error to run prior_table

[sadiexiaoyu]

Hi,

I am using the new vignettesPerform NicheNet analysis with prioritization The dataset that I used was the sample file. However, when I run

prior_table <- generate_prioritization_tables(processed_expr_table, processed_DE_table, ligand_activities, processed_condition_markers, prioritizing_weights = prioritizing_weights)

I got error report like this: Joining with by = join_by(sender, receiver, ligand, receptor) Joining with by = join_by(sender, ligand, lfc_ligand, p_val_ligand) Joining with by = join_by(ligand) Error in if (weights["de_receptor"] > 0) dplyr::inner_join(., receiver_receptor_prioritization) else (.) : missing value where TRUE/FALSE needed

Could you give me any suggestion? Thanks!

[csangara]

Hi, Is this error just from directly running the vignette? I can't seem to replicate it. Can you give me your sessionInfo() please?

[sadiexiaoyu]

Hi, Is this error just from directly running the vignette? I can't seem to replicate it. Can you give me your sessionInfo() please?

Yes, it was from directly running the vignette. I also tried my own data and it gives same error report. The sessionInfo() is:

sessionInfo()

R version 4.2.1 (2022-06-23 ucrt)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:

[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8

[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C

[5] LC_TIME=English_United Kingdom.utf8

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] export_0.3.0 SeuratObject_4.1.3 Seurat_4.3.0 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2

[7] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2 tidyverse_1.3.2

[13] RColorBrewer_1.1-3 nichenetr_2.0.0

loaded via a namespace (and not attached):

[1] scattermore_0.8 ModelMetrics_1.2.2.2 knitr_1.43 irlba_2.3.5.1

[5] data.table_1.14.8 rpart_4.1.16 hardhat_1.2.0 doParallel_1.0.17

[9] generics_0.1.3 BiocGenerics_0.44.0 cowplot_1.1.1 shadowtext_0.1.2

[13] RANN_2.6.1 proxy_0.4-27 future_1.23.0 DiagrammeR_1.0.9

[17] tzdb_0.3.0 spatstat.data_3.0-0 xml2_1.3.3 lubridate_1.9.2

[21] httpuv_1.6.9 assertthat_0.2.1 gargle_1.3.0 gower_1.0.1

[25] xfun_0.39 hms_1.1.3 evaluate_0.21 promises_1.2.0.1

[29] fansi_1.0.4 caTools_1.18.2 dbplyr_2.3.0 readxl_1.4.2

[33] igraph_1.3.5 DBI_1.1.3 htmlwidgets_1.6.2 spatstat.geom_3.0-6

[37] googledrive_2.0.0 stats4_4.2.1 ellipsis_0.3.2 ggnewscale_0.4.9

[41] backports_1.4.1 fontLiberation_0.1.0 fontBitstreamVera_0.1.1 deldir_1.0-6

[45] vctrs_0.6.3 ROCR_1.0-11 abind_1.4-5 caret_6.0-93

[49] cachem_1.0.6 withr_2.5.0 ggforce_0.4.1 progressr_0.13.0

[53] checkmate_2.2.0 sctransform_0.3.5 fdrtool_1.2.17 goftest_1.2-3

[57] cluster_2.1.3 lazyeval_0.2.2 crayon_1.5.2 crul_1.3

[61] spatstat.explore_3.0-6 recipes_1.0.4 pkgconfig_2.0.3 tweenr_2.0.2

[65] nlme_3.1-157 nnet_7.3-17 rlang_1.1.1 globals_0.16.2

[69] lifecycle_1.0.3 miniUI_0.1.1.1 fontquiver_0.2.1 httpcode_0.3.0

[73] modelr_0.1.10 cellranger_1.1.0 randomForest_4.7-1.1 polyclip_1.10-4

[77] matrixStats_1.0.0 lmtest_0.9-40 flextable_0.8.5 Matrix_1.6-0

[81] zoo_1.8-11 reprex_2.0.2 base64enc_0.1-3 ggridges_0.5.4

[85] GlobalOptions_0.1.2 googlesheets4_1.0.1 png_0.1-8 viridisLite_0.4.2

[89] rjson_0.2.21 bitops_1.0-7 KernSmooth_2.23-20 visNetwork_2.1.2

[93] pROC_1.18.0 rgl_1.0.1 shape_1.4.6 parallelly_1.36.0

[97] spatstat.random_3.1-3 S4Vectors_0.36.2 scales_1.2.1 memoise_2.0.1

[101] magrittr_2.0.3 plyr_1.8.8 ica_1.0-3 compiler_4.2.1

[105] clue_0.3-64 fitdistrplus_1.1-8 cli_3.6.0 listenv_0.9.0

[109] patchwork_1.1.2 pbapply_1.7-0 htmlTable_2.4.1 Formula_1.2-5

[113] MASS_7.3-57 tidyselect_1.2.0 stringi_1.7.12 askpass_1.1

[117] ggrepel_0.9.3 grid_4.2.1 tools_4.2.1 timechange_0.2.0

[121] future.apply_1.8.1 parallel_4.2.1 rvg_0.3.2 circlize_0.4.16

[125] rstudioapi_0.15.0 uuid_1.1-0 foreach_1.5.2 foreign_0.8-82

[129] gridExtra_2.3 stargazer_5.2.3 prodlim_2019.11.13 devEMF_4.2

[133] farver_2.1.1 Rtsne_0.16 digest_0.6.31 shiny_1.7.4

[137] lava_1.7.1 gfonts_0.2.0 Rcpp_1.0.10 broom_1.0.5

[141] later_1.3.0 RcppAnnoy_0.0.21 httr_1.4.6 gdtools_0.3.1

[145] ComplexHeatmap_2.15.4 colorspace_2.1-0 rvest_1.0.3 fs_1.6.1

[149] tensor_1.5 reticulate_1.28 IRanges_2.32.0 splines_4.2.1

[153] uwot_0.1.16 spatstat.utils_3.0-1 sp_1.6-0 plotly_4.10.1

[157] systemfonts_1.0.4 xtable_1.8-4 jsonlite_1.8.7 timeDate_4022.108

[161] ipred_0.9-13 R6_2.5.1 Hmisc_5.1-0 pillar_1.9.0

[165] htmltools_0.5.4 mime_0.12 glue_1.6.2 fastmap_1.1.0

[169] class_7.3-20 codetools_0.2-18 utf8_1.2.3 lattice_0.20-45

[173] spatstat.sparse_3.0-0 curl_5.0.0 leiden_0.4.3 officer_0.6.0

[177] zip_2.2.2 openxlsx_4.2.5.2 openssl_2.0.6 survival_3.5-3

[181] limma_3.54.2 rmarkdown_2.23 munsell_0.5.0 e1071_1.7-13

[185] GetoptLong_1.0.5 iterators_1.0.14 haven_2.5.1 reshape2_1.4.4

[189] gtable_0.3.3

[csangara]

Can you try updating NicheNet to the latest version? (v2.0.1)