Error in make_cicero_cds: "Error: is(object = cds, class2 = "CellDataSet") is not TRUE" #721
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Hello, I have a harmony-integrated scATAC-seq dataset in Signac which I converted to a CDS object using class: cell_data_set
dim: 21948 87973
metadata(0):
assays(2): counts logcounts
rownames(21948): AABR07000089.1 Vom2r6 ... Ddx3 Usp9y
rowData names(0):
colnames(87973): Rat_Amygdala_cocaine_high_AAACGAAAGAACGTCG-1
Rat_Amygdala_cocaine_high_AAACGAAAGAGCTACG-1 ...
FTL_464_M986_933000320047174_TTTGTGTGTTCATTTC-1
FTL_464_M986_933000320047174_TTTGTGTTCGCCTTAC-1
colData names(50): orig.ident nCount_peaks ... ident Size_Factor
reducedDimNames(1): UMAP
altExpNames(0):When I run I ran Error: is(object = cds, class2 = "CellDataSet") is not TRUE
Traceback:
1. make_cicero_cds(cds, reduced_coordinates = reducedDims(cds)$UMAP)
2. assertthat::assert_that(is(cds, "CellDataSet"))Here is my session info: R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS release 6.10 (Final)
Matrix products: default
BLAS/LAPACK: /iblm/netapp/home/jezhou/anaconda3/envs/snatac_pipeline/lib/libopenblasp-r0.3.10.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid splines stats4 parallel stats graphics grDevices
[8] utils datasets methods base
other attached packages:
[1] monocle3_1.0.0 SingleCellExperiment_1.12.0
[3] SummarizedExperiment_1.20.0 MatrixGenerics_1.2.0
[5] matrixStats_0.58.0 cicero_1.8.1
[7] Gviz_1.34.1 GenomicRanges_1.42.0
[9] GenomeInfoDb_1.26.0 IRanges_2.24.0
[11] S4Vectors_0.28.0 monocle_2.18.0
[13] DDRTree_0.1.5 irlba_2.3.3
[15] VGAM_1.1-5 Biobase_2.50.0
[17] BiocGenerics_0.36.0 Matrix_1.3-2
[19] patchwork_1.1.1 ggplot2_3.3.3
[21] SeuratWrappers_0.3.0 SeuratObject_4.0.0
[23] Seurat_4.0.0 Signac_1.1.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SnowballC_0.7.0 rtracklayer_1.50.0
[4] pbdZMQ_0.3-5 scattermore_0.7 GGally_2.1.0
[7] R.methodsS3_1.8.1 tidyr_1.1.2 bit64_4.0.5
[10] knitr_1.31 DelayedArray_0.16.0 R.utils_2.10.1
[13] data.table_1.13.6 rpart_4.1-15 RCurl_1.98-1.2
[16] AnnotationFilter_1.14.0 generics_0.1.0 GenomicFeatures_1.42.0
[19] leidenbase_0.1.3 cowplot_1.1.1 RSQLite_2.2.3
[22] RANN_2.6.1 combinat_0.0-8 proxy_0.4-26
[25] future_1.21.0 bit_4.0.4 spatstat.data_2.1-0
[28] xml2_1.3.2 httpuv_1.5.5 assertthat_0.2.1
[31] viridis_0.5.1 xfun_0.20 hms_1.0.0
[34] evaluate_0.14 promises_1.1.1 progress_1.2.2
[37] dbplyr_2.1.0 igraph_1.2.6 DBI_1.1.1
[40] htmlwidgets_1.5.3 sparsesvd_0.2 reshape_0.8.8
[43] purrr_0.3.4 ellipsis_0.3.1 dplyr_1.0.4
[46] backports_1.2.1 biomaRt_2.46.0 deldir_0.2-9
[49] vctrs_0.3.6 remotes_2.4.0 ensembldb_2.14.0
[52] ROCR_1.0-11 abind_1.4-5 cachem_1.0.3
[55] withr_2.4.1 ggforce_0.3.2 BSgenome_1.58.0
[58] checkmate_2.0.0 sctransform_0.3.2 GenomicAlignments_1.26.0
[61] prettyunits_1.1.1 goftest_1.2-2 cluster_2.1.0
[64] IRdisplay_1.0 lazyeval_0.2.2 crayon_1.4.1
[67] pkgconfig_2.0.3 slam_0.1-48 tweenr_1.0.1
[70] nlme_3.1-152 ProtGenerics_1.22.0 nnet_7.3-15
[73] rlang_0.4.10 globals_0.14.0 lifecycle_0.2.0
[76] miniUI_0.1.1.1 BiocFileCache_1.14.0 rsvd_1.0.5
[79] dichromat_2.0-0 polyclip_1.10-0 lmtest_0.9-38
[82] graph_1.68.0 ggseqlogo_0.1 IRkernel_1.1.1
[85] zoo_1.8-8 base64enc_0.1-3 ggridges_0.5.3
[88] pheatmap_1.0.12 png_0.1-7 viridisLite_0.3.0
[91] bitops_1.0-6 R.oo_1.24.0 KernSmooth_2.23-18
[94] Biostrings_2.58.0 blob_1.2.1 stringr_1.4.0
[97] parallelly_1.23.0 jpeg_0.1-8.1 scales_1.1.1
[100] memoise_2.0.0 magrittr_2.0.1 plyr_1.8.6
[103] ica_1.0-2 zlibbioc_1.36.0 compiler_4.0.3
[106] HSMMSingleCell_1.10.0 RColorBrewer_1.1-2 fitdistrplus_1.1-3
[109] Rsamtools_2.6.0 XVector_0.30.0 listenv_0.8.0
[112] pbapply_1.4-3 htmlTable_2.1.0 Formula_1.2-4
[115] MASS_7.3-53 mgcv_1.8-33 tidyselect_1.1.0
[118] stringi_1.5.3 densityClust_0.3 askpass_1.1
[121] latticeExtra_0.6-29 ggrepel_0.9.1 VariantAnnotation_1.36.0
[124] fastmatch_1.1-0 tools_4.0.3 future.apply_1.7.0
[127] rstudioapi_0.13 uuid_0.1-4 foreign_0.8-81
[130] lsa_0.73.2 gridExtra_2.3 farver_2.0.3
[133] Rtsne_0.15 digest_0.6.27 BiocManager_1.30.10
[136] FNN_1.1.3 shiny_1.6.0 qlcMatrix_0.9.7
[139] Rcpp_1.0.6 later_1.1.0.1 RcppAnnoy_0.0.18
[142] OrganismDbi_1.32.0 httr_1.4.2 AnnotationDbi_1.52.0
[145] ggbio_1.38.0 biovizBase_1.38.0 colorspace_2.0-0
[148] XML_3.99-0.5 tensor_1.5 reticulate_1.18
[151] uwot_0.1.10 RBGL_1.66.0 RcppRoll_0.3.0
[154] spatstat.utils_2.2-0 plotly_4.9.3 xtable_1.8-4
[157] jsonlite_1.7.2 spatstat_1.64-1 R6_2.5.0
[160] Hmisc_4.4-2 pillar_1.4.7 htmltools_0.5.1.1
[163] mime_0.9 glue_1.4.2 fastmap_1.1.0
[166] BiocParallel_1.24.0 codetools_0.2-18 lattice_0.20-41
[169] tibble_3.0.6 curl_4.3 leiden_0.3.7
[172] openssl_1.4.3 survival_3.2-7 limma_3.46.0
[175] repr_1.1.3 docopt_0.7.1 fastICA_1.2-2
[178] munsell_0.5.0 GenomeInfoDbData_1.2.4 reshape2_1.4.4
[181] gtable_0.3.0 Can someone please help me out? I don't know why I'm getting this error. I wonder if it's because the object class is It seems this issue was reported in another thread #372 as well, but has not been resolved. Thanks for your help! |
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Replies: 1 comment 1 reply
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The cicero version numbers are a little confusing, but I think you might have the wrong version installed. The latest version compatible with monocle3 is 1.3.4.11. Make sure you've installed cicero using the "monocle3" branch: https://cole-trapnell-lab.github.io/cicero-release/docs_m3/#installing-cicero |
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Hi Tim, thanks! This seemed to work. |
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The cicero version numbers are a little confusing, but I think you might have the wrong version installed. The latest version compatible with monocle3 is 1.3.4.11. Make sure you've installed cicero using the "monocle3" branch: https://cole-trapnell-lab.github.io/cicero-release/docs_m3/#installing-cicero