navinlabcode / navinlabcode/CellTrek
Errors in CellTrek::traint on example data from README
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Description
I'm attempting to get the example from the README working, but am encountering an error on the CellTrek::traint step during FindTransferAnchors:
> brain_traint <- CellTrek::traint(st_data=brain_st_cortex, sc_data=brain_sc, sc_assay='RNA', cell_names='cell_type')
Finding transfer anchors...
Using 2000 features for integration...
Running CCA
Merging objects
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
In addition: Warning messages:
1: Command ScaleData.RNA changing from SeuratCommand to SeuratCommand
2: Command ScaleData.Spatial changing from SeuratCommand to SeuratCommand
3: In RunCCA.Seurat(object1 = reference, object2 = query, features = features, :
Running CCA on different assays
Downgrading to Seurat 3.1.1 (corresponding to Version(brain_sc)) gets us past this step but encounters a new error slightly later in the execution of FindTransferAnchors. I've included that error at the end of this issue in case it is useful.
Debugging info (Seurat 4.4.0)
Traceback
> traceback()
5: `rownames<-`(x = `*tmp*`, value = Cells(x = combined.object))
4: RunCCA.Seurat(object1 = reference, object2 = query, features = features,
num.cc = max(dims), renormalize = FALSE, rescale = FALSE,
verbose = verbose)
3: RunCCA(object1 = reference, object2 = query, features = features,
num.cc = max(dims), renormalize = FALSE, rescale = FALSE,
verbose = verbose)
2: Seurat::FindTransferAnchors(reference = sc_data, query = st_data,
reference.assay = sc_assay, query.assay = st_assay, normalization.method = norm,
features = sc_st_features, reduction = "cca", ...)
1: CellTrek::traint(st_data = brain_st_cortex, sc_data = brain_sc,
sc_assay = "RNA", cell_names = "cell_type")
Session Info
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] viridis_0.6.4 viridisLite_0.4.2 dplyr_1.1.3 SeuratObject_5.0.0
[5] Seurat_4.4.0 CellTrek_0.0.94
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7
[4] magrittr_2.0.3 spatstat.utils_3.0-3 farver_2.1.1
[7] vctrs_0.6.3 ROCR_1.0-11 spatstat.explore_3.2-3
[10] rstatix_0.7.2 htmltools_0.5.6 dynamicTreeCut_1.63-1
[13] broom_1.0.5 sctransform_0.4.0 parallelly_1.36.0
[16] KernSmooth_2.23-20 htmlwidgets_1.6.2 ica_1.0-3
[19] plyr_1.8.8 plotly_4.10.2 zoo_1.8-12
[22] igraph_1.5.1 mime_0.12 lifecycle_1.0.3
[25] pkgconfig_2.0.3 Matrix_1.6-1.1 R6_2.5.1
[28] fastmap_1.1.1 magic_1.6-1 fitdistrplus_1.1-11
[31] future_1.33.0 shiny_1.7.5 digest_0.6.33
[34] colorspace_2.1-0 patchwork_1.1.3 tensor_1.5
[37] irlba_2.3.5.1 akima_0.6-3.4 ggpubr_0.6.0
[40] labeling_0.4.3 philentropy_0.7.0 progressr_0.14.0
[43] fansi_1.0.4 spatstat.sparse_3.0-2 httr_1.4.7
[46] polyclip_1.10-4 abind_1.4-5 compiler_4.3.0
[49] withr_2.5.0 backports_1.4.1 carData_3.0-5
[52] ggsignif_0.6.4 MASS_7.3-58.4 tools_4.3.0
[55] lmtest_0.9-40 httpuv_1.6.11 future.apply_1.11.0
[58] goftest_1.2-3 glue_1.6.2 dbscan_1.1-11
[61] DiagrammeR_1.0.10 nlme_3.1-162 promises_1.2.1
[64] grid_4.3.0 Rtsne_0.16 cluster_2.1.4
[67] reshape2_1.4.4 generics_0.1.3 gtable_0.3.4
[70] spatstat.data_3.0-1 tidyr_1.3.0 data.table_1.14.8
[73] sp_2.0-0 car_3.1-2 utf8_1.2.3
[76] spatstat.geom_3.2-5 RcppAnnoy_0.0.21 ggrepel_0.9.3
[79] RANN_2.6.1 pillar_1.9.0 stringr_1.5.0
[82] spam_2.10-0 later_1.3.1 splines_4.3.0
[85] lattice_0.21-8 survival_3.5-5 deldir_1.0-9
[88] tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-2
[91] gridExtra_2.3 scattermore_1.2 matrixStats_1.0.0
[94] visNetwork_2.1.2 stringi_1.7.12 lazyeval_0.2.2
[97] codetools_0.2-19 data.tree_1.0.0 tibble_3.2.1
[100] packcircles_0.3.6 cli_3.6.1 uwot_0.1.16
[103] xtable_1.8-4 geometry_0.4.7 reticulate_1.32.0
[106] randomForestSRC_3.2.2 munsell_0.5.0 Rcpp_1.0.11
[109] globals_0.16.2 spatstat.random_3.1-6 png_0.1-8
[112] fastcluster_1.2.3 parallel_4.3.0 ellipsis_0.3.2
[115] ggplot2_3.4.3 dotCall64_1.1-0 listenv_0.9.0
[118] scales_1.2.1 ggridges_0.5.4 leiden_0.4.3
[121] purrr_1.0.2 rlang_1.1.1 cowplot_1.1.1
Debugging info (Seurat 3.1.1)
Error
> brain_traint <- CellTrek::traint(st_data=brain_st_cortex, sc_data=brain_sc, sc_assay='RNA', cell_names='cell_type')
Finding transfer anchors...
Using 2000 features for integration...
Running CCA
Merging objects
Finding neighborhoods
Finding anchors
Error in !(cells1 %in% colnames(object)) || !(cells2 %in% colnames(object)) :
'length = 5860' in coercion to 'logical(1)'
In addition: Warning message:
In RunCCA.Seurat(object1 = reference, object2 = query, features = features, :
Running CCA on different assays
Traceback
> traceback()
4: FindAnchorPairs(object = object.pair, integration.name = "integrated",
k.anchor = k.anchor, verbose = verbose)
3: FindAnchors(object.pair = combined.ob, assay = c(reference.assay,
query.assay), slot = slot, cells1 = colnames(x = reference),
cells2 = colnames(x = query), reduction = reduction, internal.neighbors = list(NULL,
NULL), dims = dims, k.anchor = k.anchor, k.filter = k.filter,
k.score = k.score, max.features = max.features, nn.method = nn.method,
eps = eps, projected = projected, verbose = verbose)
2: Seurat::FindTransferAnchors(reference = sc_data, query = st_data,
reference.assay = sc_assay, query.assay = st_assay, normalization.method = norm,
features = sc_st_features, reduction = "cca", ...)
1: CellTrek::traint(st_data = brain_st_cortex, sc_data = brain_sc,
sc_assay = "RNA", cell_names = "cell_type")
Session Info
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] CellTrek_0.0.94 Seurat_3.1.1
loaded via a namespace (and not attached):
[1] mathjaxr_1.6-0 RColorBrewer_1.1-3 rstudioapi_0.15.0
[4] jsonlite_1.8.7 magrittr_2.0.3 TH.data_1.1-2
[7] vctrs_0.6.3 multtest_2.8.0 ROCR_1.0-11
[10] rstatix_0.7.2 htmltools_0.5.6 dynamicTreeCut_1.63-1
[13] plotrix_3.8-2 broom_1.0.5 sctransform_0.4.0
[16] parallelly_1.36.0 KernSmooth_2.23-20 htmlwidgets_1.6.2
[19] ica_1.0-3 plyr_1.8.8 sandwich_3.0-2
[22] plotly_4.10.2 zoo_1.8-12 igraph_1.5.1
[25] mime_0.12 lifecycle_1.0.3 pkgconfig_2.0.3
[28] rsvd_1.0.5 Matrix_1.6-1.1 R6_2.5.1
[31] fastmap_1.1.1 magic_1.6-1 rbibutils_2.2.16
[34] fitdistrplus_1.1-11 future_1.33.0 shiny_1.7.5
[37] digest_0.6.33 numDeriv_2016.8-1.1 colorspace_2.1-0
[40] irlba_2.3.5.1 akima_0.6-3.4 ggpubr_0.6.0
[43] philentropy_0.7.0 fansi_1.0.4 httr_1.4.7
[46] TFisher_0.2.0 abind_1.4-5 compiler_4.3.0
[49] mutoss_0.1-13 backports_1.4.1 carData_3.0-5
[52] R.utils_2.12.2 ggsignif_0.6.4 MASS_7.3-58.4
[55] tsne_0.1-3.1 tools_4.3.0 lmtest_0.9-40
[58] ape_5.7-1 metap_1.9 httpuv_1.6.11
[61] future.apply_1.11.0 qqconf_1.3.2 R.oo_1.25.0
[64] glue_1.6.2 dbscan_1.1-11 DiagrammeR_1.0.10
[67] promises_1.2.1 nlme_3.1-162 grid_4.3.0
[70] Rtsne_0.16 cluster_2.1.4 reshape2_1.4.4
[73] generics_0.1.3 gtable_0.3.4 R.methodsS3_1.8.2
[76] tidyr_1.3.0 sn_2.1.1 data.table_1.14.8
[79] sp_2.0-0 car_3.1-2 utf8_1.2.3
[82] BiocGenerics_0.48.0 RcppAnnoy_0.0.21 ggrepel_0.9.3
[85] RANN_2.6.1 pillar_1.9.0 stringr_1.5.0
[88] later_1.3.1 splines_4.3.0 dplyr_1.1.3
[91] lattice_0.21-8 survival_3.5-5 tidyselect_1.2.0
[94] pbapply_1.7-2 gridExtra_2.3 stats4_4.3.0
[97] Biobase_2.62.0 matrixStats_1.0.0 visNetwork_2.1.2
[100] stringi_1.7.12 lazyeval_0.2.2 codetools_0.2-19
[103] data.tree_1.0.0 tibble_3.2.1 packcircles_0.3.6
[106] cli_3.6.1 uwot_0.1.16 geometry_0.4.7
[109] xtable_1.8-4 reticulate_1.32.0 randomForestSRC_3.2.2
[112] Rdpack_2.5 munsell_0.5.0 Rcpp_1.0.11
[115] globals_0.16.2 png_0.1-8 fastcluster_1.2.3
[118] parallel_4.3.0 ellipsis_0.3.2 ggplot2_3.4.3
[121] listenv_0.9.0 viridisLite_0.4.2 mvtnorm_1.2-3
[124] SDMTools_1.1-221 scales_1.2.1 ggridges_0.5.4
[127] leiden_0.4.3 purrr_1.0.2 rlang_1.1.1
[130] cowplot_1.1.1 multcomp_1.4-25 mnormt_2.1.1
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the README example with the reported CellTrek::traint call and the listed R, Seurat 4.4.0, and Seurat 3.1.1 environments. Trace the FindTransferAnchors call and its RunCCA or FindAnchorPairs failures; done means the example progresses past anchor finding without either reported error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100