-
-
Notifications
You must be signed in to change notification settings - Fork 14
Open
Labels
SeuratIssues related to Seurat object conversionIssues related to Seurat object conversion
Description
Example:
library(anndataR)
adata <- AnnData(X = matrix(nrow = 10, ncol = 0))
adata$as_Seurat()
#> Warning: No "counts" or "data" layer found in `names(layers_mapping)`, this may lead to
#> unexpected results when using the resulting <Seurat> object.
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
#> Error: No feature overlap between existing object and new layer data
Created on 2025-09-25 with reprex v2.1.1
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.5.1 (2025-06-13)
#> os Ubuntu 24.04.3 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_AU:en
#> collate en_AU.UTF-8
#> ctype en_AU.UTF-8
#> tz Europe/Berlin
#> date 2025-09-25
#> pandoc 3.6.3 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
#> quarto 1.7.32 @ /usr/local/bin/quarto
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> abind 1.4-8 2024-09-12 [1] RSPM
#> anndataR * 0.99.2 2025-09-25 [1] Bioconductor
#> cli 3.6.5 2025-04-23 [1] RSPM
#> cluster 2.1.8.1 2025-03-12 [2] CRAN (R 4.5.1)
#> codetools 0.2-20 2024-03-31 [2] CRAN (R 4.5.1)
#> cowplot 1.2.0 2025-07-07 [1] RSPM
#> data.table 1.17.8 2025-07-10 [1] RSPM
#> deldir 2.0-4 2024-02-28 [1] RSPM
#> digest 0.6.37 2024-08-19 [1] RSPM
#> dotCall64 1.2 2024-10-04 [1] RSPM
#> dplyr 1.1.4 2023-11-17 [1] RSPM
#> evaluate 1.0.4 2025-06-18 [1] RSPM
#> farver 2.1.2 2024-05-13 [1] RSPM
#> fastDummies 1.7.5 2025-01-20 [1] RSPM
#> fastmap 1.2.0 2024-05-15 [1] RSPM
#> fitdistrplus 1.2-4 2025-07-03 [1] RSPM
#> fs 1.6.6 2025-04-12 [1] RSPM
#> future 1.67.0 2025-07-29 [1] RSPM
#> future.apply 1.20.0 2025-06-06 [1] RSPM
#> generics 0.1.4 2025-05-09 [1] RSPM
#> ggplot2 3.5.2 2025-04-09 [1] RSPM
#> ggrepel 0.9.6 2024-09-07 [1] RSPM
#> ggridges 0.5.6 2024-01-23 [1] RSPM
#> globals 0.18.0 2025-05-08 [1] RSPM
#> glue 1.8.0 2024-09-30 [1] RSPM
#> goftest 1.2-3 2021-10-07 [1] RSPM
#> gridExtra 2.3 2017-09-09 [1] RSPM
#> gtable 0.3.6 2024-10-25 [1] RSPM
#> htmltools 0.5.8.1 2024-04-04 [1] RSPM
#> htmlwidgets 1.6.4 2023-12-06 [1] RSPM
#> httpuv 1.6.16 2025-04-16 [1] RSPM
#> httr 1.4.7 2023-08-15 [1] RSPM
#> ica 1.0-3 2022-07-08 [1] RSPM
#> igraph 2.1.4 2025-01-23 [1] RSPM
#> irlba 2.3.5.1 2022-10-03 [1] RSPM
#> jsonlite 2.0.0 2025-03-27 [1] RSPM
#> KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.5.1)
#> knitr 1.50 2025-03-16 [1] RSPM
#> later 1.4.2 2025-04-08 [1] RSPM
#> lattice 0.22-7 2025-04-02 [1] RSPM
#> lazyeval 0.2.2 2019-03-15 [1] RSPM
#> lifecycle 1.0.4 2023-11-07 [1] RSPM
#> listenv 0.9.1 2024-01-29 [1] RSPM
#> lmtest 0.9-40 2022-03-21 [1] RSPM
#> magrittr 2.0.3 2022-03-30 [1] RSPM
#> MASS 7.3-65 2025-02-28 [2] CRAN (R 4.5.1)
#> Matrix 1.7-3 2025-03-11 [2] CRAN (R 4.5.1)
#> matrixStats 1.5.0 2025-01-07 [1] RSPM
#> mime 0.13 2025-03-17 [1] RSPM
#> miniUI 0.1.2 2025-04-17 [1] RSPM
#> nlme 3.1-168 2025-03-31 [2] CRAN (R 4.5.1)
#> parallelly 1.45.1 2025-07-24 [1] RSPM
#> patchwork 1.3.1 2025-06-21 [1] RSPM
#> pbapply 1.7-4 2025-07-20 [1] RSPM
#> pillar 1.11.0 2025-07-04 [1] RSPM
#> pkgconfig 2.0.3 2019-09-22 [1] RSPM
#> plotly 4.11.0 2025-06-19 [1] RSPM
#> plyr 1.8.9 2023-10-02 [1] RSPM
#> png 0.1-8 2022-11-29 [1] RSPM
#> polyclip 1.10-7 2024-07-23 [1] RSPM
#> progressr 0.15.1 2024-11-22 [1] RSPM
#> promises 1.3.3 2025-05-29 [1] RSPM
#> purrr 1.1.0 2025-07-10 [1] RSPM
#> R6 2.6.1 2025-02-15 [1] RSPM
#> RANN 2.6.2 2024-08-25 [1] RSPM
#> RColorBrewer 1.1-3 2022-04-03 [1] RSPM
#> Rcpp 1.1.0 2025-07-02 [1] RSPM
#> RcppAnnoy 0.0.22 2024-01-23 [1] RSPM
#> RcppHNSW 0.6.0 2024-02-04 [1] RSPM
#> reprex 2.1.1 2024-07-06 [1] RSPM
#> reshape2 1.4.4 2020-04-09 [1] RSPM
#> reticulate 1.43.0 2025-07-21 [1] RSPM
#> rlang 1.1.6 2025-04-11 [1] RSPM
#> rmarkdown 2.29 2024-11-04 [1] RSPM
#> ROCR 1.0-11 2020-05-02 [1] RSPM
#> RSpectra 0.16-2 2024-07-18 [1] RSPM
#> rstudioapi 0.17.1 2024-10-22 [1] RSPM
#> Rtsne 0.17 2023-12-07 [1] RSPM
#> scales 1.4.0 2025-04-24 [1] RSPM
#> scattermore 1.2 2023-06-12 [1] RSPM
#> sctransform 0.4.2 2025-04-30 [1] RSPM
#> sessioninfo 1.2.3 2025-02-05 [1] RSPM
#> Seurat 5.3.0 2025-04-23 [1] RSPM
#> SeuratObject 5.1.0 2025-04-22 [1] RSPM
#> shiny 1.11.1 2025-07-03 [1] RSPM
#> sp 2.2-0 2025-02-01 [1] RSPM
#> spam 2.11-1 2025-01-20 [1] RSPM
#> spatstat.data 3.1-6 2025-03-17 [1] RSPM
#> spatstat.explore 3.5-2 2025-07-22 [1] RSPM
#> spatstat.geom 3.5-0 2025-07-20 [1] RSPM
#> spatstat.random 3.4-1 2025-05-20 [1] CRAN (R 4.5.0)
#> spatstat.sparse 3.1-0 2024-06-21 [1] RSPM
#> spatstat.univar 3.1-4 2025-07-13 [1] RSPM
#> spatstat.utils 3.1-5 2025-07-17 [1] RSPM
#> stringi 1.8.7 2025-03-27 [1] RSPM
#> stringr 1.5.1 2023-11-14 [1] RSPM
#> survival 3.8-3 2024-12-17 [2] CRAN (R 4.5.1)
#> tensor 1.5.1 2025-06-17 [1] RSPM
#> tibble 3.3.0 2025-06-08 [1] RSPM
#> tidyr 1.3.1 2024-01-24 [1] RSPM
#> tidyselect 1.2.1 2024-03-11 [1] RSPM
#> uwot 0.2.3 2025-02-24 [1] RSPM
#> vctrs 0.6.5 2023-12-01 [1] RSPM
#> viridisLite 0.4.2 2023-05-02 [1] RSPM
#> withr 3.0.2 2024-10-28 [1] RSPM
#> xfun 0.52 2025-04-02 [1] RSPM
#> xtable 1.8-4 2019-04-21 [1] RSPM
#> yaml 2.3.10 2024-07-26 [1] RSPM
#> zoo 1.8-14 2025-04-10 [1] RSPM
#>
#> [1] /home/luke/R/x86_64-pc-linux-gnu-library/4.5
#> [2] /opt/R/4.5.1/lib/R/library
#> * ── Packages attached to the search path.
#>
#> ──────────────────────────────────────────────────────────────────────────────
It might not be possible to create a Seurat
with this shape, in which case we should add a check and give a more useful error.
Metadata
Metadata
Assignees
Labels
SeuratIssues related to Seurat object conversionIssues related to Seurat object conversion