size_inches(3, 2)
fig.set_dpi(72)
x = np.arange(0, 2*np.pi, 0.01)
line, = ax.plot(x, np.sin(x))
def animate(i):
line.set_ydata(np.sin(x + 2 * np.pi * i / 50)) # update the data.
return line,
ani = animation.FuncAnimation(fig, animate, interval=20, blit=True, save_count=50)
# pillow is the "python imaging library", included with matplotlib
ani.save("animation_python.gif", writer = "pillow", fps = 20)
# Default writer is ffmpeg
ani.save("animation_python.mp4", fps = 20)
# Close the figure to prevent an image of the last frame from displaying automatically
plt.close(fig)
MPEG (does not loop in Canvas)
knitr::include_graphics("animation_python.mp4")While we can set loop and autoplay
attributes as shown below, Canvas will strip them from the question
html. Thus, the following will loop if you knit it separately, but not
in Canvas.