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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Error: is(object = cds, class2 = "CellDataSet") is not TRUE #1661

Closed Raghav1881 closed 6 months ago

Raghav1881 commented 6 months ago

Hello, I am aware of issue #721 and followed the instructions, but I have been having a problem with trying to create co-accessibility networks with my data. It appears like the class the as.cell_data_set function creates a 'cell_data_set' object, whereas make_cicero_cds expects a 'CellDataSet' object. I am not sure if it is a version compatibility issue with SeuratWrappers or something else that could be causing issues.

hip.cds <- as.cell_data_set(x = oligo)
View(hip.cds)
class(hip.cds)
[1] "cell_data_set"
attr(,"package")
[1] "monocle3"
hip.cicero <- make_cicero_cds(hip.cds, reduced_coordinates = reducedDims(hip.cds)$UMAP)
Error: is(object = cds, class2 = "CellDataSet") is not TRUE
Session info ```R sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 22.04.4 LTS Matrix products: default BLAS/LAPACK: /home/raghav1881/miniconda3/envs/R-4.2/lib/libopenblasp-r0.3.25.so locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 [4] LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid splines stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] dplyr_1.1.4 chromVARmotifs_0.2.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3 [4] BSgenome_1.66.3 rtracklayer_1.58.0 Biostrings_2.66.0 [7] XVector_0.38.0 patchwork_1.1.1 SeuratWrappers_0.2.0 [10] cicero_1.3.9 Gviz_1.42.1 monocle_2.26.0 [13] VennDiagram_1.7.3 futile.logger_1.4.3 Signac_1.10.0 [16] Seurat_4.4.0 TFBSTools_1.36.0 DDRTree_0.1.5 [19] irlba_2.3.5.1 VGAM_1.1-10 ggplot2_3.4.4 [22] Biobase_2.58.0 Matrix_1.6-5 SeuratObject_4.1.4 [25] sp_2.1-2 GenomicRanges_1.50.0 GenomeInfoDb_1.39.6 [28] IRanges_2.32.0 S4Vectors_0.36.0 BiocGenerics_0.44.0 loaded via a namespace (and not attached): [1] rsvd_1.0.5 Hmisc_5.1-1 ica_1.0-2 [4] RcppRoll_0.3.0 ps_1.7.0 Rsamtools_2.14.0 [7] foreach_1.5.2 lmtest_0.9-40 crayon_1.5.1 [10] MASS_7.3-57 nlme_3.1-157 backports_1.4.1 [13] qlcMatrix_0.9.7 monocle3_1.0.0 GOSemSim_2.24.0 [16] rlang_1.1.3 HDO.db_0.99.1 ROCR_1.0-11 [19] callr_3.7.3 limma_3.54.0 filelock_1.0.3 [22] BiocParallel_1.32.5 rjson_0.2.21 CNEr_1.34.0 [25] bit64_4.0.5 glue_1.6.2 pheatmap_1.0.12 [28] poweRlaw_0.80.0 sctransform_0.4.1 processx_3.8.3 [31] parallel_4.2.3 vipor_0.4.7 spatstat.sparse_3.0-3 [34] AnnotationDbi_1.60.2 DOSE_3.24.2 spatstat.geom_3.2-7 [37] tidyselect_1.2.1 SummarizedExperiment_1.28.0 fitdistrplus_1.1-11 [40] XML_3.99-0.16.1 tidyr_1.3.1 zoo_1.8-10 [43] GenomicAlignments_1.34.1 xtable_1.8-4 magrittr_2.0.3 [46] evaluate_0.15 cli_3.6.2 zlibbioc_1.44.0 [49] rstudioapi_0.13 miniUI_0.1.1.1 rpart_4.1.16 [52] fastmatch_1.1-4 ensembldb_2.22.0 lambda.r_1.2.4 [55] shiny_1.7.1 xfun_0.31 clue_0.3-65 [58] leidenbase_0.1.27 pkgbuild_1.4.3 cluster_2.1.3 [61] caTools_1.18.2 KEGGREST_1.38.0 tibble_3.2.1 [64] ggrepel_0.9.5 biovizBase_1.46.0 listenv_0.8.0 [67] TFMPvalue_0.0.9 png_0.1-7 future_1.26.1 [70] withr_2.5.0 bitops_1.0-7 slam_0.1-50 [73] plyr_1.8.7 sparsesvd_0.2-2 AnnotationFilter_1.22.0 [76] pracma_2.4.4 pillar_1.9.0 GlobalOptions_0.1.2 [79] cachem_1.0.6 GenomicFeatures_1.50.4 GetoptLong_1.0.5 [82] vctrs_0.6.5 ellipsis_0.3.2 generics_0.1.3 [85] tools_4.2.3 foreign_0.8-82 beeswarm_0.4.0 [88] munsell_0.5.0 fgsea_1.24.0 DelayedArray_0.24.0 [91] fastmap_1.1.0 HSMMSingleCell_1.18.0 compiler_4.2.3 [94] abind_1.4-5 httpuv_1.6.5 plotly_4.10.0 [97] GenomeInfoDbData_1.2.9 gridExtra_2.3 lattice_0.20-45 [100] deldir_1.0-6 utf8_1.2.2 later_1.3.0 [103] BiocFileCache_2.6.1 jsonlite_1.8.0 scales_1.2.0 [106] docopt_0.7.1 pbapply_1.5-0 lazyeval_0.2.2 [109] promises_1.2.0.1 doParallel_1.0.17 latticeExtra_0.6-30 [112] R.utils_2.12.3 goftest_1.2-3 spatstat.utils_3.0-4 [115] reticulate_1.25 checkmate_2.3.1 rmarkdown_2.14 [118] openxlsx_4.2.5.2 cowplot_1.1.1 textshaping_0.3.7 [121] Rtsne_0.16 dichromat_2.0-0.1 uwot_0.1.16 [124] igraph_1.6.0 survival_3.3-1 yaml_2.3.5 [127] systemfonts_1.0.5 htmltools_0.5.2 memoise_2.0.1 [130] VariantAnnotation_1.44.1 BiocIO_1.8.0 viridisLite_0.4.0 [133] digest_0.6.29 assertthat_0.2.1 mime_0.12 [136] rappdirs_0.3.3 futile.options_1.0.1 RSQLite_2.3.4 [139] future.apply_1.9.0 remotes_2.4.2.1 data.table_1.14.2 [142] blob_1.2.3 R.oo_1.26.0 ragg_1.2.7 [145] fastICA_1.2-4 Formula_1.2-5 labeling_0.4.2 [148] ProtGenerics_1.30.0 RCurl_1.98-1.13 hms_1.1.1 [151] colorspace_2.0-3 base64enc_0.1-3 BiocManager_1.30.22 [154] ggbeeswarm_0.7.2 shape_1.4.6 ggrastr_1.0.2 [157] nnet_7.3-17 Rcpp_1.0.12 RANN_2.6.1 [160] circlize_0.4.15 ggseqlogo_0.2 fansi_1.0.3 [163] tzdb_0.3.0 parallelly_1.31.1 R6_2.5.1 [166] ggridges_0.5.3 lifecycle_1.0.4 formatR_1.12 [169] zip_2.3.0 curl_5.2.0 leiden_0.4.3.1 [172] qvalue_2.30.0 desc_1.4.3 RcppAnnoy_0.0.19 [175] RColorBrewer_1.1-3 iterators_1.0.14 spatstat.explore_3.2-5 [178] stringr_1.5.1 htmlwidgets_1.5.4 polyclip_1.10-0 [181] biomaRt_2.54.1 purrr_1.0.2 seqLogo_1.64.0 [184] ComplexHeatmap_2.14.0 globals_0.15.0 htmlTable_2.4.2 [187] spatstat.random_3.2-2 progressr_0.10.0 codetools_0.2-18 [190] matrixStats_0.62.0 GO.db_3.16.0 gtools_3.9.2.1 [193] prettyunits_1.1.1 SingleCellExperiment_1.20.0 dbplyr_2.1.1 [196] R.methodsS3_1.8.2 gtable_0.3.0 DBI_1.1.2 [199] tensor_1.5 httr_1.4.3 KernSmooth_2.23-20 [202] stringi_1.8.3 progress_1.2.2 reshape2_1.4.4 [205] farver_2.1.0 annotate_1.76.0 viridis_0.6.4 [208] xml2_1.3.3 combinat_0.0-8 restfulr_0.0.15 [211] interp_1.1-6 readr_2.1.2 scattermore_1.2 [214] bit_4.0.4 jpeg_0.1-10 MatrixGenerics_1.10.0 [217] spatstat.data_3.0-3 pkgconfig_2.0.3 DirichletMultinomial_1.40.0 [220] knitr_1.39 ```
Raghav1881 commented 6 months ago

Package attachment issues, fixed.