I'm not sure if this is the correct place to ask this, so maybe some can point me in the right direction if it isn't.

I have exported an chart from the R programming language as a PDF, and it needs some manual edits before it can be included in a publication.

If I open the PDF in acrobat it looks fine. But if I open it in illustrator, there are parts missing:


enter image description here


enter image description here

The missing part is a filled path. If I open the file, and then save it without making any changes, the missing information is now missing in Acrobat also.

If anyone has any ideas what might be happening, or how it might be fixed, I'd be very grateful.

Edit: Here is a link to the original PDF

  • Hi. Welcome to GDSE. I notice that everything is pixelated in your Illustrator example, suggesting it's a low resolution raster image, rendered without any anti-aliasing. Can you share an example PDF that demonstrates the problem? – Billy Kerr Dec 20 '19 at 15:15
  • Thanks. Yes, sorry, its a screen cap, I don't know why stackexchange has chosen to show it so large. I've added a link to the file. – Ian Sudbery Dec 20 '19 at 15:34
  • I can confirm the fourth darker blue line doesn't go all the way to the end. Can't really tell why. However, there seem to be a ridiculous number of clilpping groups, which are probably confusing poor old Illustrator. In fact when I opened the file, Illustrator was unresponsive for quite a few seconds. I thought it was going to crash. – Billy Kerr Dec 20 '19 at 15:46
  • The wireframe comparison between illustrator and Acrobat are showing up completely different for me. I can't rule out the clipping issue because PitStop is crashing when I try and unmask any objects. Perhaps inkscape would have better results? imgur.com/a/tBn9rH7 – superluminal Dec 20 '19 at 17:57
  • R has a habit of putting a clipping mask around everything when it converts to PDF. Its very annoying. Good call on inkscape. – Ian Sudbery Dec 21 '19 at 10:54

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