Update convenience.R Xenium new blank unassigned assay

[Ceallaig33]

With new version of Xenium output, the output matrix "Blank Codeword" was changed to "Unassigned Codeword". Suggesting change to allow import of this updated Xenium output. Not sure if a data version check needs to also be included. Thanks @aclark5 for finding this.

Note

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[Ceallaig33]

Note that the fix is already completed on the develop branch, but does not seem to updated on the seurat5 branch

[Margokap]

Hi there, I've also encountered this issue with Human Xenium data from 10x genomics (https://www.10xgenomics.com/resources/datasets/xenium-human-brain-preview-data-1-standard)

The features.tsv file from this experiment contains "Unassigned Codeword" in lieu of "Blank Codeword"

ie:

data <- ReadXenium(data.dir = data.dir, type =c('centroids', 'segmentation'))
10X data contains more than one type and is being returned as a list containing matrices of each type.
|--------------------------------------------------|
|==================================================|
data$matrix[["Blank Codeword"]]
NULL

however:

data$matrix[["Unassigned Codeword"]]
161 x 24406 sparse Matrix of class "dgCMatrix"
[[ suppressing 39 column names ‘barcodes’, ‘1’, ‘2’ ... ]]
[[ suppressing 39 column names ‘barcodes’, ‘1’, ‘2’ ... ]]

BLANK_0001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0007 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0026 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......

..............................
........suppressing 24367 columns and 136 rows in show(); maybe adjust 'options(max.print= *, width = *)'
..............................
[[ suppressing 39 column names ‘barcodes’, ‘1’, ‘2’ ... ]]

BLANK_0460 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0471 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0473 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0483 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0484 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0487 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0490 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......

data$matrix[["Unassigned Codeword"]]
161 x 24406 sparse Matrix of class "dgCMatrix"
[[ suppressing 39 column names ‘barcodes’, ‘1’, ‘2’ ... ]]
[[ suppressing 39 column names ‘barcodes’, ‘1’, ‘2’ ... ]]

BLANK_0001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0007 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0026 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......

..............................
........suppressing 24367 columns and 136 rows in show(); maybe adjust 'options(max.print= *, width = *)'
..............................
[[ suppressing 39 column names ‘barcodes’, ‘1’, ‘2’ ... ]]

BLANK_0460 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0471 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0473 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0483 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0484 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0487 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0490 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......
BLANK_0494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

To try to resolve this issue, I used the following:

remotes::install_github(repo = 'Ceallaig33/seurat', ref = 'patch-1')

but am still unable to load the Xenium data:
reprex:

xeni-human <- LoadXenium(data.dir = data.dir)
10X data contains more than one type and is being returned as a list containing matrices of each type.
|--------------------------------------------------|
|==================================================|
Warning: Feature names cannot have underscores (''), replacing with dashes ('-')
Warning: Feature names cannot have underscores (''), replacing with dashes ('-')
Warning: Feature names cannot have underscores (''), replacing with dashes ('-')
Warning: Feature names cannot have underscores (''), replacing with dashes ('-')
Warning: Feature names cannot have underscores (''), replacing with dashes ('-')
Warning: Feature names cannot have underscores (''), replacing with dashes ('-')
Error in [[<-:
! Cannot add new cells with [[<-
Run rlang::last_trace() to see where the error occurred

Thank you very much for any possible help or suggestions! I posted this at #7491 and got a little help, was directed here.

&session info:

sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4

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

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

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

other attached packages:
[1] ggplot2_3.4.2 future_1.32.0 dplyr_1.1.2 Seurat_4.9.9.9045 SeuratObject_4.9.9.9086
[6] sp_2.0-0

loaded via a namespace (and not attached):
[1] Rtsne_0.16 colorspace_2.1-0 deldir_1.0-9 ellipsis_0.3.2 ggridges_0.5.4 rprojroot_2.0.3
[7] rstudioapi_0.14 spatstat.data_3.0-1 leiden_0.4.3 listenv_0.9.0 farver_2.1.1 remotes_2.4.2
[13] ggrepel_0.9.3 bit64_4.0.5 fansi_1.0.4 codetools_0.2-18 splines_4.2.1 R.methodsS3_1.8.2
[19] polyclip_1.10-4 spam_2.9-1 jsonlite_1.8.5 ica_1.0-3 cluster_2.1.4 png_0.1-8
[25] R.oo_1.25.0 uwot_0.1.15 shiny_1.7.4 sctransform_0.3.5 spatstat.sparse_3.0-2 compiler_4.2.1
[31] httr_1.4.6 Matrix_1.5-1 fastmap_1.1.1 lazyeval_0.2.2 cli_3.6.1 later_1.3.1
[37] prettyunits_1.1.1 htmltools_0.5.5 tools_4.2.1 igraph_1.5.0 dotCall64_1.0-2 gtable_0.3.3
[43] glue_1.6.2 RANN_2.6.1 reshape2_1.4.4 Rcpp_1.0.10 scattermore_1.2 vctrs_0.6.3
[49] spatstat.explore_3.2-1 nlme_3.1-160 progressr_0.13.0 lmtest_0.9-40 spatstat.random_3.1-5 stringr_1.5.0
[55] ps_1.7.5 globals_0.16.2 mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.3 irlba_2.3.5.1
[61] goftest_1.2-3 MASS_7.3-58.1 zoo_1.8-12 scales_1.2.1 promises_1.2.0.1 spatstat.utils_3.0-3
[67] parallel_4.2.1 RColorBrewer_1.1-3 curl_5.0.1 reticulate_1.30 pbapply_1.7-2 gridExtra_2.3
[73] stringi_1.7.12 desc_1.4.2 pkgbuild_1.4.0 rlang_1.1.1 pkgconfig_2.0.3 matrixStats_1.0.0
[79] lattice_0.20-45 ROCR_1.0-11 purrr_1.0.1 tensor_1.5 patchwork_1.1.2 htmlwidgets_1.6.2
[85] labeling_0.4.2 processx_3.8.1 bit_4.0.5 cowplot_1.1.1 tidyselect_1.2.0 parallelly_1.36.0
[91] RcppAnnoy_0.0.20 plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 generics_0.1.3 pillar_1.9.0
[97] withr_2.5.0 fitdistrplus_1.1-11 survival_3.4-0 abind_1.4-5 tibble_3.2.1 future.apply_1.11.0
[103] crayon_1.5.2 KernSmooth_2.23-20 utf8_1.2.3 spatstat.geom_3.2-1 plotly_4.10.2 grid_4.2.1
[109] data.table_1.14.8 callr_3.7.3 digest_0.6.32 xtable_1.8-4 tidyr_1.3.0 httpuv_1.6.11
[115] R.utils_2.12.2 munsell_0.5.0 viridisLite_0.4.2

[alikhuseynov]

I guess, before adding FOVs one should subset them to have the same cells as the object.

coords %<>% 
    # only consider the cells we have counts and a segmentation.
    subset(x = .,
           cells = intersect(x = Cells(x = .[["segmentation"]]),
                               y = Cells(x = xenium.obj)))
xenium.obj[[fov]] <- coords