Error while running get_expressed_genes

[Samir1703]

Hello, I'm a bit new to coding and I'm encountering the following error. I'm following the step by step vignette and after running :

get_expressed_genes from sender and receiver cell types

list_expressed_genes_sender = sender_celltypes %>% unique() %>%
lapply(get_expressed_genes, seurat_object)
expressed_genes_sender = list_expressed_genes_sender %>% unlist() %>% unique()

I get the following error : Error in FUN(X[[i]], ...) :
no slot of name "data" for this object of class "Assay5"

I inspected the seurat object and I do indeed have a slot for data on my object so I'm a bit confused.

[csangara]

Hi, can you provide me your sessionInfo()? This seems to be a problem with Seurat v5 which we have not fully integrated with.

[Samir1703]

Hello and happy new year !
Here's the session info

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5

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-x86_64/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/Paris
tzcode source: internal

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

other attached packages:
[1] nichenetr_2.0.4 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[5] dplyr_1.1.4 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0
[9] tibble_3.2.1 ggplot2_3.4.4 tidyverse_2.0.0 Seurat_5.0.1
[13] SeuratObject_5.0.1 sp_2.1-2

loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.21 splines_4.3.2 later_1.3.2
[4] bitops_1.0-7 polyclip_1.10-6 hardhat_1.3.0
[7] pROC_1.18.5 rpart_4.1.21 fastDummies_1.7.3
[10] lifecycle_1.0.4 doParallel_1.0.17 globals_0.16.2
[13] lattice_0.21-9 MASS_7.3-60 backports_1.4.1
[16] magrittr_2.0.3 rmarkdown_2.25 Hmisc_5.1-1
[19] limma_3.58.1 plotly_4.10.3 httpuv_1.6.13
[22] sctransform_0.4.1 spam_2.10-0 spatstat.sparse_3.0-3
[25] reticulate_1.34.0 cowplot_1.1.2 pbapply_1.7-2
[28] RColorBrewer_1.1-3 abind_1.4-5 Rtsne_0.17
[31] BiocGenerics_0.48.1 nnet_7.3-19 tweenr_2.0.2
[34] ipred_0.9-14 circlize_0.4.15 lava_1.7.3
[37] S4Vectors_0.40.2 IRanges_2.36.0 ggrepel_0.9.4
[40] irlba_2.3.5.1 listenv_0.9.0 spatstat.utils_3.0-4
[43] goftest_1.2-3 RSpectra_0.16-1 spatstat.random_3.2-2
[46] fitdistrplus_1.1-11 parallelly_1.36.0 leiden_0.4.3.1
[49] codetools_0.2-19 ggforce_0.4.1 shape_1.4.6
[52] tidyselect_1.2.0 farver_2.1.1 base64enc_0.1-3
[55] matrixStats_1.2.0 stats4_4.3.2 spatstat.explore_3.2-5
[58] jsonlite_1.8.8 caret_6.0-94 GetoptLong_1.0.5
[61] e1071_1.7-14 Formula_1.2-5 ellipsis_0.3.2
[64] progressr_0.14.0 ggridges_0.5.5 survival_3.5-7
[67] iterators_1.0.14 foreach_1.5.2 tools_4.3.2
[70] ggnewscale_0.4.9 ica_1.0-3 Rcpp_1.0.11
[73] glue_1.6.2 prodlim_2023.08.28 gridExtra_2.3
[76] xfun_0.41 mgcv_1.9-0 withr_2.5.2
[79] fastmap_1.1.1 fansi_1.0.6 caTools_1.18.2
[82] digest_0.6.33 timechange_0.2.0 R6_2.5.1
[85] mime_0.12 colorspace_2.1-0 scattermore_1.2
[88] tensor_1.5 spatstat.data_3.0-3 DiagrammeR_1.0.10
[91] utf8_1.2.4 generics_0.1.3 data.table_1.14.10
[94] recipes_1.0.9 class_7.3-22 httr_1.4.7
[97] htmlwidgets_1.6.4 uwot_0.1.16 ModelMetrics_1.2.2.2
[100] pkgconfig_2.0.3 gtable_0.3.4 timeDate_4032.109
[103] ComplexHeatmap_2.18.0 lmtest_0.9-40 shadowtext_0.1.2
[106] htmltools_0.5.7 dotCall64_1.1-1 clue_0.3-65
[109] scales_1.3.0 png_0.1-8 gower_1.0.1
[112] knitr_1.45 rstudioapi_0.15.0 tzdb_0.4.0
[115] reshape2_1.4.4 rjson_0.2.21 checkmate_2.3.1
[118] visNetwork_2.1.2 nlme_3.1-163 proxy_0.4-27
[121] zoo_1.8-12 GlobalOptions_0.1.2 KernSmooth_2.23-22
[124] parallel_4.3.2 miniUI_0.1.1.1 vipor_0.4.7
[127] foreign_0.8-85 ggrastr_1.0.2 pillar_1.9.0
[130] grid_4.3.2 vctrs_0.6.5 RANN_2.6.1
[133] randomForest_4.7-1.1 promises_1.2.1 xtable_1.8-4
[136] cluster_2.1.4 htmlTable_2.4.2 beeswarm_0.4.0
[139] evaluate_0.23 cli_3.6.2 compiler_4.3.2
[142] rlang_1.1.2 crayon_1.5.2 future.apply_1.11.1
[145] fdrtool_1.2.17 labeling_0.4.3 plyr_1.8.9
[148] ggbeeswarm_0.7.2 stringi_1.8.3 viridisLite_0.4.2
[151] deldir_2.0-2 munsell_0.5.0 lazyeval_0.2.2
[154] spatstat.geom_3.2-7 Matrix_1.6-4 RcppHNSW_0.5.0
[157] hms_1.1.3 patchwork_1.1.3 future_1.33.1
[160] statmod_1.5.0 shiny_1.8.0 ROCR_1.0-11
[163] igraph_1.6.0

[csangara]

Thanks for providing your session.

I implemented a fix in the "get-expressed-genes" branch, which you can already install using

devtools::install_github("saeyslab/nichenetr", ref="get-expressed-genes")

I haven't fully tested it on all scenarios yet, but it should work on the vignette now. I'll push it to the main branch once I have more time to run tests on it.

Let me know if you still have errors!

[csangara]

@godstick0517
@Samir1703

This has now been merged with the master branch. Feel free to reinstall NicheNet to version 2.0.5 now. When I posted the previous comment, I swapped the order of the arguments because I thought it was better practice to have the main (Seurat) object as the first argument (#247). However, I decided to rewrite this again so that it wouldn't break the current vignettes (#250). Sorry if this ends up breaking your code.

[Samir1703]

Thank you so much !!! I will try to do run it again and will let you know how it goes

Best

Samir