fix invalid class "GGbio" object: invalid object for slot "ggplot"

[zhewa]

Currently, even though no changes to scruff was made, there is an unexpected new build error at https://bioconductor.org/checkResults/release/bioc-LATEST/scruff/nebbiolo1-buildsrc.html.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scruff
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* checking for file ‘scruff/DESCRIPTION’ ... OK
* preparing ‘scruff’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘scruff.Rmd’ using rmarkdown

Quitting from scruff.Rmd:218-227 [visualize_reads]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'geom_arrow' for signature 'data = "ggplot2::mapping"'
---
Backtrace:
    ▆
 1. └─scruff::rview(bamExample, chr = "MT", start = start, end = end)
 2.   └─ggbio::geom_arrow(ggplot2::aes(color = umi))
 3.     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scruff.Rmd' failed with diagnostics:
unable to find an inherited method for function 'geom_arrow' for signature 'data = "ggplot2::mapping"'
--- failed re-building ‘scruff.Rmd’

SUMMARY: processing the following file failed:
  ‘scruff.Rmd’

Error: Vignette re-building failed.
Execution halted

This is probably due to the changes in ggbio package. Changes in this PR circumvents the error introduced in ggbio.

• Fix Bioconductor build error: class "GGbio" object: invalid object for slot "ggplot".
• Use patchwork to combine plots in vignette.
• Updated .themePublication.

[joshua-d-campbell]

Thanks for updating this @zhewa! Could you just update the version numbers of the ".github/workflows/R-CMD-check.yaml" files so the checks can run? I think you can update the versions to the following:

    steps:
      - uses: actions/checkout@v4

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r@v2

      - uses: r-lib/actions/setup-r-dependencies@v2