Comments (4)
browaeysrobin
commented on September 26, 2024
1
Hi @jaquol
Normally, the nichenetr function prepare_ligand_target_visualization should use the cor and dist functions of base R and not of the proxyC package (and they work perfectly fine with non-sparse matrices). There is probably some conflict there, although I could not reproduce the error by loading the proxyC package myself... Can you maybe tell me 1) how you load in the packages; 2) how you installed nichenetr, and 3) whether it works if you don't load the proxyC package (and preferably no other package than nichenetr, Seurat, tidyverse) ?
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browaeysrobin
commented on September 26, 2024
Hi @jaquol ,
Can you give some information of potential other packages that you loaded in your workspace (except for nichenetr, tidyverse and Seurat) ?
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jaquol
commented on September 26, 2024
Thank you for your quick reply! Below is the output of sessionInfo():
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] nichenetr_0.1.0 future.apply_1.5.0 future_1.17.0
[4] leiden_0.3.3 SingleR_1.0.6 DoubletFinder_2.0.3
[7] MAST_1.12.0 SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.1
[10] DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.56.0
[13] Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[16] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
[19] Seurat_3.1.5 loomR_0.2.1.9000 hdf5r_1.3.2
[22] R6_2.4.1 limma_3.42.2 msigdbr_7.1.1
[25] DT_0.13 scales_1.1.0 ggrepel_0.8.2
[28] UpSetR_1.4.0 doParallel_1.0.15 iterators_1.0.12
[31] foreach_1.5.0 proxyC_0.1.5 circlize_0.4.8
[34] ComplexHeatmap_2.2.0 ggpubr_0.2.5 magrittr_1.5
[37] patchwork_1.0.0.9000 rio_0.5.16 data.table_1.12.8
[40] broom_0.5.6 forcats_0.5.0 stringr_1.4.0
[43] dplyr_0.8.5 purrr_0.3.4 readr_1.3.1
[46] tidyr_1.0.2 tibble_3.0.1 ggplot2_3.3.0
[49] tidyverse_1.3.0 fs_1.4.1
loaded via a namespace (and not attached):
[1] reticulate_1.15 tidyselect_1.1.0 RSQLite_2.2.0
[4] AnnotationDbi_1.48.0 htmlwidgets_1.5.1 Rtsne_0.15
[7] pROC_1.16.2 munsell_0.5.0 codetools_0.2-16
[10] ica_1.0-2 withr_2.2.0 colorspace_1.4-1
[13] knitr_1.28 rstudioapi_0.11 ROCR_1.0-11
[16] ggsignif_0.6.0 listenv_0.8.0 GenomeInfoDbData_1.2.2
[19] bit64_0.9-7 vctrs_0.2.4 generics_0.0.2
[22] ipred_0.9-9 xfun_0.14 BiocFileCache_1.10.2
[25] randomForest_4.6-14 clue_0.3-57 rsvd_1.0.3
[28] bitops_1.0-6 assertthat_0.2.1 promises_1.1.0
[31] nnet_7.3-14 gtable_0.3.0 globals_0.12.5
[34] timeDate_3043.102 rlang_0.4.6 GlobalOptions_0.1.1
[37] splines_3.6.3 lazyeval_0.2.2 acepack_1.4.1
[40] ModelMetrics_1.2.2.2 checkmate_2.0.0 BiocManager_1.30.10
[43] yaml_2.2.1 reshape2_1.4.4 abind_1.4-5
[46] modelr_0.1.8 backports_1.1.6 httpuv_1.5.2
[49] Hmisc_4.4-0 DiagrammeR_1.0.6.1 caret_6.0-86
[52] lava_1.6.7 tools_3.6.3 ellipsis_0.3.0
[55] RColorBrewer_1.1-2 ggridges_0.5.2 Rcpp_1.0.4.6
[58] plyr_1.8.6 base64enc_0.1-3 visNetwork_2.0.9
[61] zlibbioc_1.32.0 RCurl_1.98-1.1 rpart_4.1-15
[64] pbapply_1.4-2 GetoptLong_0.1.8 cowplot_1.0.0
[67] zoo_1.8-7 haven_2.2.0 cluster_2.1.0
[70] openxlsx_4.1.4 lmtest_0.9-37 reprex_0.3.0
[73] RANN_2.6.1 fitdistrplus_1.1-1 hms_0.5.3
[76] mime_0.9 xtable_1.8-4 jpeg_0.1-8.1
[79] readxl_1.3.1 gridExtra_2.3 shape_1.4.4
[82] compiler_3.6.3 KernSmooth_2.23-17 crayon_1.3.4
[85] htmltools_0.4.0 later_1.0.0 Formula_1.2-3
[88] RcppParallel_5.0.0 lubridate_1.7.8 DBI_1.1.0
[91] ExperimentHub_1.12.0 dbplyr_1.4.3 MASS_7.3-51.6
[94] rappdirs_0.3.1 Matrix_1.2-18 cli_2.0.2
[97] gower_0.2.1 igraph_1.2.5 pkgconfig_2.0.3
[100] foreign_0.8-75 plotly_4.9.2.1 recipes_0.1.12
[103] xml2_1.3.2 XVector_0.26.0 prodlim_2019.11.13
[106] rvest_0.3.5 digest_0.6.25 sctransform_0.2.1
[109] RcppAnnoy_0.0.16 tsne_0.1-3 cellranger_1.1.0
[112] htmlTable_1.13.3 uwot_0.1.8 DelayedMatrixStats_1.8.0
[115] curl_4.3 shiny_1.4.0.2 rjson_0.2.20
[118] lifecycle_0.2.0 nlme_3.1-147 jsonlite_1.6.1
[121] BiocNeighbors_1.4.2 viridisLite_0.3.0 fansi_0.4.1
[124] pillar_1.4.4 lattice_0.20-41 fastmap_1.0.1
[127] httr_1.4.1 survival_3.1-12 interactiveDisplayBase_1.24.0
[130] glue_1.4.0 fdrtool_1.2.15 zip_2.0.4
[133] png_0.1-7 BiocVersion_3.10.1 bit_1.1-15.2
[136] class_7.3-17 stringi_1.4.6 blob_1.2.1
[139] AnnotationHub_2.18.0 caTools_1.18.0 latticeExtra_0.6-29
[142] memoise_1.1.0 irlba_2.3.3 ape_5.3
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jaquol
commented on September 26, 2024
Loading only nichenetr, Seurat and tydiverse (plus rio and fs for data importing), I do not run into the issue above! Thank you a lot!
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Related Issues (20)
- Warning message in `predict_ligand_activities`
- `generate_prioritization_tables` warnings and documentation
- Error when passing the recorrect_umi argument in get_lfc_celltype HOT 1
- Error in WhichCells.Seurat(object = object, idents = ident.2) : Cannot find the following identities in the object: Adjacent HOT 1
- Error in `Idents<-`: ! 'value' must be a factor or vector HOT 3
- Different results running. the same. code in different version. of HOT 6
- Protein complex HOT 1
- Function generate_info_tables return an error HOT 3
- Low AUPR values in analyses HOT 4
- RankActiveLigands Error
- Can NicheNet be used for analyzing three groups? HOT 1
- Parallelization error when optimizing parameters for NicheNet HOT 4
- How is the Ligand-Target-Matrix generated? HOT 2
- Receiver cells in differential analysis HOT 1
- when sender cell type is only one, HOT 1
- Only activating interactions or also repressing? HOT 1
- Naming convention in prioritization table
- Change error in `alias_to_symbol_seurat()` to warning
- discrepancy in results output HOT 2
- assign_ligands_to_celltype erroe message HOT 1
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