change plotting to work with ggplot2 >=v3.5

[immanuelazn]

Details

ggplot2 version 3.5 had added a myriad of changes to legend objects, converting from S3 objects, to ggproto. Additionally, the legend interface had been heavily rewritten, with the grobs now having attr for legends in four positions rather than the one shared position in a plot previously. Lastly, empty grob objects, which were previously dropped, are no longer dropped, breaking our internal logic (<simpleError in g$grobs[[legend]]: no such index at level 2>)

This broke ArchR's ability to create legends, since we use this information when fixing plot sizes. This fixes plotting issues by validating that any legends detecting in a plot's grob are indeed non-empty.

Fixes issues #2150, #2123, #2130, #2168, #2234, #2210

Tests

• Ran with all unit tests. Confirm that previous errors resulting from ggplot have been reduced to 0

[mohsinbadat]

Sorry this may be a really basic question, but I've been having this issue, what's the fix I need to apply to sort things out? Thanks a lot! I know I need to change the VisualizeData.R script with the inserted lines but not sure how to find this file...

[immanuelazn]

Hi @mohsinbadat , no problem at all! This change has been added to the dev branch of ArchR. This means you can just load in the new ArchR dev branch through remotes::install_github("GreenleafLab/ArchR", ref ="dev")

[mohsinbadat]

Thanks @immanuelazn that's really helpful! I loaded it and it didn't work first time (R4.4.2, ggplot 3.5.1) but when I loaded ggplot 3.5.0 it's been working a dream, in case this is useful info.