Error when using giottoToSeuratV5 (CosMX data)

[guillermoturiel]

I have been trying to convert my Giotto object to Seurat using the function giottoToSeuratV5(). However I get the following error:

fov_s <- giottoToSeuratV5(fov_join)

Error in (function (cl, name, valueClass) :
‘meta.data’ is not a slot in class “Assay”

The function works perfectly for me while using the example for this function in the documentation

g <- GiottoData::loadGiottoMini("visium")

1. read Giotto object
2. read Giotto feature information
3. read Giotto spatial information
   3.1 read Giotto spatial shape information
   cell_spatInfo_spatVector.shp
   cell

3.2 read Giotto spatial centroid information
cell

3.3 read Giotto spatial overlap information
No overlaps were found, overlap loading will be
skipped

4. read Giotto image information

no external python path was provided,
but a giotto python environment was found and
will be used
Warning message:
This giotto object was created in a newer version of
GiottoClass (v0.3.2)

giottoToSeuratV5(g)

An object of class Seurat
634 features across 624 samples within 1 assay
Active assay: rna (634 features, 0 variable features)
3 layers present: counts, data, scale.data
6 dimensional reductions calculated: pca, custom_pca, umap, custom_umap, tsne, spatial
2 images present: alignment, image
Warning messages:
1: Keys should be one or more alphanumeric characters followed by an underscore, setting key from custom_pca_ to custompca_
2: Keys should be one or more alphanumeric characters followed by an underscore, setting key from custom_umap_ to customumap_

However while trying the same with the example cosmx dataset I get the same error:

g <- GiottoData::loadGiottoMini("cosmx")

1. read Giotto object
2. read Giotto feature information
   /home/guruiz/R/x86_64-pc-linux-gnu-library/4.4/GiottoData/Mini_datasets/CosMx/CosMxObject/Features/neg_probe_feature_spatVector.shp
   neg_probe
   /home/guruiz/R/x86_64-pc-linux-gnu-library/4.4/GiottoData/Mini_datasets/CosMx/CosMxObject/Features/rna_feature_spatVector.shp
   rna
3. read Giotto spatial information
   3.1 read Giotto spatial shape information
   cell_spatInfo_spatVector.shp
   cell

3.2 read Giotto spatial centroid information
cell

3.3 read Giotto spatial overlap information
neg_probe_cell_spatInfo_spatVectorOverlaps.shp
rna_cell_spatInfo_spatVectorOverlaps.shp
poly_ID feat_ID feat_ID_uniq
cell and neg_probe
poly_ID feat_ID feat_ID_uniq
cell and rna

4. read Giotto image information

no external python path was provided,
but a giotto python environment was found and
will be used

giottoToSeuratV5(g)

Error in (function (cl, name, valueClass) :
‘meta.data’ is not a slot in class “Assay”

I guess then it is a problem of the function itself with CosMX data rather than a problem with my data.

Could you please provide any solution to this?

Thank you very much.

sessionInfo()

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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: Europe/Zurich
tzcode source: system (glibc)

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

other attached packages:
[1] sp_2.1-4 ggplot2_3.5.1 GiottoUtils_0.1.8 Giotto_4.0.8
[5] GiottoClass_0.3.1

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.8 magrittr_2.0.3
[4] spatstat.utils_3.0-5 magick_2.8.3 farver_2.1.2
[7] zlibbioc_1.50.0 vctrs_0.6.5 ROCR_1.0-11
[10] spatstat.explore_3.2-7 terra_1.7-78 htmltools_0.5.8.1
[13] S4Arrays_1.4.1 SparseArray_1.4.8 sctransform_0.4.1
[16] parallelly_1.37.1 KernSmooth_2.23-20 htmlwidgets_1.6.4
[19] ica_1.0-3 plyr_1.8.9 plotly_4.10.4
[22] zoo_1.8-12 igraph_2.0.3 mime_0.12
[25] lifecycle_1.0.4 pkgconfig_2.0.3 rsvd_1.0.5
[28] Matrix_1.7-0 R6_2.5.1 fastmap_1.2.0
[31] magic_1.6-1 MatrixGenerics_1.16.0 fitdistrplus_1.2-1
[34] future_1.33.2 shiny_1.8.1.1 digest_0.6.35
[37] colorspace_2.1-0 patchwork_1.2.0 S4Vectors_0.42.0
[40] Seurat_5.1.0 tensor_1.5 RSpectra_0.16-1
[43] irlba_2.3.5.1 beachmat_2.20.0 labeling_0.4.3
[46] progressr_0.14.0 spatstat.sparse_3.1-0 fansi_1.0.6
[49] polyclip_1.10-6 httr_1.4.7 abind_1.4-5
[52] compiler_4.4.1 withr_3.0.0 backports_1.5.0
[55] BiocParallel_1.38.0 fastDummies_1.7.3 MASS_7.3-55
[58] rappdirs_0.3.3 DelayedArray_0.30.1 gtools_3.9.5
[61] GiottoVisuals_0.2.3 tools_4.4.1 lmtest_0.9-40
[64] httpuv_1.6.15 future.apply_1.11.2 goftest_1.2-3
[67] glue_1.7.0 dbscan_1.1-12 nlme_3.1-155
[70] promises_1.3.0 grid_4.4.1 checkmate_2.3.1
[73] Rtsne_0.17 cluster_2.1.2 reshape2_1.4.4
[76] generics_0.1.3 spatstat.data_3.1-2 gtable_0.3.5
[79] tidyr_1.3.1 data.table_1.15.4 BiocSingular_1.20.0
[82] ScaledMatrix_1.12.0 utf8_1.2.4 XVector_0.44.0
[85] spatstat.geom_3.2-9 BiocGenerics_0.50.0 RcppAnnoy_0.0.22
[88] ggrepel_0.9.5 RANN_2.6.1 pillar_1.9.0
[91] stringr_1.5.1 spam_2.10-0 RcppHNSW_0.5.0
[94] later_1.3.2 splines_4.4.1 dplyr_1.1.4
[97] lattice_0.20-45 survival_3.2-13 deldir_2.0-4
[100] tidyselect_1.2.1 pbapply_1.7-2 miniUI_0.1.1.1
[103] gridExtra_2.3 IRanges_2.38.0 scattermore_1.2
[106] stats4_4.4.1 Biobase_2.62.0 matrixStats_1.3.0
[109] stringi_1.8.4 lazyeval_0.2.2 codetools_0.2-18
[112] GiottoData_0.2.13 tibble_3.2.1 colorRamp2_0.1.0
[115] cli_3.6.2 uwot_0.2.2 geometry_0.4.7
[118] xtable_1.8-4 reticulate_1.38.0 munsell_0.5.1
[121] Rcpp_1.0.12 spatstat.random_3.2-3 globals_0.16.3
[124] png_0.1-8 parallel_4.4.1 dotCall64_1.1-1
[127] listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0
[130] ggridges_0.5.6 SeuratObject_5.0.2 leiden_0.4.3.1
[133] purrr_1.0.2 crayon_1.5.2 rlang_1.1.4
[136] cowplot_1.1.3

[iqraAmin]

@guillermoturiel The changes have been implemented in PR #210. It should be fixed now.

[jiajic]

This fix is now in the currently released version. Closing as completed, please reopen if I am mistaken.