timoast
commented
1 month ago The CoveragePlot function requires access to a fragment file. If you move the object to a different computer you need to also move the fragment file and fragment file index, and update the path to the file. See here: https://stuartlab.org/signac/articles/data_structures#changing-the-fragment-file-path-in-an-existing-fragment-object
nelmari
After adding the motifs to a seurat object I saved it as an RDS to access more easily. I opened it in another computer (same version of Signac and Seurat but SeuratObjects is 5.0.1 instead of 5.0.2) and I am able to use the object to generate plots without issues. However, I am not able to run CoveragePlot when I open the same object in the computer I created the object. It shows: "Error: TabixFile: Fragment file is not indexed."
I verified and it does the same with multiple RDS files I have generated over time, although they open fine in another computer. Below is my sessioninfo from the computer with issues:
R version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] TFBSTools_1.40.0 Seurat_5.0.3 Signac_1.13.0 SeuratObject_5.0.2 [5] sp_2.1-4
loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.3
[3] later_1.3.2 BiocIO_1.12.0
[5] bitops_1.0-7 cellranger_1.1.0
[7] R.oo_1.26.0 tibble_3.2.1
[9] polyclip_1.10-6 XML_3.99-0.16.1
[11] DirichletMultinomial_1.44.0 fastDummies_1.7.3
[13] lifecycle_1.0.4 globals_0.16.3
[15] lattice_0.22-6 MASS_7.3-60.0.1
[17] magrittr_2.0.3 plotly_4.10.4
[19] yaml_2.3.8 httpuv_1.6.15
[21] sctransform_0.4.1 spam_2.10-0
[23] spatstat.sparse_3.0-3 reticulate_1.36.1
[25] cowplot_1.1.3 pbapply_1.7-2
[27] DBI_1.2.2 CNEr_1.38.0
[29] RColorBrewer_1.1-3 abind_1.4-5
[31] zlibbioc_1.48.2 Rtsne_0.17
[33] GenomicRanges_1.54.1 R.utils_2.12.3
[35] purrr_1.0.2 BiocGenerics_0.48.1
[37] RCurl_1.98-1.14 pracma_2.4.4
[39] GenomeInfoDbData_1.2.11 IRanges_2.36.0
[41] S4Vectors_0.40.2 ggrepel_0.9.5
[43] irlba_2.3.5.1 listenv_0.9.1
[45] spatstat.utils_3.0-4 seqLogo_1.68.0
[47] goftest_1.2-3 RSpectra_0.16-1
[49] annotate_1.80.0 spatstat.random_3.2-3
[51] fitdistrplus_1.1-11 parallelly_1.37.1
[53] leiden_0.4.3.1 codetools_0.2-19
[55] DelayedArray_0.28.0 RcppRoll_0.3.0
[57] tidyselect_1.2.1 ggseqlogo_0.2
[59] matrixStats_1.3.0 stats4_4.3.3
[61] spatstat.explore_3.2-7 GenomicAlignments_1.38.2
[63] jsonlite_1.8.8 progressr_0.14.0
[65] ggridges_0.5.6 survival_3.5-8
[67] tools_4.3.3 TFMPvalue_0.0.9
[69] ica_1.0-3 Rcpp_1.0.12
[71] glue_1.7.0 gridExtra_2.3
[73] SparseArray_1.2.4 MatrixGenerics_1.14.0
[75] GenomeInfoDb_1.38.8 dplyr_1.1.4
[77] withr_3.0.0 fastmap_1.1.1
[79] fansi_1.0.6 caTools_1.18.2
[81] digest_0.6.35 R6_2.5.1
[83] mime_0.12 colorspace_2.1-0
[85] GO.db_3.18.0 scattermore_1.2
[87] poweRlaw_0.80.0 gtools_3.9.5
[89] tensor_1.5 spatstat.data_3.0-4
[91] RSQLite_2.3.6 R.methodsS3_1.8.2
[93] utf8_1.2.4 tidyr_1.3.1
[95] generics_0.1.3 data.table_1.15.4
[97] rtracklayer_1.62.0 httr_1.4.7
[99] htmlwidgets_1.6.4 S4Arrays_1.2.1
[101] uwot_0.2.2 pkgconfig_2.0.3
[103] gtable_0.3.5 blob_1.2.4
[105] lmtest_0.9-40 XVector_0.42.0
[107] htmltools_0.5.8.1 dotCall64_1.1-1
[109] scales_1.3.0 Biobase_2.62.0
[111] png_0.1-8 rstudioapi_0.16.0
[113] tzdb_0.4.0 reshape2_1.4.4
[115] rjson_0.2.21 nlme_3.1-164
[117] zoo_1.8-12 cachem_1.0.8
[119] stringr_1.5.1 KernSmooth_2.23-22
[121] parallel_4.3.3 miniUI_0.1.1.1
[123] AnnotationDbi_1.64.1 restfulr_0.0.15
[125] pillar_1.9.0 grid_4.3.3
[127] vctrs_0.6.5 RANN_2.6.1
[129] promises_1.3.0 xtable_1.8-4
[131] cluster_2.1.6 readr_2.1.5
[133] cli_3.6.2 compiler_4.3.3
[135] Rsamtools_2.18.0 rlang_1.1.3
[137] crayon_1.5.2 future.apply_1.11.2
[139] plyr_1.8.9 stringi_1.8.4
[141] viridisLite_0.4.2 deldir_2.0-4
[143] BiocParallel_1.36.0 munsell_0.5.1
[145] Biostrings_2.70.3 lazyeval_0.2.2
[147] spatstat.geom_3.2-9 Matrix_1.6-5
[149] BSgenome_1.70.2 RcppHNSW_0.6.0
[151] hms_1.1.3 patchwork_1.2.0
[153] bit64_4.0.5 future_1.33.2
[155] ggplot2_3.5.1 KEGGREST_1.42.0
[157] shiny_1.8.1.1 SummarizedExperiment_1.32.0 [159] ROCR_1.0-11 igraph_2.0.3
[161] memoise_2.0.1 fastmatch_1.1-4
[163] bit_4.0.5 readxl_1.4.3