Hi There,
thanks for the great tool, I was trying to plot a gene with multiple genomic locations supplying a GRanges object but get an error that Granges does not support [[, as.list, lapply at the moment
the cause is that whilst the GRanges object has a length > 1 it can only be accessed by single brackets and not like a list or vector, thus an additional check is required when dealing with GRanges objects or to transform those into a list.
so I guess this can be circumvented by supplying a GRangesList or by calling GRangesToString but would need an update of the function documentation
# gene has two isoforms on two chromosomes, create separate plots as otherwise a single chromsome is plotted with max span of coordinates
# get gene coordinates in GRanges format
gene_idx <- which(so_neural@assays$ATAC@annotation$gene_name == 'SLC5A7' & so_neural@assays$ATAC@annotation$type == 'cds')
plot_regions <- GRanges(so_neural@assays$ATAC@annotation[c(gene_idx[1],gene_idx[length(gene_idx)]),])
CoveragePlot(so_neural,
assay = 'ATAC',
expression.assay = 'SCT',
region = plot_regions,
feature = 'SLC5A7',
group.by = 'predicted.id.neural',
extend.upstream = 1000,
extend.downstream = 1000,
peaks = TRUE
)Error in getListElement(x, i, ...) :
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
> sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /nfs/scistore07/clustersw/debian/bookworm/R/4.5.2/lib/R/lib/libRblas.so
LAPACK: /nfs/scistore07/clustersw/debian/bookworm/R/4.5.2/lib/R/lib/libRlapack.so; LAPACK version 3.12.1
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Vienna
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomeInfoDb_1.46.0 future_1.67.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3
[4] BSgenome.Drerio.UCSC.danRer11_1.4.2 BSgenome_1.78.0 rtracklayer_1.70.0
[7] BiocIO_1.20.0 Biostrings_2.78.0 XVector_0.50.0
[10] GenomicRanges_1.62.0 Seqinfo_1.0.0 IRanges_2.44.0
[13] S4Vectors_0.48.0 motifmatchr_1.32.0 TFBSTools_1.48.0
[16] JASPAR2024_0.99.7 chromVAR_1.32.0 AnnotationHub_4.0.0
[19] BiocFileCache_3.0.0 dbplyr_2.5.1 BiocGenerics_0.56.0
[22] generics_0.1.4 ggplot2_4.0.0 Signac_1.16.0
[25] dplyr_1.1.4 CyteTypeR_0.1.5 Seurat_5.3.1
[28] SeuratObject_5.2.0 sp_2.2-0
loaded via a namespace (and not attached):
[1] matrixStats_1.5.0 spatstat.sparse_3.1-0 bitops_1.0-9
[4] DirichletMultinomial_1.52.0 httr_1.4.7 RColorBrewer_1.1-3
[7] tools_4.5.2 sctransform_0.4.2 utf8_1.2.6
[10] R6_2.6.1 DT_0.34.0 lazyeval_0.2.2
[13] uwot_0.2.3 withr_3.0.2 gridExtra_2.3
[16] clustermq_0.9.9 progressr_0.18.0 textshaping_1.0.4
[19] cli_3.6.5 Biobase_2.70.0 spatstat.explore_3.5-3
[22] fastDummies_1.7.5 labeling_0.4.3 sass_0.4.10
[25] S7_0.2.0 spatstat.data_3.1-9 ggridges_0.5.7
[28] pbapply_1.7-4 Rsamtools_2.26.0 systemfonts_1.3.1
[31] dichromat_2.0-0.1 parallelly_1.45.1 rstudioapi_0.17.1
[34] RSQLite_2.4.3 gtools_3.9.5 ica_1.0-3
[37] spatstat.random_3.4-2 Matrix_1.7-4 logger_0.4.1
[40] abind_1.4-8 lifecycle_1.0.4 yaml_2.3.10
[43] SummarizedExperiment_1.40.0 SparseArray_1.10.1 Rtsne_0.17
[46] glmGamPoi_1.22.0 grid_4.5.2 blob_1.2.4
[49] promises_1.5.0 crayon_1.5.3 pwalign_1.6.0
[52] miniUI_0.1.2 lattice_0.22-7 beachmat_2.26.0
[55] cowplot_1.2.0 cigarillo_1.0.0 KEGGREST_1.50.0
[58] pillar_1.11.1 knitr_1.50 rjson_0.2.23
[61] future.apply_1.20.0 codetools_0.2-20 fastmatch_1.1-6
[64] glue_1.8.0 spatstat.univar_3.1-4 data.table_1.17.8
[67] vctrs_0.6.5 png_0.1-8 spam_2.11-1
[70] gtable_0.3.6 cachem_1.1.0 xfun_0.54
[73] S4Arrays_1.10.0 mime_0.13 survival_3.8-3
[76] RcppRoll_0.3.1 fitdistrplus_1.2-4 ROCR_1.0-11
[79] nlme_3.1-168 bit64_4.6.0-1 filelock_1.0.3
[82] RcppAnnoy_0.0.22 bslib_0.9.0 irlba_2.3.5.1
[85] KernSmooth_2.23-26 otel_0.2.0 seqLogo_1.76.0
[88] DBI_1.2.3 tidyselect_1.2.1 bit_4.6.0
[91] compiler_4.5.2 curl_7.0.0 httr2_1.2.1
[94] DelayedArray_0.36.0 plotly_4.11.0 scales_1.4.0
[97] caTools_1.18.3 lmtest_0.9-40 rappdirs_0.3.3
[100] stringr_1.6.0 digest_0.6.37 goftest_1.2-3
[103] presto_1.0.0 spatstat.utils_3.2-0 rmarkdown_2.30
[106] htmltools_0.5.8.1 pkgconfig_2.0.3 sparseMatrixStats_1.22.0
[109] MatrixGenerics_1.22.0 fastmap_1.2.0 rlang_1.1.6
[112] htmlwidgets_1.6.4 UCSC.utils_1.6.0 shiny_1.11.1
[115] DelayedMatrixStats_1.32.0 farver_2.1.2 jquerylib_0.1.4
[118] zoo_1.8-14 jsonlite_2.0.0 BiocParallel_1.44.0
[121] RCurl_1.98-1.17 magrittr_2.0.4 dotCall64_1.2
[124] patchwork_1.3.2 Rcpp_1.1.0 reticulate_1.44.0
[127] stringi_1.8.7 MASS_7.3-65 plyr_1.8.9
[130] parallel_4.5.2 listenv_0.10.0 ggrepel_0.9.6
[133] deldir_2.0-4 splines_4.5.2 tensor_1.5.1
[136] igraph_2.2.1 spatstat.geom_3.6-0 RcppHNSW_0.6.0
[139] reshape2_1.4.4 pkgload_1.4.1 TFMPvalue_0.0.9
[142] BiocVersion_3.22.0 XML_3.99-0.19 evaluate_1.0.5
[145] BiocManager_1.30.27 tweenr_2.0.3 httpuv_1.6.16
[148] RANN_2.6.2 tidyr_1.3.1 purrr_1.2.0
[151] polyclip_1.10-7 scattermore_1.2 ggforce_0.5.0
[154] xtable_1.8-4 restfulr_0.0.16 RSpectra_0.16-2
[157] later_1.4.4 ragg_1.5.0 viridisLite_0.4.2
[160] tibble_3.3.0 memoise_2.0.1 AnnotationDbi_1.72.0
[163] GenomicAlignments_1.46.0 cluster_2.1.8.1 globals_0.18.0
Hi There,
thanks for the great tool, I was trying to plot a gene with multiple genomic locations supplying a GRanges object but get an error that Granges does not support [[, as.list, lapply at the moment
the cause is that whilst the GRanges object has a length > 1 it can only be accessed by single brackets and not like a list or vector, thus an additional check is required when dealing with GRanges objects or to transform those into a list.
so I guess this can be circumvented by supplying a GRangesList or by calling
GRangesToStringbut would need an update of the function documentation