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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:

enter image description here

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.

Os GS
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    does applying a constrained or tight layout help: `fig = plt.figure(figsize=(10,8), layout='constrained')`? – Stef Aug 12 '22 at 13:22
  • @Stef So, this fixes it for this graph, like it is no longer cropped. But for some of my other graphs that have a legend box, the graph still seems squished and the legend box overlaps the data/curves meanwhile the same plot in python is fine. – Os GS Aug 12 '22 at 14:31
  • What about `{r fig4, out.width = '40%',out.height = '40%'}` for the R chunks? does this work as well? – Daniel_j_iii Aug 12 '22 at 15:17
  • I'm not having this issue, no matter how much I try to recreate it. Do you have any global chunk options set in the RMD? As in `knitr::opts_chunk$set`? What's in your YAML? I even tried different plots via `matplotlib`, `plotly`, `plotly` as a backend, and so on. I tried it with and without global figure sizes, too. – Kat Aug 12 '22 at 15:37
  • I just thought to add: if your output is set to `html_document` or similar, it defaults to a body max-width of 940px. You can set styles to unset that for `.main-container`. Another option is to add Resize Sensor to your head (if the output is HTML). If Resize Sensor is something you're interested in trying, let me know. I can give you the code to add it. I don't know if it will help, so I didn't want to provide it as an answer. – Kat Aug 12 '22 at 16:06
  • @Kat Indeed, I am using an html_notebook output. I'd be interested in seeing the code for the Resize Sensor ! Thanks – Os GS Aug 12 '22 at 17:54

1 Answers1

1

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.

Kat
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