Error in plotMahal

[aaron-tantk]

I was able to carry out all steps up until this.

plotMahal(sce, which = "B3")

I was thrown an error: Error in assay(x, assay)[bc_chs, cs] : subscript out of bounds

Here is my sessioninfo()

sessionInfo() R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.2.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] ggplot2_3.4.1 flowCore_2.10.0 cowplot_1.1.1 CATALYST_1.22.0 SingleCellExperiment_1.20.0 [6] SummarizedExperiment_1.28.0 Biobase_2.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[11] S4Vectors_0.36.1 BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_0.63.0

loaded via a namespace (and not attached): [1] utf8_1.2.3 spatstat.explore_3.0-6 reticulate_1.28 tidyselect_1.2.0 htmlwidgets_1.6.1
[6] BiocParallel_1.32.5 grid_4.2.2 Rtsne_0.16 ScaledMatrix_1.6.0 munsell_0.5.0
[11] codetools_0.2-19 ica_1.0-3 future_1.31.0 miniUI_0.1.1.1 withr_2.5.0
[16] spatstat.random_3.1-3 colorspace_2.1-0 progressr_0.13.0 knitr_1.42 rstudioapi_0.14
[21] Seurat_4.3.0 ROCR_1.0-11 ggsignif_0.6.4 tensor_1.5 listenv_0.9.0
[26] labeling_0.4.2 GenomeInfoDbData_1.2.9 polyclip_1.10-4 farver_2.1.1 parallelly_1.34.0
[31] vctrs_0.5.2 generics_0.1.3 TH.data_1.1-1 xfun_0.37 R6_2.5.1
[36] doParallel_1.0.17 ggbeeswarm_0.7.1 clue_0.3-64 rsvd_1.0.5 bitops_1.0-7
[41] spatstat.utils_3.0-1 DelayedArray_0.24.0 promises_1.2.0.1 scales_1.2.1 multcomp_1.4-22
[46] beeswarm_0.4.0 gtable_0.3.1 beachmat_2.14.0 globals_0.16.2 goftest_1.2-3
[51] RProtoBufLib_2.10.0 sandwich_3.0-2 rlang_1.0.6 GlobalOptions_0.1.2 splines_4.2.2
[56] rstatix_0.7.2 lazyeval_0.2.2 spatstat.geom_3.0-6 broom_1.0.3 BiocManager_1.30.19
[61] yaml_2.3.7 reshape2_1.4.4 abind_1.4-5 backports_1.4.1 httpuv_1.6.8
[66] tools_4.2.2 ellipsis_0.3.2 RColorBrewer_1.1-3 sessioninfo_1.2.2 ggridges_0.5.4
[71] Rcpp_1.0.10 plyr_1.8.8 sparseMatrixStats_1.10.0 zlibbioc_1.44.0 purrr_1.0.1
[76] RCurl_1.98-1.10 FlowSOM_2.6.0 ggpubr_0.6.0 deldir_1.0-6 viridis_0.6.2
[81] pbapply_1.7-0 GetoptLong_1.0.5 zoo_1.8-11 SeuratObject_4.1.3 ggrepel_0.9.3
[86] cluster_2.1.4 colorRamps_2.3.1 magrittr_2.0.3 data.table_1.14.6 scattermore_0.8
[91] circlize_0.4.15 lmtest_0.9-40 RANN_2.6.1 mvtnorm_1.1-3 ggnewscale_0.4.8
[96] fitdistrplus_1.1-8 patchwork_1.1.2.9000 mime_0.12 evaluate_0.20 xtable_1.8-4
[101] XML_3.99-0.13 gridExtra_2.3 shape_1.4.6 scater_1.26.1 compiler_4.2.2
[106] tibble_3.1.8 KernSmooth_2.23-20 crayon_1.5.2 htmltools_0.5.4 later_1.3.0
[111] tidyr_1.3.0 DBI_1.1.3 tweenr_2.0.2 ComplexHeatmap_2.14.0 MASS_7.3-58.2
[116] Matrix_1.5-3 car_3.1-1 cli_3.6.0 parallel_4.2.2 igraph_1.4.0
[121] pkgconfig_2.0.3 sp_1.6-0 scuttle_1.8.4 plotly_4.10.1 spatstat.sparse_3.0-0
[126] foreach_1.5.2 vipor_0.4.5 XVector_0.38.0 drc_3.0-1 stringr_1.5.0
[131] digest_0.6.31 sctransform_0.3.5 RcppAnnoy_0.0.20 ConsensusClusterPlus_1.62.0 spatstat.data_3.0-0
[136] rmarkdown_2.20 leiden_0.4.3 uwot_0.1.14 DelayedMatrixStats_1.20.0 shiny_1.7.4
[141] gtools_3.9.4 rjson_0.2.21 lifecycle_1.0.3 nlme_3.1-162 jsonlite_1.8.4
[146] BiocNeighbors_1.16.0 carData_3.0-5 viridisLite_0.4.1 fansi_1.0.4 pillar_1.8.1
[151] lattice_0.20-45 fastmap_1.1.0 httr_1.4.4 plotrix_3.8-2 survival_3.5-0
[156] glue_1.6.2 png_0.1-8 iterators_1.0.14 ggforce_0.4.1 stringi_1.7.12
[161] nnls_1.4 BiocSingular_1.14.0 dplyr_1.1.0 cytolib_2.10.0 irlba_2.3.5.1
[166] future.apply_1.10.0

[HelenaLC]

Could you please post the output of sce (i.e., just printing the object), table(sce$bc_id), metadata(sce)$bc_key, and rownames(sce)[rowData(sce)$is_bc]? ...it generally helps a lot to see some data in order to understand what might cause an error.

[aaron-tantk]

This is the sce object_

table(sce$bc_id) < table of extent 0 >

metadata(sce)$bc_key NULL

rownames(sce)[rowData(sce)$is_bc] character(0)

[HelenaLC]

Yeah, so that explains a lot. Looks like you didn't run the debarcoding, and preliminary barcode assignments are necessary for plotMahal. So, if you run assignPrelim(sce, ...) you should be good.