DimPlot error with Seurat v5

[udhaya2991]

Hi, I am getting an following error when I tried to plot the UMAP using DimPlot function from seurat v5. I have used several analysis with seurat and used the same function many times with the previous seurat version (v4 not sure of the subversion). Your suggestion or help will be much appreciated. 1) multiomic data (joint snRNA+snATAC-seq) analysed using seurat v4 and signac. 2) I did not have any problem analyzing the same sample before, but now I have opened the same environment that I saved earlier with all the objects and parameters with seurat v4 in seurat v5, the dimplot function doesnt work.

Error: Error in Ops.data.frame(guide_loc, panel_loc) : '==' only defined for equally-sized data frames

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. See this previous issue from a few months ago https://github.com/satijalab/seurat/issues/8170. I would recommend updating ggplot2 and seeing if issue persists. If it does can you please provide the full code that you are running as well as the output of sessionInfo()?

Best, Sam

[udhaya2991]

Hi samuel,

Thank you for your response. I have tried as per the #8170, still same error. command: DimPlot(seurat_integrated, reduction = "umap_rna", label = TRUE, pt.size = 0.2) error: Error in Ops.data.frame(guide_loc, panel_loc) : '==' only defined for equally-sized data frames

I have provided the session info below.

sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages: [1] calibrate_1.7.7 MASS_7.3-58.2 celldex_1.8.0
[4] SignacX_2.2.5 AnnotationHub_3.6.0 BiocFileCache_2.6.1
[7] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[10] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[13] tidyr_1.3.0 tibble_3.2.1 tidyverse_2.0.0
[16] dbplyr_2.4.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.66.3
[19] Biostrings_2.66.0 XVector_0.38.0 rtracklayer_1.58.0
[22] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.22.0 AnnotationFilter_1.22.0
[25] GenomicFeatures_1.50.4 AnnotationDbi_1.60.2 Signac_1.12.0
[28] scater_1.26.1 ggplot2_3.5.0.9000 scran_1.26.2
[31] scuttle_1.8.4 SingleCellExperiment_1.20.1 SingleCellMultiModal_1.10.1
[34] MultiAssayExperiment_1.24.0 SummarizedExperiment_1.28.0 Biobase_2.58.0
[37] MatrixGenerics_1.10.0 matrixStats_1.2.0 Seurat_5.0.1
[40] SeuratObject_5.0.1 sp_2.1-3 GenomicRanges_1.50.2
[43] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2
[46] BiocGenerics_0.44.0

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 scattermore_1.2 SpatialExperiment_1.8.1 R.methodsS3_1.8.2
[5] bit64_4.0.5 irlba_2.3.5.1 DelayedArray_0.24.0 R.utils_2.12.3
[9] data.table_1.15.0 KEGGREST_1.38.0 RCurl_1.98-1.10 generics_0.1.3
[13] ScaledMatrix_1.6.0 callr_3.7.5 cowplot_1.1.1 usethis_2.1.6
[17] RSQLite_2.3.5 RANN_2.6.1 future_1.33.1 tzdb_0.4.0
[21] bit_4.0.5 spatstat.data_3.0-4 xml2_1.3.6 httpuv_1.6.14
[25] viridis_0.6.5 hms_1.1.3 promises_1.2.0.1 fansi_1.0.6
[29] restfulr_0.0.15 progress_1.2.3 igraph_1.5.1 DBI_1.2.2
[33] htmlwidgets_1.6.4 spatstat.geom_3.2-9 ellipsis_0.3.2 RSpectra_0.16-1
[37] biomaRt_2.54.1 deldir_1.0-6 sparseMatrixStats_1.10.0 vctrs_0.6.5
[41] remotes_2.4.2.1 ROCR_1.0-11 abind_1.4-5 cachem_1.0.8
[45] withr_2.5.0 progressr_0.14.0 presto_1.0.0 sctransform_0.4.1
[49] GenomicAlignments_1.34.1 prettyunits_1.1.1 goftest_1.2-3 cluster_2.1.4
[53] ExperimentHub_2.6.0 dotCall64_1.1-1 lazyeval_0.2.2 crayon_1.5.2
[57] spatstat.explore_3.2-6 labeling_0.4.2 edgeR_3.40.2 pkgconfig_2.0.3
[61] pkgload_1.3.2 ProtGenerics_1.30.0 nlme_3.1-162 vipor_0.4.5
[65] devtools_2.4.5 rlang_1.1.3 globals_0.16.2 lifecycle_1.0.3
[69] miniUI_0.1.1.1 filelock_1.0.3 fastDummies_1.7.3 rsvd_1.0.5
[73] rprojroot_2.0.4 polyclip_1.10-4 RcppHNSW_0.6.0 lmtest_0.9-40
[77] Matrix_1.6-5 Rhdf5lib_1.20.0 zoo_1.8-11 beeswarm_0.4.0
[81] processx_3.8.0 ggridges_0.5.4 png_0.1-8 viridisLite_0.4.2
[85] rjson_0.2.21 bitops_1.0-7 R.oo_1.26.0 KernSmooth_2.23-20
[89] spam_2.10-0 rhdf5filters_1.10.1 blob_1.2.4 DelayedMatrixStats_1.20.0
[93] parallelly_1.37.0 spatstat.random_3.2-2 beachmat_2.14.2 scales_1.3.0
[97] memoise_2.0.1 magrittr_2.0.3 plyr_1.8.9 ica_1.0-3
[101] zlibbioc_1.44.0 compiler_4.2.1 dqrng_0.3.0 BiocIO_1.8.0
[105] RColorBrewer_1.1-3 fitdistrplus_1.1-8 Rsamtools_2.14.0 cli_3.6.2
[109] urlchecker_1.0.1 listenv_0.9.1 ps_1.7.2 patchwork_1.1.2
[113] pbapply_1.7-2 tidyselect_1.2.0 stringi_1.8.3 yaml_2.3.8
[117] BiocSingular_1.14.0 locfit_1.5-9.7 ggrepel_0.9.5 grid_4.2.1
[121] timechange_0.3.0 fastmatch_1.1-4 tools_4.2.1 future.apply_1.11.1
[125] parallel_4.2.1 rstudioapi_0.14 bluster_1.8.0 metapod_1.6.0
[129] gridExtra_2.3 farver_2.1.1 Rtsne_0.17 DropletUtils_1.18.1
[133] digest_0.6.34 BiocManager_1.30.19 shiny_1.8.0 Rcpp_1.0.12
[137] BiocVersion_3.16.0 later_1.3.2 RcppAnnoy_0.0.22 httr_1.4.7
[141] colorspace_2.1-0 fs_1.6.3 XML_3.99-0.16.1 tensor_1.5
[145] reticulate_1.35.0 splines_4.2.1 uwot_0.1.14 RcppRoll_0.3.0
[149] statmod_1.5.0 spatstat.utils_3.0-4 sessioninfo_1.2.2 plotly_4.10.4
[153] xtable_1.8-4 jsonlite_1.8.8 R6_2.5.1 profvis_0.3.7
[157] pillar_1.9.0 htmltools_0.5.7 mime_0.12 glue_1.6.2
[161] fastmap_1.1.1 BiocParallel_1.32.6 BiocNeighbors_1.16.0 interactiveDisplayBase_1.36.0 [165] codetools_0.2-19 pkgbuild_1.4.0 utf8_1.2.4 lattice_0.20-45
[169] spatstat.sparse_3.0-3 curl_5.2.0 ggbeeswarm_0.7.1 leiden_0.4.3
[173] magick_2.8.3 survival_3.5-3 limma_3.54.2 desc_1.4.2
[177] munsell_0.5.0 rhdf5_2.42.1 GenomeInfoDbData_1.2.9 HDF5Array_1.26.0
[181] reshape2_1.4.4 gtable_0.3.4

[samuel-marsh]

Hi,

so it appears you still have a dev version of ggplot2 installed. I would suggest removing that and installing 3.5.0 from CRAN and see if that solves issue.

Best, Sam

[udhaya2991]

Hi samuel, I removed the development version of ggplot2 and installed ggplot2 v3.5.0. Now, the dimPlot function from seurat works. thank you

[samuel-marsh]

Great!

[z-bluesky]

Hi! I get the same error when I use the vlnplot and dimplot functions in the Seurat package. I run very simple code, but I get this error. My code is as follows： VlnPlot(scRNAlist[[i]], features = c("nFeature_RNA")) Error in Ops.data.frame(guide_loc, panel_loc) : ‘==’ only defined for equally-sized data frames But I use this line of code, restart the session and it works, finally!！！！ remotes::install_github("thomasp85/patchwork")

[Ruthwww]

Hi! I get the same error when I use the vlnplot and dimplot functions in the Seurat package. I run very simple code, but I get this error. My code is as follows： VlnPlot(scRNAlist[[i]], features = c("nFeature_RNA")) Error in Ops.data.frame(guide_loc, panel_loc) : ‘==’ only defined for equally-sized data frames But I use this line of code, restart the session and it works, finally!！！！ remotes::install_github("thomasp85/patchwork")

Thank you so much, I also solved this problem by this way~