Error in g$grobs[[legend]]: no such index at level 2

[danli349]

When run the tutorial "https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html" The output figures are all correct but when I tried to save them:

#Save Plot
plotPDF(p1, p2, p3, name = "UMAP-scATAC-scRNA-Combined", addDOC = FALSE)

Plotting Ggplot!

Error in g$grobs[[legend]]: no such index at level 2

Traceback:

1. tryCatch({
 .     pdf(filename, width = width, height = height, useDingbats = useDingbats)
 .     for (i in seq_along(plotList)) {
 .         if (inherits(plotList[[i]], "gg")) {
 .             if (inherits(plotList[[i]], "patchwork")) {
 .                 if (getArchRVerbose()) 
 .                   message("Plotting Patchwork!")
 .                 print(plotList[[i]])
 .             }
 .             else {
 .                 if (getArchRVerbose()) 
 .                   message("Plotting Ggplot!")
 .                 if (!is.null(attr(plotList[[i]], "ratioYX"))) {
 .                   .fixPlotSize(plotList[[i]], plotWidth = width, 
 .                     plotHeight = height, height = attr(plotList[[i]], 
 .                       "ratioYX"), newPage = FALSE)
 .                 }
 .                 else {
 .                   .fixPlotSize(plotList[[i]], plotWidth = width, 
 .                     plotHeight = height, newPage = FALSE)
 .                 }
 .             }
 .             if (i != length(plotList)) {
 .                 grid::grid.newpage()
 .             }
 .         }
 .         else if (inherits(plotList[[i]], "gtable")) {
 .             if (getArchRVerbose()) 
 .                 message("Plotting Gtable!")
 .             print(grid::grid.draw(plotList[[i]]))
 .             if (i != length(plotList)) {
 .                 grid::grid.newpage()
 .             }
 .         }
 .         else if (inherits(plotList[[i]], "HeatmapList") | inherits(plotList[[i]], 
 .             "Heatmap")) {
 .             if (getArchRVerbose()) 
 .                 message("Plotting ComplexHeatmap!")
 .             padding <- 15
 .             draw(plotList[[i]], padding = unit(c(padding, padding, 
 .                 padding, padding), "mm"), heatmap_legend_side = "bot", 
 .                 annotation_legend_side = "bot")
 .         }
 .         else {
 .             if (getArchRVerbose()) 
 .                 message("Plotting Other")
 .             print(plotList[[i]])
 .         }
 .     }
 .     dev.off()
 . }, error = function(x) {
 .     if (getArchRVerbose()) 
 .         message(x)
 . })
2. tryCatchList(expr, classes, parentenv, handlers)
3. tryCatchOne(expr, names, parentenv, handlers[[1L]])
4. value[[3L]](cond)
5. message(x)
6. withRestarts({
 .     signalCondition(cond)
 .     defaultHandler(cond)
 . }, muffleMessage = function() NULL)
7. withOneRestart(expr, restarts[[1L]])
8. doWithOneRestart(return(expr), restart)
9. signalCondition(cond)

How to solve this problem? Thanks!

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0

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

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
 [1] nabor_0.5.0                       Seurat_5.1.0                     
 [3] SeuratObject_5.0.2                sp_2.1-4                         
 [5] Rsamtools_2.20.0                  BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [7] BSgenome_1.72.0                   rtracklayer_1.64.0               
 [9] BiocIO_1.14.0                     Biostrings_2.72.1                
[11] XVector_0.44.0                    rhdf5_2.48.0                     
[13] SummarizedExperiment_1.34.0       Biobase_2.64.0                   
[15] MatrixGenerics_1.16.0             Rcpp_1.0.13                      
[17] Matrix_1.7-0                      GenomicRanges_1.56.1             
[19] GenomeInfoDb_1.40.1               IRanges_2.38.1                   
[21] S4Vectors_0.42.1                  BiocGenerics_0.50.0              
[23] matrixStats_1.4.1                 data.table_1.16.0                
[25] stringr_1.5.1                     plyr_1.8.9                       
[27] magrittr_2.0.3                    ggplot2_3.5.1                    
[29] gtable_0.3.5                      gtools_3.9.5                     
[31] gridExtra_2.3                     ArchR_1.0.2                      

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22         splines_4.4.1            later_1.3.2             
  [4] pbdZMQ_0.3-11            bitops_1.0-8             tibble_3.2.1            
  [7] polyclip_1.10-7          XML_3.99-0.17            fastDummies_1.7.3       
 [10] lifecycle_1.0.4          globals_0.16.3           lattice_0.22-6          
 [13] MASS_7.3-61              plotly_4.10.4            yaml_2.3.10             
 [16] httpuv_1.6.15            sctransform_0.4.1        spam_2.10-0             
 [19] spatstat.sparse_3.1-0    reticulate_1.38.0        cowplot_1.1.3           
 [22] pbapply_1.7-2            RColorBrewer_1.1-3       abind_1.4-8             
 [25] zlibbioc_1.50.0          Rtsne_0.17               purrr_1.0.2             
 [28] RCurl_1.98-1.16          GenomeInfoDbData_1.2.12  ggrepel_0.9.6           
 [31] irlba_2.3.5.1            listenv_0.9.1            spatstat.utils_3.0-5    
 [34] goftest_1.2-3            RSpectra_0.16-2          spatstat.random_3.3-1   
 [37] fitdistrplus_1.2-1       parallelly_1.38.0        leiden_0.4.3.1          
 [40] codetools_0.2-20         DelayedArray_0.30.1      tidyselect_1.2.1        
 [43] UCSC.utils_1.0.0         farver_2.1.2             base64enc_0.1-3         
 [46] spatstat.explore_3.3-1   GenomicAlignments_1.40.0 jsonlite_1.8.9          
 [49] progressr_0.14.0         ggridges_0.5.6           survival_3.7-0          
 [52] tools_4.4.1              ica_1.0-3                glue_1.7.0              
 [55] SparseArray_1.4.8        IRdisplay_1.1            dplyr_1.1.4             
 [58] withr_3.0.1              fastmap_1.2.0            rhdf5filters_1.16.0     
 [61] fansi_1.0.6              digest_0.6.37            R6_2.5.1                
 [64] mime_0.12                colorspace_2.1-1         scattermore_1.2         
 [67] Cairo_1.6-2              tensor_1.5               spatstat.data_3.1-2     
 [70] utf8_1.2.4               tidyr_1.3.1              generics_0.1.3          
 [73] httr_1.4.7               htmlwidgets_1.6.4        S4Arrays_1.4.1          
 [76] uwot_0.2.2               pkgconfig_2.0.3          lmtest_0.9-40           
 [79] htmltools_0.5.8.1        dotCall64_1.1-1          scales_1.3.0            
 [82] png_0.1-8                spatstat.univar_3.0-0    reshape2_1.4.4          
 [85] rjson_0.2.23             uuid_1.2-1               nlme_3.1-166            
 [88] curl_5.2.3               repr_1.1.7               zoo_1.8-12              
 [91] KernSmooth_2.23-24       miniUI_0.1.1.1           restfulr_0.0.15         
 [94] pillar_1.9.0             vctrs_0.6.5              RANN_2.6.1              
 [97] promises_1.3.0           xtable_1.8-4             cluster_2.1.6           
[100] evaluate_1.0.0           cli_3.6.3                compiler_4.4.1          
[103] rlang_1.1.4              crayon_1.5.3             future.apply_1.11.2     
[106] labeling_0.4.3           stringi_1.8.4            deldir_2.0-4            
[109] viridisLite_0.4.2        BiocParallel_1.38.0      munsell_0.5.1           
[112] lazyeval_0.2.2           spatstat.geom_3.3-2      IRkernel_1.3.2          
[115] RcppHNSW_0.6.0           patchwork_1.2.0          future_1.34.0           
[118] Rhdf5lib_1.26.0          shiny_1.9.1              ROCR_1.0-11             
[121] igraph_2.0.3            

ggsave can save the plot, but I don't know why plotPDF doesn't work.

ggsave(
  "./UMAP-scATAC-scRNA-Combined_p2.pdf", p2,
  scale = 1,
  width = 8,
  height = 8,
  dpi = 600)

[rcorces]

Hi @danli349! 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.

[slundh]

It's an issue with newer versions of ggplot2 with archR. I had to downgrade to version 3.4.0. Other people say that 3.4.2 works as well.

[danli349]

@slundh Thanks a lot for the information!

When I install ggplot2_3.4.2, there is an Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double), how did you solve this problem?

packageurl <- "https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.4.2.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) :
  invalid non-character version specification 'x' (type: double)
Error: unable to load R code in package ‘ggplot2’
Execution halted
ERROR: lazy loading failed for package ‘ggplot2’
* removing ‘/home/dan/R/x86_64-pc-linux-gnu-library/4.03/ggplot2’
Warning message:
In install.packages(packageurl, repos = NULL, type = "source") :
  installation of package ‘/tmp/Rtmpwk4sB5/downloaded_packages/ggplot2_3.4.2.tar.gz’ had non-zero exit status

[immanuelazn]

Hey @danli349, sorry for the super late reply. I added in a fix for this, and this will be included in the 1.0.3 release

[danli349]

Hey @danli349, sorry for the super late reply. I added in a fix for this, and this will be included in the 1.0.3 release

That's great! Thanks a lot