Colors not preserved when exporting PDF

[bernienlab]

I'm using Illustrator 30.0 to prepare some scientific figures. I use matplotlib to output a PDF, which I then "Place" in my Illustrator file, and after making my edits I would export the file as a new PDF. However, when I do this, the output files' colors seem messed up on every PDF viewer I use (Acrobat, Chrome, Firefox, even Illustrator). For example, here's a screengrab of the matplotlib output, which looks as expected:

Here's the preview in Illustrator, before export:

And here's after export. Document color mode is RGB, exporting using the [PDF/X-4:2008] preset, though other settings have given me similar results:

If I change the document color mode to CMYK before export, it looks slightly different, but still bad:

And here's my color settings, if it's any clue:

I don't expect a perfect color match on the output, but this seems dramatically far off. Is there some combination of settings which I can use to preserve the appearance of my output? Here's a Creative Cloud link to my example file: https://illustrator.adobe.com/id/urn:aaid:sc:US:265137ba-9f92-49b1-ada9-1f68341c16c4 

[Doug A Roberts]

I think you need to give edit access to enable your file to be downloaded.

[bernienlab]

Thanks for the heads up, "Save a copy" should now be enabled for anyone with the link

[Doug A Roberts]

The matplotlib output is a 5x5 px raster image upscaled 2800%. Is this normal for your output?

Your compression settings are what matter here, the image is showing compression artefacts.

Change to 'Do not downsample' and 'Compression: None'.

[bernienlab]

This blow-up is a bit more dramatic, but yes, my output will be a few-pixel raster image upscaled to a larger size.
On the export settings, if I go to Compression, turn off all downsampling, and uncheck the "Compress text and line art" box, I get the following output, which still doesn't look right:

[Ton Frederiks]

Line art is for black and white images. What do you use for color? Don't use jpeg, because it is a lossy format that throws away and averages colors.

[Doug A Roberts · Accepted solution]

Did you set Compression to None?

[bernienlab · Accepted solution]

Aha, this was it! I was under the false impression that setting "Do not downsample" meant the rest of the compression settings would be disabled by default; switching these to "None" did the trick. Thanks!