GGplot Errors for Fragment Size Distribution and DoubletScores

[shamer3]

I am getting errors with anything related to ggplot. I have done as suggested in previous thread by reinstalling Cairo, Quartz and ggrastr, however this has not fixed the problem. The issue is observed firstly, in Arrow file generation:

Continuing through after error ggplot for TSS by Frags

And then again during doublet scoring ggplot generation:

RROR Found in ggplot for Untreated (4 of 5) :  
LogFile = ArchRLogs/ArchR-addDoubletScores...

<simpleError in g$grobs[[legend]]: no such index at level 2
>

In each case pdf files are generated for the specific plot hone when I try and access them I am met with an error message that the file is broken or damaged as shown below ( also tried opening is two different pdf viewers and was met with similar issues) :

Session information is as follows:

R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] Seurat_5.0.2                      SeuratObject_5.0.1               
 [3] sp_2.1-3                          BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [5] BSgenome_1.70.2                   rtracklayer_1.62.0               
 [7] BiocIO_1.12.0                     Biostrings_2.70.2                
 [9] XVector_0.42.0                    ggrastr_1.0.2                    
[11] harmony_1.2.0                     Cairo_1.6-2                      
[13] rhdf5_2.46.1                      SummarizedExperiment_1.32.0      
[15] Biobase_2.62.0                    MatrixGenerics_1.14.0            
[17] Rcpp_1.0.12                       Matrix_1.6-5                     
[19] GenomicRanges_1.54.1              GenomeInfoDb_1.38.7              
[21] IRanges_2.36.0                    S4Vectors_0.40.2                 
[23] BiocGenerics_0.48.1               matrixStats_1.2.0                
[25] data.table_1.15.2                 stringr_1.5.1                    
[27] plyr_1.8.9                        magrittr_2.0.3                   
[29] ggplot2_3.5.0                     gtable_0.3.4                     
[31] gtools_3.9.5                      gridExtra_2.3                    
[33] ArchR_1.0.2                       devtools_2.4.5                   
[35] usethis_2.2.3                     reticulate_1.35.0                

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22         shinythemes_1.2.0        splines_4.3.2           
  [4] later_1.3.2              bitops_1.0-7             tibble_3.2.1            
  [7] polyclip_1.10-6          XML_3.99-0.16.1          fastDummies_1.7.3       
 [10] lifecycle_1.0.4          doParallel_1.0.17        rprojroot_2.0.4         
 [13] globals_0.16.3           processx_3.8.3           lattice_0.22-5          
 [16] MASS_7.3-60              plotly_4.10.4            yaml_2.3.8              
 [19] remotes_2.4.2.1          httpuv_1.6.14            sctransform_0.4.1       
 [22] spam_2.10-0              spatstat.sparse_3.0-3    sessioninfo_1.2.2       
 [25] pkgbuild_1.4.3           cowplot_1.1.3            pbapply_1.7-2           
 [28] RColorBrewer_1.1-3       abind_1.4-5              pkgload_1.3.4           
 [31] zlibbioc_1.48.0          Rtsne_0.17               presto_1.0.0            
 [34] purrr_1.0.2              RCurl_1.98-1.14          rappdirs_0.3.3          
 [37] circlize_0.4.16          GenomeInfoDbData_1.2.11  ggrepel_0.9.5           
 [40] irlba_2.3.5.1            spatstat.utils_3.0-4     listenv_0.9.1           
 [43] pheatmap_1.0.12          goftest_1.2-3            RSpectra_0.16-1         
 [46] spatstat.random_3.2-3    fitdistrplus_1.1-11      parallelly_1.37.1       
 [49] leiden_0.4.3.1           codetools_0.2-19         DelayedArray_0.28.0     
 [52] tidyselect_1.2.0         shape_1.4.6.1            rhandsontable_0.3.8     
 [55] spatstat.explore_3.2-6   GenomicAlignments_1.38.2 jsonlite_1.8.8          
 [58] GetoptLong_1.0.5         ellipsis_0.3.2           progressr_0.14.0        
 [61] ggridges_0.5.6           survival_3.5-7           iterators_1.0.14        
 [64] foreach_1.5.2            tools_4.3.2              ica_1.0-3               
 [67] glue_1.7.0               SparseArray_1.2.4        here_1.0.1              
 [70] dplyr_1.1.4              withr_3.0.0              BiocManager_1.30.22     
 [73] fastmap_1.1.1            rhdf5filters_1.14.1      fansi_1.0.6             
 [76] callr_3.7.5              digest_0.6.34            R6_2.5.1                
 [79] mime_0.12                colorspace_2.1-0         scattermore_1.2         
 [82] tensor_1.5               spatstat.data_3.0-4      utf8_1.2.4              
 [85] tidyr_1.3.1              generics_0.1.3           httr_1.4.7              
 [88] htmlwidgets_1.6.4        S4Arrays_1.2.1           uwot_0.1.16             
 [91] pkgconfig_2.0.3          ComplexHeatmap_2.18.0    lmtest_0.9-40           
 [94] htmltools_0.5.7          profvis_0.3.8            dotCall64_1.1-1         
 [97] clue_0.3-65              scales_1.3.0             png_0.1-8               
[100] rstudioapi_0.15.0        reshape2_1.4.4           rjson_0.2.21            
[103] nlme_3.1-164             curl_5.2.1               cachem_1.0.8            
[106] zoo_1.8-12               GlobalOptions_0.1.2      KernSmooth_2.23-22      
[109] vipor_0.4.7              miniUI_0.1.1.1           restfulr_0.0.15         
[112] desc_1.4.3               pillar_1.9.0             vctrs_0.6.5             
[115] RANN_2.6.1               urlchecker_1.0.1         promises_1.2.1          
[118] xtable_1.8-4             cluster_2.1.6            beeswarm_0.4.0          
[121] Rsamtools_2.18.0         cli_3.6.2                compiler_4.3.2          
[124] rlang_1.1.3              crayon_1.5.2             future.apply_1.11.1     
[127] ps_1.7.6                 ggbeeswarm_0.7.2         fs_1.6.3                
[130] stringi_1.8.3            BiocParallel_1.36.0      deldir_2.0-4            
[133] viridisLite_0.4.2        munsell_0.5.0            lazyeval_0.2.2          
[136] spatstat.geom_3.2-9      RcppHNSW_0.6.0           patchwork_1.2.0         
[139] future_1.33.1            Rhdf5lib_1.24.2          shiny_1.8.0             
[142] ROCR_1.0-11              igraph_2.0.2             memoise_2.0.1 

[rcorces]

Hi @shamer3! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

[juliabelk]

For me, downgrading specifically ggplot fixed this. This worked for me: conda install conda-forge::r-ggplot2=3.3

[shamer3]

Hi Julia, thanks so much I can confirm downgrading to ggplot 3.3.0 has solved the plotting issue. Something with ggplot 3.5.0 is bugging all the plots out. Thanks!!

[saeedfc]

@rcorces

It is an incredible set of tools that you have built and would indeed be a shame if it cannot be updated. For this specific issue with ggplot2, it is even more crucial as almost all packages use it and to keep it downgraded for a long time could be a challenge. Over time this indeed could force people to not use ArchR. Hopefully you are able to get a comp-biologist to work on it. Good luck :-).

I am going to try downgrading now the ggplot2. Hopefully it doesn't bother other packages. Will keep this thread posted Thanks again for ArchR!

[rcorces]

@saeedfc - I know this is frustrating and I do apologize. The good news is that we have a full-time developer joining the team in a month and then we will be working to push a new stable release of ArchR. More to come on that in a month.

[saeedfc]

@rcorces Looking forwward!

@shamer3 @juliabelk Thanks. I tried this. But then I cannot load Seurat. Because then says ggplot 3.4.0 is required even though Seurat CRAN webpage only says ggplot2 3.3.0 is required . Same if I try to downgrade Seurat as well to 4.0.4.

So I looked through the dependencies of Seurat which requires ggplot2 3.4.0 ggridges and cowplot.

For anyone having a similar issue; Try to use renv so you have a project specific iosolated library for R packges.

Install Seurat

install.packages('Seurat')

Then start downgrading the below 3 packages;

ggplot_url <- "https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz"
install.packages(ggplot_url, repos=NULL, type="source")
packageurl <- "https://cran.r-project.org/src/contrib/Archive/cowplot/cowplot_1.1.1.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
packageurl <- "https://cran.r-project.org/src/contrib/Archive/ggridges/ggridges_0.5.4.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

Beware when you install tidyverse blindly as only upto tidyverse 1.3.0 that you can go with ggplot 3.3.0