I have created the plot below using R and exported the figure as a PDF-file. I would like to add additional elements to the plot, and I typically use Illustrator 2020 for such jobs.

Original R plot

However, when I open the PDF-file in Illustrator the points (the cirles) are turned into small squares with a cross inside (I have enlarged on point so it is easier to see). If I make the plot in R with squares instead I do not have the problem. PDF opened in Illustrator

Does anyone know how to fix it?

The PDF-fil can be downloaded here: https://github.com/PDRohde/illustrator_problem

Cheers Palle

  • Checked your file. The circles are indeed 100% gone and replaced with text boxes for some reason. You probably need to experiment and adjust your code. – Lucian Jun 19 '20 at 12:29
  • Thanks - it is strange because it is only for some symbols that I get this problem. Triangles dosen't work, but diamonds and squares does :) – Palle Duun Rohde Jun 19 '20 at 12:37
  • Make sure you're not placing TEXT symbols, but use actual circle shapes instead. That could be it. – Lucian Jun 19 '20 at 12:45
  • The box with an X through it indicates a missing glyph in a font. When you output the PDF, do you have an option in R that can convert text to outlines? I've never used that software so I don't know if it's possible. – Billy Kerr Jun 19 '20 at 12:48

Since I was beaten to the better answer I will offer an alternative :)

In this case, you can also resolve within Acrobat Pro if you have it.

First, change the font of the circles. This can be achieved with Edit PDF. Change them to a common font or one installed on your system like Arial. In this case I just dragged a box over all the circles and changed the font on mass. If you have add ons like PitStop pro, then there will be tools that replace fonts on mass more easily.

Next convert the font to outline via Preflight. This tool can be found under Print Production. Just type outline font and it will appear on the list. This function will make you save the PDF as a new file.

Open the .PDF in illustrator and it should have the circles in tact. There is a draw back and that is the text around the axis and the legend will also be outlined. However you can easily retype or just pull from the original version.


A guess: The circles are actually pieces of text. The font is included to the PDF and it's available for the PDF reader but Illustrator refuses to read it because Adobe doesn't help uncontrolled font distributing. You would have a theoretical possibility to write something without paying for a font.

Try to open the PDF in Inkscape. Import can work because Inkscape isn't font seller. The unfotunate thing in Inkscape's PDF imports is unpredictable deep multilevel groupings. You may need to apply Ungroup several times or to apply extension Deep Ungroup.

Maybe you can insert a link to the PDF to stop guesses and to get some reasoned help. Use a cloud which doesn't need login.

ADD after the link was made available: The guess was right, the dots are pieces of writing.

I released in Illustrator the clipping mask, selected one of the dots, then selected all of them by applying Select > Same > Appearance. Applying Type > Font > Arial restored the circles. In the next image only a part of texts is changed to Arial:

enter image description here

When editing PDFs in Illustrator you may need to release and delete numerous clipping masks before you can select the wanted objects. This case needed only 2.

How do I know Arial is the right choice? I don't. It was only a guess. Illustrator tells when you open a PDF what's missing and Acrobat can give also a list of needed fonts. Original is the original. I tried also Windings as a substitute. It seemed to work, too.

In this case Illustrator said "The font AdobePiStd is missing. Affected text will be displayed using a substitute font."

Tried also Inkscape 1.0 It imported the PDF. Import mode "Internal" worked, Poppler-Cairo import didn't.

  • Thanks for the suggestion! And have updated my question with link to the file. – Palle Duun Rohde Jun 19 '20 at 12:24
  • Amazing - it worked! Thanks – Palle Duun Rohde Jun 22 '20 at 7:10

Make sure you're not placing TEXT symbols, but use actual circle shapes instead.

Otherwise, the circles may still be there, but may have been enclosed into rectangular clipping masks and turned the fills into outlines.

This kind of thing happens sometimes when importing work generated from other software into AI.

What you can do is hit CTRL+Y which switches to outline view, which is a shape-only view with no formatting shown, at which point you're probably going to see the circles again.

If so, then hit A and start manually removing the rectangular shapes around your circles — there are different ways of doing this.

If you don't see the circles in CTRL+Y mode, these may have just been converted to squares on import. Play around with the R to PDF options, see if it can produce different types of PDF — yes, there are multiple kinds of PDF and AI could differentiate between these on import.

Also try exporting to SVG. Its a try until it works thing.

  • Thanks for your suggestions, Lucian. Unfortunately it is the same; just in black ;) – Palle Duun Rohde Jun 19 '20 at 12:04
  • Updated my answer with more suggestions. – Lucian Jun 19 '20 at 12:09

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