knitr: python engine output not in .md or .html

ghz 2days ago ⋅ 5 views

When I process my .Rmd file, there is no matplotlib img displayed. Is there a chunk option, or a different matplotlib method that is needed?

title: "Viz Examples" output: html_document: keep_md: true

from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
for c, z in zip(['r', 'g', 'b', 'y'], [30, 20, 10, 0]):
xs = np.arange(20)
ys = np.random.rand(20)

# You can provide either a single color or an array. To demonstrate this,
# the first bar of each set will be colored cyan.
cs = [c] * len(xs)
cs[0] = 'c'
ax.bar(xs, ys, zs=z, zdir='y', color=cs, alpha=0.8)

ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')

plt.print()

Answer

In your .Rmd file, the issue with the missing matplotlib image is likely due to the fact that matplotlib's rendering doesn't automatically display when used within an engine="python" chunk in R Markdown. To make sure that the plot appears in the output, there are a few things you need to ensure:

  1. Matplotlib Plotting in IPython / Jupyter: When using matplotlib in a Python chunk within an RMarkdown file, you need to explicitly tell matplotlib to display the plot. In some environments, this can be done by using %matplotlib inline or similar commands.

  2. Correct Plot Rendering: Instead of using plt.print(), which doesn't exist, you need to use plt.show() to display the plot.

Here’s how to modify your RMarkdown chunk to make sure the plot appears in the HTML output:

Revised Code

---
title: "Viz Examples"
output:
  html_document:
    keep_md: true
---

```{r testplot, engine="python"}
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np

# Ensure the plot will display inline
%matplotlib inline

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

for c, z in zip(['r', 'g', 'b', 'y'], [30, 20, 10, 0]):
    xs = np.arange(20)
    ys = np.random.rand(20)

    cs = [c] * len(xs)
    cs[0] = 'c'  # First bar colored cyan
    ax.bar(xs, ys, zs=z, zdir='y', color=cs, alpha=0.8)

ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')

# Display the plot
plt.show()

Key Changes:

  1. %matplotlib inline: This directive is used to enable inline plotting when using Jupyter/IPython-style execution. It's not strictly necessary in some environments, but it often ensures that plots render correctly.

  2. plt.show(): This is the correct method to render a matplotlib plot in a script or notebook.

Additional Considerations:

  • Ensure Plotting is Enabled: Depending on the setup of your RMarkdown and how Python is being executed, matplotlib might need some environment configuration (e.g., if you're running this through Jupyter, it typically works well with inline plotting enabled).
  • Check keep_md Output: Since you’ve set keep_md: true, you can check the intermediate Markdown output to see if there are any issues or errors in the rendering process.

Let me know if this resolves the issue!

#py