Error in plotPDF()

[sokratiag]

Hi,

I am getting an error when trying to use plotPDF() function (sessioninfo below):

Plotting Ggplot!

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

Traceback:

1. plotPDF(p1, p2, p3, p4, name = "Plot-UMAP-Own_UMAP_Clusters_sample_multiome_EJ1.pdf",
   . ArcRProj = proj_multiome, addDOC = FALSE, width = 10,
   . height = 10)
2. 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)
   . })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[3L]
6. message(x)
7. withRestarts({
   . signalCondition(cond)
   . defaultHandler(cond)
   . }, muffleMessage = function() NULL)
8. withOneRestart(expr, restarts[[1L]])
9. doWithOneRestart(return(expr), restart)

R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /mnt/mr01-home01/b28763sg/anaconda3/envs/r_mul/lib/libopenblasp-r0.3.26.so; LAPACK version 3.12.0

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/London
tzcode source: system (glibc)

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

other attached packages:
[1] remotes_2.5.0 scDblFinder_1.16.0
[3] viridis_0.6.5 viridisLite_0.4.2
[5] SingleR_2.4.1 scran_1.30.2
[7] scater_1.30.1 scuttle_1.12.0
[9] scales_1.3.0 KernSmooth_2.23-22
[11] igraph_2.0.3 ggrepel_0.9.5
[13] ggforce_0.4.2 ggbeeswarm_0.7.2
[15] enrichR_3.2 DropletUtils_1.22.0
[17] SingleCellExperiment_1.24.0 cowplot_1.1.3
[19] bluster_1.12.0 AnnotationHub_3.10.0
[21] BiocFileCache_2.10.2 dbplyr_2.5.0
[23] SeuratObject_5.0.1 Seurat_4.3.0
[25] hdf5r_1.3.10 HDF5Array_1.30.1
[27] DelayedArray_0.28.0 SparseArray_1.2.4
[29] S4Arrays_1.2.1 abind_1.4-5
[31] lubridate_1.9.3 forcats_1.0.0
[33] dplyr_1.1.4 purrr_1.0.2
[35] readr_2.1.5 tidyr_1.3.1
[37] tibble_3.2.1 tidyverse_2.0.0
[39] rhdf5_2.46.1 SummarizedExperiment_1.32.0
[41] Biobase_2.62.0 MatrixGenerics_1.14.0
[43] Rcpp_1.0.12 Matrix_1.6-5
[45] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[47] IRanges_2.36.0 S4Vectors_0.40.2
[49] BiocGenerics_0.48.1 matrixStats_1.3.0
[51] data.table_1.15.4 stringr_1.5.1
[53] plyr_1.8.9 magrittr_2.0.3
[55] ggplot2_3.4.2 gtable_0.3.4
[57] gtools_3.9.5 gridExtra_2.3
[59] ArchR_1.0.2

loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-3 bitops_1.0-7
[3] httr_1.4.7 RColorBrewer_1.1-3
[5] repr_1.1.7 tools_4.3.3
[7] sctransform_0.4.1 utf8_1.2.4
[9] R6_2.5.1 lazyeval_0.2.2
[11] uwot_0.2.1 rhdf5filters_1.14.1
[13] withr_3.0.0 sp_2.1-3
[15] progressr_0.14.0 cli_3.6.2
[17] Cairo_1.6-2 spatstat.explore_3.2-7
[19] labeling_0.4.3 spatstat.data_3.0-4
[21] ggridges_0.5.6 pbapply_1.7-2
[23] Rsamtools_2.18.0 pbdZMQ_0.3-11
[25] R.utils_2.12.3 parallelly_1.37.1
[27] WriteXLS_6.5.0 BSgenome_1.70.2
[29] limma_3.58.1 RSQLite_2.3.6
[31] BiocIO_1.12.0 generics_0.1.3
[33] ica_1.0-3 spatstat.random_3.2-3
[35] fansi_1.0.6 R.methodsS3_1.8.2
[37] lifecycle_1.0.4 yaml_2.3.8
[39] edgeR_4.0.16 Rtsne_0.17
[41] blob_1.2.4 promises_1.3.0
[43] dqrng_0.3.2 crayon_1.5.2
[45] miniUI_0.1.1.1 lattice_0.22-6
[47] beachmat_2.18.0 KEGGREST_1.42.0
[49] metapod_1.10.1 pillar_1.9.0
[51] rjson_0.2.21 xgboost_1.7.7.1
[53] future.apply_1.11.2 codetools_0.2-20
[55] leiden_0.4.3.1 glue_1.7.0
[57] vctrs_0.6.5 png_0.1-8
[59] spam_2.10-0 cachem_1.0.8
[61] mime_0.12 survival_3.5-8
[63] statmod_1.5.0 interactiveDisplayBase_1.40.0
[65] fitdistrplus_1.1-11 ROCR_1.0-11
[67] nlme_3.1-164 bit64_4.0.5
[69] filelock_1.0.3 RcppAnnoy_0.0.22
[71] irlba_2.3.5.1 vipor_0.4.7
[73] colorspace_2.1-0 DBI_1.2.2
[75] tidyselect_1.2.1 bit_4.0.5
[77] compiler_4.3.3 curl_5.2.1
[79] BiocNeighbors_1.20.2 BSgenome.Mmusculus.UCSC.mm10_1.4.3
[81] plotly_4.10.4 rtracklayer_1.62.0
[83] lmtest_0.9-40 rappdirs_0.3.3
[85] digest_0.6.35 goftest_1.2-3
[87] spatstat.utils_3.0-4 XVector_0.42.0
[89] htmltools_0.5.8.1 pkgconfig_2.0.3
[91] base64enc_0.1-3 sparseMatrixStats_1.14.0
[93] fastmap_1.1.1 rlang_1.1.3
[95] htmlwidgets_1.6.4 shiny_1.8.1.1
[97] DelayedMatrixStats_1.24.0 farver_2.1.1
[99] zoo_1.8-12 jsonlite_1.8.8
[101] BiocParallel_1.36.0 R.oo_1.26.0
[103] BiocSingular_1.18.0 RCurl_1.98-1.14
[105] GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[107] patchwork_1.2.0 Rhdf5lib_1.24.2
[109] IRkernel_1.3.2 munsell_0.5.1
[111] reticulate_1.36.0 stringi_1.8.3
[113] zlibbioc_1.48.2 MASS_7.3-60.0.1
[115] parallel_4.3.3 listenv_0.9.1
[117] deldir_2.0-4 Biostrings_2.70.3
[119] IRdisplay_1.1 splines_4.3.3
[121] tensor_1.5 hms_1.1.3
[123] locfit_1.5-9.9 uuid_1.2-0
[125] spatstat.geom_3.2-9 reshape2_1.4.4
[127] ScaledMatrix_1.10.0 XML_3.99-0.16.1
[129] BiocVersion_3.18.1 evaluate_0.23
[131] BiocManager_1.30.22 tzdb_0.4.0
[133] tweenr_2.0.3 httpuv_1.6.15
[135] RANN_2.6.1 polyclip_1.10-6
[137] future_1.33.2 scattermore_1.2
[139] rsvd_1.0.5 xtable_1.8-4
[141] restfulr_0.0.15 later_1.3.2
[143] GenomicAlignments_1.38.2 memoise_2.0.1
[145] beeswarm_0.4.0 AnnotationDbi_1.64.1
[147] cluster_2.1.6 timechange_0.3.0
[149] globals_0.16.3

I would appreciate your help.

Thanks!

[rcorces]

Hi @sokratiag! 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.

[hhlhhlhhl]

I also encountered the same error. Have you solved this error?

[sokratiag]

Hi,

I downgraded some packages and it works now - I think the issue was with ggplot2, I downgraded to version 3.4.2. I also used: options("Seurat.object.assay.version" = "v3").

R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /mnt/mr01-home01/b28763sg/anaconda3/envs/r42/lib/libopenblasp-r0.3.27.so

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome_1.66.3
[3] rtracklayer_1.58.0 Biostrings_2.66.0
[5] XVector_0.38.0 scDblFinder_1.12.0
[7] viridis_0.6.5 viridisLite_0.4.2
[9] SingleR_2.0.0 scran_1.26.2
[11] scater_1.26.1 scuttle_1.8.4
[13] scales_1.3.0 KernSmooth_2.23-22
[15] igraph_2.0.3 ggrepel_0.9.5
[17] ggforce_0.4.2 ggbeeswarm_0.7.2
[19] enrichR_3.2 DropletUtils_1.18.1
[21] SingleCellExperiment_1.20.1 cowplot_1.1.3
[23] bluster_1.8.0 AnnotationHub_3.6.0
[25] BiocFileCache_2.6.1 dbplyr_2.5.0
[27] Seurat_5.0.3 SeuratObject_5.0.1
[29] sp_2.1-3 hdf5r_1.3.10
[31] HDF5Array_1.26.0 DelayedArray_0.24.0
[33] lubridate_1.9.3 forcats_1.0.0
[35] dplyr_1.1.4 purrr_1.0.2
[37] readr_2.1.5 tidyr_1.3.1
[39] tibble_3.2.1 tidyverse_2.0.0
[41] rhdf5_2.42.1 SummarizedExperiment_1.28.0
[43] Biobase_2.58.0 MatrixGenerics_1.10.0
[45] Rcpp_1.0.12 Matrix_1.6-5
[47] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[49] IRanges_2.32.0 S4Vectors_0.36.2
[51] BiocGenerics_0.44.0 matrixStats_1.3.0
[53] data.table_1.15.4 stringr_1.5.1
[55] plyr_1.8.9 magrittr_2.0.3
[57] ggplot2_3.4.2 gtable_0.3.5
[59] gtools_3.9.5 gridExtra_2.3
[61] ArchR_1.0.2

loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 pbdZMQ_0.3-11
[3] scattermore_1.2 R.methodsS3_1.8.2
[5] bit64_4.0.5 irlba_2.3.5.1
[7] R.utils_2.12.3 KEGGREST_1.38.0
[9] RCurl_1.98-1.14 generics_0.1.3
[11] ScaledMatrix_1.6.0 RSQLite_2.3.6
[13] RANN_2.6.1 future_1.33.2
[15] bit_4.0.5 tzdb_0.4.0
[17] spatstat.data_3.0-4 httpuv_1.6.15
[19] hms_1.1.3 evaluate_0.23
[21] promises_1.3.0 fansi_1.0.6
[23] restfulr_0.0.15 DBI_1.2.2
[25] htmlwidgets_1.6.4 spatstat.geom_3.2-9
[27] RSpectra_0.16-1 deldir_2.0-4
[29] sparseMatrixStats_1.10.0 vctrs_0.6.5
[31] ROCR_1.0-11 abind_1.4-5
[33] cachem_1.0.8 withr_3.0.0
[35] progressr_0.14.0 sctransform_0.4.1
[37] GenomicAlignments_1.34.1 goftest_1.2-3
[39] cluster_2.1.6 IRdisplay_1.1
[41] dotCall64_1.1-1 lazyeval_0.2.2
[43] crayon_1.5.2 spatstat.explore_3.2-7
[45] edgeR_3.40.2 pkgconfig_2.0.3
[47] tweenr_2.0.3 nlme_3.1-164
[49] vipor_0.4.7 rlang_1.1.3
[51] globals_0.16.3 lifecycle_1.0.4
[53] miniUI_0.1.1.1 filelock_1.0.3
[55] fastDummies_1.7.3 rsvd_1.0.5
[57] polyclip_1.10-6 RcppHNSW_0.6.0
[59] lmtest_0.9-40 IRkernel_1.3.2
[61] Rhdf5lib_1.20.0 zoo_1.8-12
[63] base64enc_0.1-3 beeswarm_0.4.0
[65] ggridges_0.5.6 png_0.1-8
[67] rjson_0.2.21 bitops_1.0-7
[69] R.oo_1.26.0 spam_2.10-0
[71] rhdf5filters_1.10.1 blob_1.2.4
[73] DelayedMatrixStats_1.20.0 parallelly_1.37.1
[75] spatstat.random_3.2-3 beachmat_2.14.2
[77] memoise_2.0.1 ica_1.0-3
[79] zlibbioc_1.44.0 compiler_4.2.3
[81] dqrng_0.3.2 BiocIO_1.8.0
[83] RColorBrewer_1.1-3 fitdistrplus_1.1-11
[85] Rsamtools_2.14.0 cli_3.6.2
[87] listenv_0.9.1 patchwork_1.2.0
[89] pbapply_1.7-2 MASS_7.3-60.0.1
[91] tidyselect_1.2.1 stringi_1.8.3
[93] yaml_2.3.8 BiocSingular_1.14.0
[95] locfit_1.5-9.9 tools_4.2.3
[97] timechange_0.3.0 future.apply_1.11.2
[99] parallel_4.2.3 uuid_1.2-0
[101] metapod_1.6.0 farver_2.1.1
[103] Rtsne_0.17 digest_0.6.35
[105] BiocManager_1.30.22 shiny_1.8.1.1
[107] BiocVersion_3.16.0 later_1.3.2
[109] RcppAnnoy_0.0.22 WriteXLS_6.5.0
[111] httr_1.4.7 AnnotationDbi_1.60.2
[113] colorspace_2.1-0 XML_3.99-0.16.1
[115] tensor_1.5 reticulate_1.36.1
[117] splines_4.2.3 uwot_0.2.2
[119] statmod_1.5.0 spatstat.utils_3.0-4
[121] xgboost_1.7.7.1 plotly_4.10.4
[123] xtable_1.8-4 jsonlite_1.8.8
[125] R6_2.5.1 pillar_1.9.0
[127] htmltools_0.5.8.1 mime_0.12
[129] glue_1.7.0 fastmap_1.1.1
[131] BiocParallel_1.32.6 BiocNeighbors_1.16.0
[133] interactiveDisplayBase_1.36.0 codetools_0.2-20
[135] utf8_1.2.4 lattice_0.22-6
[137] spatstat.sparse_3.0-3 curl_5.2.1
[139] leiden_0.4.3.1 survival_3.6-4
[141] limma_3.54.2 repr_1.1.7
[143] munsell_0.5.1 GenomeInfoDbData_1.2.9
[145] reshape2_1.4.4