ArchR
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20 hours ago •
GreenleafLab
GreenleafLab
simpleError in validObject(.Object): invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order
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When run the tutorial "https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html"
#Add Clusters
proj <- addClusters(proj, reducedDims = "LSI_Combined", name = "Clusters", resolution = 0.4, force = TRUE)
There is error: simpleError in validObject(.Object): invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order
How can I solve this?
Thanks a lot
The LogFile is:
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
Logging With ArchR!
Start Time : 2024-09-27 16:40:00.132495
------- ArchR Info
ArchRThreads = 10
ArchRGenome = Hg38
------- System Info
Computer OS = unix
Total Cores = 12
------- Session Info
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] nabor_0.5.0 Seurat_5.1.0
[3] SeuratObject_5.0.2 sp_2.1-4
[5] Rsamtools_2.20.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[7] BSgenome_1.72.0 rtracklayer_1.64.0
[9] BiocIO_1.14.0 Biostrings_2.72.1
[11] XVector_0.44.0 rhdf5_2.48.0
[13] SummarizedExperiment_1.34.0 Biobase_2.64.0
[15] MatrixGenerics_1.16.0 Rcpp_1.0.13
[17] Matrix_1.7-0 GenomicRanges_1.56.1
[19] GenomeInfoDb_1.40.1 IRanges_2.38.1
[21] S4Vectors_0.42.1 BiocGenerics_0.50.0
[23] matrixStats_1.4.1 data.table_1.16.0
[25] stringr_1.5.1 plyr_1.8.9
[27] magrittr_2.0.3 ggplot2_3.5.1
[29] gtable_0.3.5 gtools_3.9.5
[31] gridExtra_2.3 ArchR_1.0.2
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.1 later_1.3.2
[4] pbdZMQ_0.3-11 bitops_1.0-8 tibble_3.2.1
[7] polyclip_1.10-7 XML_3.99-0.17 fastDummies_1.7.3
[10] lifecycle_1.0.4 globals_0.16.3 lattice_0.22-6
[13] MASS_7.3-61 plotly_4.10.4 yaml_2.3.10
[16] httpuv_1.6.15 sctransform_0.4.1 spam_2.10-0
[19] spatstat.sparse_3.1-0 reticulate_1.38.0 cowplot_1.1.3
[22] pbapply_1.7-2 RColorBrewer_1.1-3 abind_1.4-8
[25] zlibbioc_1.50.0 Rtsne_0.17 purrr_1.0.2
[28] RCurl_1.98-1.16 GenomeInfoDbData_1.2.12 ggrepel_0.9.6
[31] irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.0-5
[34] goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.3-1
[37] fitdistrplus_1.2-1 parallelly_1.38.0 leiden_0.4.3.1
[40] codetools_0.2-20 DelayedArray_0.30.1 tidyselect_1.2.1
[43] UCSC.utils_1.0.0 farver_2.1.2 base64enc_0.1-3
[46] spatstat.explore_3.3-1 GenomicAlignments_1.40.0 jsonlite_1.8.9
[49] progressr_0.14.0 ggridges_0.5.6 survival_3.7-0
[52] tools_4.4.1 ica_1.0-3 glue_1.7.0
[55] SparseArray_1.4.8 IRdisplay_1.1 dplyr_1.1.4
[58] withr_3.0.1 fastmap_1.2.0 rhdf5filters_1.16.0
[61] fansi_1.0.6 digest_0.6.37 R6_2.5.1
[64] mime_0.12 colorspace_2.1-1 scattermore_1.2
[67] Cairo_1.6-2 tensor_1.5 spatstat.data_3.1-2
[70] utf8_1.2.4 tidyr_1.3.1 generics_0.1.3
[73] httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.4.1
[76] uwot_0.2.2 pkgconfig_2.0.3 lmtest_0.9-40
[79] htmltools_0.5.8.1 dotCall64_1.1-1 scales_1.3.0
[82] png_0.1-8 spatstat.univar_3.0-0 reshape2_1.4.4
[85] rjson_0.2.23 uuid_1.2-1 nlme_3.1-166
[88] curl_5.2.3 repr_1.1.7 zoo_1.8-12
[91] KernSmooth_2.23-24 miniUI_0.1.1.1 restfulr_0.0.15
[94] pillar_1.9.0 vctrs_0.6.5 RANN_2.6.1
[97] promises_1.3.0 xtable_1.8-4 cluster_2.1.6
[100] evaluate_1.0.0 cli_3.6.3 compiler_4.4.1
[103] rlang_1.1.4 crayon_1.5.3 future.apply_1.11.2
[106] labeling_0.4.3 stringi_1.8.4 deldir_2.0-4
[109] viridisLite_0.4.2 BiocParallel_1.38.0 munsell_0.5.1
[112] lazyeval_0.2.2 spatstat.geom_3.3-2 IRkernel_1.3.2
[115] RcppHNSW_0.6.0 patchwork_1.2.0 future_1.34.0
[118] Rhdf5lib_1.26.0 shiny_1.9.1 ROCR_1.0-11
[121] igraph_2.0.3
------- Log Info
2024-09-27 16:40:00.246428 : addClusters Input-Parameters, Class = list
addClusters Input-Parameters$: length = 1
1 function (name)
2 .Internal(args(name))
addClusters Input-Parameters$input: length = 1
addClusters Input-Parameters$reducedDims: length = 1
[1] "LSI_Combined"
addClusters Input-Parameters$name: length = 1
[1] "Clusters"
addClusters Input-Parameters$sampleCells: length = 0
NULL
addClusters Input-Parameters$seed: length = 1
[1] 1
addClusters Input-Parameters$method: length = 1
[1] "Seurat"
addClusters Input-Parameters$dimsToUse: length = 0
NULL
addClusters Input-Parameters$scaleDims: length = 0
NULL
addClusters Input-Parameters$corCutOff: length = 1
[1] 0.75
addClusters Input-Parameters$knnAssign: length = 1
[1] 10
addClusters Input-Parameters$nOutlier: length = 1
[1] 5
addClusters Input-Parameters$maxClusters: length = 1
[1] 25
addClusters Input-Parameters$testBias: length = 1
[1] TRUE
addClusters Input-Parameters$filterBias: length = 1
[1] FALSE
addClusters Input-Parameters$biasClusters: length = 1
[1] 0.01
addClusters Input-Parameters$biasCol: length = 1
[1] "nFrags"
addClusters Input-Parameters$biasVals: length = 0
NULL
addClusters Input-Parameters$biasQuantiles: length = 2
[1] 0.05 0.95
addClusters Input-Parameters$biasEnrich: length = 1
[1] 10
addClusters Input-Parameters$biasProportion: length = 1
[1] 0.5
addClusters Input-Parameters$biasPval: length = 1
[1] 0.05
addClusters Input-Parameters$nPerm: length = 1
[1] 500
addClusters Input-Parameters$prefix: length = 1
[1] "C"
addClusters Input-Parameters$ArchRProj: length = 0
NULL
addClusters Input-Parameters$verbose: length = 1
[1] TRUE
addClusters Input-Parameters$tstart: length = 0
NULL
addClusters Input-Parameters$force: length = 1
[1] TRUE
addClusters Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addClusters-3a00529df302-Date-2024-09-27_Time-16-40-00.128721.log"
addClusters Input-Parameters$...: length = 1
2024-09-27 16:40:00.357858 : Running Seurats FindClusters (Stuart et al. Cell 2019), 0.001 mins elapsed.
************************************************************
2024-09-27 16:40:00.52974 : ERROR Found in FindNeighbors for
LogFile = ArchRLogs/ArchR-addClusters-3a00529df302-Date-2024-09-27_Time-16-40-00.128721.log
<simpleError in validObject(.Object): invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order>
2024-09-27 16:40:00.530944 : errorList, Class = list
errorList$: length = 1
1 function (name)
2 .Internal(args(name))
errorList$e: length = 2
$message
[1] "invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order"
$call
validObject(.Object)
************************************************************
************************************************************
2024-09-27 16:40:00.536953 : ERROR Found in runClusters for
LogFile = ArchRLogs/ArchR-addClusters-3a00529df302-Date-2024-09-27_Time-16-40-00.128721.log
<simpleError in .logError(e, fn = "FindNeighbors", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-09-27 16:40:00.538637 : errorList, Class = list
errorList$resolution: length = 1
[1] 0.4
errorList$verbose: length = 1
[1] TRUE
errorList$tstart: length = 1
[1] "2024-09-27 16:40:00 EDT"
************************************************************
Hi @danli349! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
@danli349
The issue is with the names of the reducedDims after combining RNA and ATAC. Running the following prior to addClusters(proj, reducedDims = "LSI_Combined" ... should fix the problem.
colnames(proj@reducedDims$LSI_Combined$matRD) <- paste0('LSI',1:length(colnames(getReducedDims(proj,'LSI_Combined'))))
