kstreet13
commented
2 years ago Hi @HousLi ,
Thanks for the question! This is expected behavior with newer versions of the package, as the default output format has changed from a SlingshotDataSet to a PseudotimeOrdering (which does not contain a lineages slot). In general, I would advise against using the @ operator with either of these object types and instead use the more flexible accessor functions. In this case, slingLineages(lnes) should work regardless of what type of object it is (including SingleCellExperiment objects).
Best, Kelly
HousLi
Hello,
I was trying to run slingshot functions on Rstudio 4.1.0, but I got an error when running the following commands,
Below is my session info,
Matrix products: default BLAS: /usr/lib64/libblas.so.3.4.2 LAPACK: /usr/lib64/liblapack.so.3.4.2
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] splines parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] scRepertoire_1.3.2 corrplot_0.90 ggthemes_4.2.4
[4] ggbeeswarm_0.6.0 Polychrome_1.3.1 scater_1.20.1
[7] ggplot2_3.3.5 scuttle_1.2.1 gam_1.20
[10] foreach_1.5.1 slingshot_2.1.1 TrajectoryUtils_1.0.0
[13] princurve_2.1.6 SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0 [16] Biobase_2.52.0 GenomicRanges_1.44.0 GenomeInfoDb_1.28.4
[19] IRanges_2.26.0 S4Vectors_0.30.2 BiocGenerics_0.38.0
[22] MatrixGenerics_1.4.3 matrixStats_0.61.0 SeuratObject_4.0.2
[25] Seurat_4.0.4
loaded via a namespace (and not attached): [1] VGAM_1.1-5 plyr_1.8.6 igraph_1.2.6
[4] lazyeval_0.2.2 powerTCR_1.12.0 BiocParallel_1.26.2
[7] listenv_0.8.0 scattermore_0.7 digest_0.6.28
[10] htmltools_0.5.2 viridis_0.6.1 ggalluvial_0.12.3
[13] fansi_0.5.0 truncdist_1.0-2 magrittr_2.0.1
[16] ScaledMatrix_1.0.0 doParallel_1.0.16 tensor_1.5
[19] cluster_2.1.2 ROCR_1.0-11 remotes_2.4.1
[22] globals_0.14.0 spatstat.sparse_2.0-0 colorspace_2.0-2
[25] ggrepel_0.9.1 dplyr_1.0.7 crayon_1.4.1
[28] RCurl_1.98-1.5 jsonlite_1.7.2 spatstat.data_2.1-0
[31] survival_3.2-13 zoo_1.8-9 iterators_1.0.13
[34] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0
[37] zlibbioc_1.38.0 XVector_0.32.0 leiden_0.3.9
[40] DelayedArray_0.18.0 evd_2.3-3 BiocSingular_1.8.1
[43] future.apply_1.8.1 SparseM_1.81 abind_1.4-5
[46] scales_1.1.1 DBI_1.1.1 miniUI_0.1.1.1
[49] Rcpp_1.0.7 viridisLite_0.4.0 xtable_1.8-4
[52] reticulate_1.22 spatstat.core_2.3-0 rsvd_1.0.5
[55] htmlwidgets_1.5.4 httr_1.4.2 RColorBrewer_1.1-2
[58] ellipsis_0.3.2 ica_1.0-2 pkgconfig_2.0.3
[61] uwot_0.1.10 deldir_1.0-5 utf8_1.2.2
[64] tidyselect_1.1.1 rlang_0.4.11 reshape2_1.4.4
[67] later_1.3.0 munsell_0.5.0 tools_4.1.0
[70] generics_0.1.0 ggridges_0.5.3 stringr_1.4.0
[73] fastmap_1.1.0 goftest_1.2-3 evmix_2.12
[76] fitdistrplus_1.1-6 purrr_0.3.4 RANN_2.6.1
[79] pbapply_1.5-0 future_1.22.1 nlme_3.1-153
[82] sparseMatrixStats_1.4.2 mime_0.12 compiler_4.1.0
[85] beeswarm_0.4.0 plotly_4.10.0 png_0.1-7
[88] spatstat.utils_2.2-0 tibble_3.1.5 gsl_2.1-7
[91] stringi_1.7.5 cubature_2.0.4.2 lattice_0.20-45
[94] Matrix_1.3-4 permute_0.9-5 vegan_2.5-7
[97] vctrs_0.3.8 stringdist_0.9.8 pillar_1.6.3
[100] lifecycle_1.0.1 spatstat.geom_2.2-2 lmtest_0.9-38
[103] RcppAnnoy_0.0.19 BiocNeighbors_1.10.0 data.table_1.14.2
[106] cowplot_1.1.1 bitops_1.0-7 irlba_2.3.3
[109] httpuv_1.6.3 patchwork_1.1.1 R6_2.5.1
[112] promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3
[115] vipor_0.4.5 parallelly_1.28.1 codetools_0.2-18
[118] MASS_7.3-54 assertthat_0.2.1 withr_2.4.2
[121] sctransform_0.3.2 GenomeInfoDbData_1.2.6 mgcv_1.8-36
[124] grid_4.1.0 rpart_4.1-15 beachmat_2.8.1
[127] tidyr_1.1.4 DelayedMatrixStats_1.14.3 Rtsne_0.15
[130] scatterplot3d_0.3-41 shiny_1.7.1
Is this due to a compatibility issue? Can you help me resolve this problem?
Thanks a lot ! Li