How to prevent RMarkdown from cutting off my Python graphs when using the R-reticulate package?-CodePudding

I have some simple plots in an Rmarkdown file plotted with matplotlib in a python chunk using the R-Reticulate package. But for some reason, the graphs always get squished no matter how I specify the figsize in python. It seems as if it is a problem with RMarkdown because I have plotted the same graphs in a .py file and they come out fine. Does anyone know how to prevent this resizing from RMarkdown?

Here is the code:

```{python, message=FALSE, results='hide', fig.keep='all'}
fig = plt.figure(figsize=(10,8))
plt.xlabel('Log Dispersion (km/s)', fontsize='x-large', fontweight='bold')
plt.ylabel(r'Log Black Hole Mass ($M_\odot$)', fontsize='x-large', fontweight='bold')
plt.scatter(data.SIG, data.MBH, label='data')
plt.show()
```

Here is the output in RMarkdown:

As you can see, it gets cutoff. Meanwhile, this same code in a .py file is totally fine. I have tried changing the figure size in fig = plt.figure(figsize=(10,8)) and it does absolutely nothing.

CodePudding user response：

I'm still not able to duplicate the issue you're having. The following is a chunk that will add Resize Sensor to the page.

```{r spicy, engine="js", include=FALSE, results="asis"}

scrp = ["https://cdnjs.cloudflare.com/ajax/libs/css-element-queries/1.2.3/ElementQueries.min.js",
        "https://cdnjs.cloudflare.com/ajax/libs/css-element-queries/1.2.3/ResizeSensor.js"];

setTimeout(function(){ // this function adds the URLs to the HTML <head>
  for(i=0; i < scrp.length; i  ) {
    script = document.createElement('script');
    script.src = scrp[i];
    script.type = "text/javascript";
    document.head.appendChild(script);
  }
  ElementQueries.listen(); // just listen!!
}, 200); //wait a sec!

```

Since this is a notebook, you may want to add echo=F to the chunk options.

If this doesn't work, look at any other global settings you've set.

For example, do you have any configurations established in your YAML?
Or is it just who, when, and output?
Did you set default figure sizes?
Are some plots okay and others not? If so, what differs?
Do you have columns or rows specified?
Do you have styles specified?

Another thing that's worth mentioning—base R plots and ggplot render as images, while graphs from packages like plotly or highchart render as HTML. Matplotlib renders as an image.