Cytomappershiny - Error: Graphics API version mismatch

[jparkinson375]

Hi, apologies if this is duplicated somewhere else, but I couldn't find anything about it in the past issues.

I have used the Steinbock analysis pipeline and am now using Cytomapper (version 1.8.0) to analyse the data. When I try to run Cytomappershiny, the GUI loads and I can load and view images/channels in the first "Scatterplot" tab. However, in the "Images" tab I get the error: Graphics API version mismatch in the expression section and nothing appears in the right section.

When I close back to R I get the following information.

Any idea what could be causing this?

Many thanks.

[nilseling]

Hi @jparkinson375,

could you please post the output of sessionInfo() here and the function call that you used to open the shiny app. The warning can be ignored for now.

[jparkinson375]

Thanks for the speedy reply nilseling,

Here is the output of sessionInfo()

I am using this code to open the app:

if (interactive()) {

images <- readRDS("./images.rds")
masks <- readRDS("./masks.rds")

cytomapperShiny(object = spe, mask = masks, image = images, 
                cell_id = "ObjectNumber", img_id = "sample_id")

}

From your guide here: https://bodenmillergroup.github.io/IMCDataAnalysis/cell-phenotyping.html#classification

[nilseling]

Thanks! Unfortunately I can't reproduce the error on my side. Would it be possible if you send me the spe object of a single image as well as the matching multi-channel image and segmentation mask as CytoImageList object via mail: nils.eling@uzh.ch.

[jparkinson375]

Thanks, I have just emailed the data to you.

[nilseling]

Hi @jparkinson375,

thanks for sending the data! I was not able to reproduce the error on my side. But I have only loaded cytomapper v1.9.1 and no other packages. So I'm assuming there is a function clash with another package that you have loaded. Could you please try to run the command only when loading cytomapper?

[jparkinson375]

No problem at all.

I tried starting a completely fresh instance of Rstudio and loading only Cytomapper and the required data, I even tried running it in R (4.2.1) without using Rstudio and I still get the same error. I was able to get some more info on the error though, I am not sure if this is any help.

This is what my sessionInfo() outputs when I only load cytomapper, does this look right, is any package being loaded that isn't on your machine?

[nilseling]

Hmm, so the issue is really the graphics device. Would install.packages("svglite", type = "source") (reinstalling svglite) solve the issue?

[jparkinson375]

That worked! It seems to be working normally now.

Thank you for all the help.

[nilseling]

That's great :) closing now